afni.nimh.nih.gov
AFNI Message Board
Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| March 03, 2023 07:03AM | |
Okay, all done (thank you IT!)
The outputs (with some trimming) and QC images are below.
Many thanks!
Sam
@animal_warper -input center_aligned_T1.nii -base /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz -atlas /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_atlas_v2.0.nii.gz
++ Start @animal_warper, ver = 3.39
++ Prepare for running @djunct_overlap_check (ver = 0.42)
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aw_results/QC/__workdir_olap_BF2DtBfz9Vc/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aw_results/QC/__workdir_olap_BF2DtBfz9Vc/olapch_1_cp_olay.nii
++ Quietly run: 3drefit -space D99_Macaque olapch_0_cp_ulay.nii
++ olay_alpha has known value: No
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 3 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -set_dicom_xyz 0 0 0
++ Using AFNI ver : AFNI_21.2.09
++ chauffeur ver : 6.29
------------------ start of optionizing ------------------
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 3
++ Making temporary work directory to copy vis files: ./__tmp_chauf_5DPqsY1gM2c
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 2265.500000]
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_5DPqsY1gM2c/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_5DPqsY1gM2c/tmp_olay.nii
++ For olay, the 98%ile value leads to
--> upper range value: 208.000000
++ Dimensions (xyzt): 275 347 245 1
++ (initial) Slice spacing ordered (x,y,z) is: 275 347 245
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
------------------- end of optionizing -------------------
-- trying to start Xvfb :822
[1] 23135
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=3 mont=1x1:275:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=3 mont=1x1:347:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=3 mont=1x1:245:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 2265.500000 -com SET_FUNC_RANGE 208.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 0 0 0 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com QUITT ./__tmp_chauf_5DPqsY1gM2c
+/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/QC/__workdir_olap_BF2DtBfz9Vc/__tmp_chauf_5DPqsY1gM2c++ Writing one 550x694 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.axi.jpg'
++ Writing one 694x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.sag.jpg'
++ Writing one 550x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.cor.jpg'
AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_5DPqsY1gM2c'.
[1] + Done Xvfb :822 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 550x694) into a 3x1 matrix.
+++ Transforming all input to rgb for a good reason
+++ Writing image to ../init_qc_00_inp_base.jpg
You can view image ../init_qc_00_inp_base.jpg with:
aiv ../init_qc_00_inp_base.jpg
+* Removing temporary workdir 'aw_results/QC/__workdir_olap_BF2DtBfz9Vc*'
++ DONE! Image output:
aw_results/QC/init_qc_00_inp_base
++ Making 'base' abbrev:
... D99_Macaque
--> D99_Macaque
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Making list of 'atlas_follower' abbrevs:
... D99_atlas_v2.0 --> D99_atlas_v2.0
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ 3drefit: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./intermediate/center_aligned_T1_pshft.nii.gz
+ deoblique
+ loading and re-writing dataset ./intermediate/center_aligned_T1_pshft.nii.gz (/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_pshft.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Prepare for running @djunct_overlap_check (ver = 0.42)
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__workdir_olap_V6nDvfjZlLN/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__workdir_olap_V6nDvfjZlLN/olapch_1_cp_olay.nii
++ Quietly run: 3drefit -space D99_Macaque olapch_0_cp_ulay.nii
++ olay_alpha has known value: No
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 3 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -set_dicom_xyz 0 0 0
++ Using AFNI ver : AFNI_21.2.09
++ chauffeur ver : 6.29
------------------ start of optionizing ------------------
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 3
++ Making temporary work directory to copy vis files: ./__tmp_chauf_2MFLsOmdtou
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 2265.500000]
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_2MFLsOmdtou/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_2MFLsOmdtou/tmp_olay.nii
++ For olay, the 98%ile value leads to
--> upper range value: 208.000000
++ Dimensions (xyzt): 275 347 245 1
++ (initial) Slice spacing ordered (x,y,z) is: 275 347 245
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
------------------- end of optionizing -------------------
-- trying to start Xvfb :300
[1] 23550
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=3 mont=1x1:275:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=3 mont=1x1:347:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=3 mont=1x1:245:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 2265.500000 -com SET_FUNC_RANGE 208.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 0 0 0 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com QUITT ./__tmp_chauf_2MFLsOmdtou
+/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/QC/__workdir_olap_V6nDvfjZlLN/__tmp_chauf_2MFLsOmdtou++ Writing one 550x694 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.axi.jpg'
++ Writing one 694x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.sag.jpg'
++ Writing one 550x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.cor.jpg'
AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_2MFLsOmdtou'.
[1] + Done Xvfb :300 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 550x694) into a 3x1 matrix.
+++ Transforming all input to rgb for a good reason
+++ Writing image to ../init_qc_01_inpsh_base.jpg
You can view image ../init_qc_01_inpsh_base.jpg with:
aiv ../init_qc_01_inpsh_base.jpg
+* Removing temporary workdir 'QC/__workdir_olap_V6nDvfjZlLN*'
++ DONE! Image output:
QC/init_qc_01_inpsh_base
#++ align_epi_anat version: 1.62
#++ turning off tshift, volume registration, resampling
#++ turning off tshift, volume registration, resampling
#Script is running (command trimmed):
3dAttribute DELTA ./intermediate/center_aligned_T1_pshft.nii.gz
#Script is running (command trimmed):
3dAttribute DELTA ./intermediate/center_aligned_T1_pshft.nii.gz
#Script is running:
3dAttribute DELTA /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz
#++ Multi-cost is lpa+ZZ
# User has selected a new output directory /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/
#Script is running (command trimmed):
mkdir ./intermediate/
mkdir: cannot create directory ‘./intermediate/’: File exists
cd /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/
#++ Removing all the temporary files
#Script is running (command trimmed):
\rm -f ./__tt_center_aligned_T1_pshft*
#Script is running (command trimmed):
\rm -f ./__tt_D99_template*
#Script is running (command trimmed):
3dcopy /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz ./__tt_D99_template+orig
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#Script is running (command trimmed):
3dinfo ./__tt_D99_template+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/__tt_D99_template+orig is not oblique
#Script is running (command trimmed):
3dinfo ./center_aligned_T1_pshft.nii.gz | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_pshft.nii.gz is not oblique
#++ Copying NIFTI EPI input to AFNI format
#Script is running (command trimmed):
3dcopy ./center_aligned_T1_pshft.nii.gz ./__tt_center_aligned_T1_pshft+tlrc
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix ./__tt_center_aligned_T1_pshft_ts ./__tt_center_aligned_T1_pshft+tlrc'[0]'
++ 3dbucket: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#++ removing skull or area outside brain
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_center_aligned_T1_pshft_ts+tlrc
#++ Applying threshold of 2200.000000 on /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/__tt_center_aligned_T1_pshft_ts+tlrc
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_center_aligned_T1_pshft_ts_wt -a ./__tt_center_aligned_T1_pshft_ts+tlrc -expr 'min(1,(a/2200.000000))'
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
#++ Aligning dset1 data to dset2 data
#Script is running (command trimmed):
3dAllineate -lpa+ZZ -wtprefix ./__tt_D99_template_al2std_wtal -weight ./__tt_center_aligned_T1_pshft_ts_wt+tlrc -source ./__tt_D99_template+orig -prefix ./__tt_D99_template_al2std -base ./__tt_center_aligned_T1_pshft_ts+tlrc -cmass -1Dmatrix_save ./D99_template_al2std_mat.aff12.1D -master BASE -mast_dxyz 0.250000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -twoblur 1.000000 -blok "RHDD(0.500000)" -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 0.5 -source_automask+2
++ 3dAllineate: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ lpa+ parameters: hel=1.00 mi=0.00 nmi=0.20 crA=0.40 ov=0.00 [to be zeroed at Final iteration]
++ Option '-cmass' enables center-of-mass code = 7 = +xyz
*+ WARNING: Small value 0.25 after -mast_dxyz
++ Source dataset: ./__tt_D99_template+orig.HEAD
++ Base dataset: ./__tt_center_aligned_T1_pshft_ts+tlrc.HEAD
++ Loading datasets into memory
++ 7006921 voxels in -source_automask+2
++ Zero-pad: xbot=30 xtop=26
++ Zero-pad: ybot=16 ytop=43
++ Zero-pad: zbot=21 ztop=17
++ 7388107 voxels [19.4%] in weight mask
++ Number of points for matching = 7388107
++ Local correlation: blok type = 'RHDD(1.63065)'
++ lpa+ parameters: hel=1.00 mi=0.00 nmi=0.20 crA=0.40 ov=0.00 [to be zeroed at Final iteration]
++ base center of mass = 165.789 223.093 139.041 (index)
+ source center of mass = 136.500 147.653 125.509 (index)
+ source-target CM = 0.428 -2.186 1.867 (xyz)
+ estimated center of mass shifts = 0.428 -2.186 1.867
< parameter values removed>
# Finished alignment successfully
++ 3dAFNItoNIFTI: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ 3drefit: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset intermediate/center_aligned_T1_shft.nii.gz
+ deoblique
+ loading and re-writing dataset intermediate/center_aligned_T1_shft.nii.gz (/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_shft.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ 3dAllineate: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_shft.nii.gz
++ Base dataset: /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz
++ Loading datasets into memory
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be TERRIBLY large!
*+ WARNING: - at least one is more than 50% of search range
+ -cmass x y z shifts = 9.290 39.922 54.804
+ shift search range is +/- = 21.989 27.767 19.581
+ 42.2% 143.8% 279.9%
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset intermediate/center_aligned_T1_shft_aff.nii.gz
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2.2
++ ###########################################################
+
++ ***********************************************************
*+ WARNING: -cmass was turned off, but might have been needed :(
+ Please check your results - PLEASE PLEASE PLEASE
++ ***********************************************************
++ Prepare for running @djunct_overlap_check (ver = 0.42)
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__workdir_olap_Cz0OKk26mCn/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__workdir_olap_Cz0OKk26mCn/olapch_1_cp_olay.nii
++ Quietly run: 3drefit -space D99_Macaque olapch_0_cp_ulay.nii
++ olay_alpha has known value: No
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 3 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -set_dicom_xyz 0 0 0
++ Using AFNI ver : AFNI_21.2.09
++ chauffeur ver : 6.29
------------------ start of optionizing ------------------
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 3
++ Making temporary work directory to copy vis files: ./__tmp_chauf_2sjmch3CY7E
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 0]
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_2sjmch3CY7E/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_2sjmch3CY7E/tmp_olay.nii
++ For olay, the 98%ile value leads to
--> upper range value: 208.000000
++ Dimensions (xyzt): 275 347 245 1
++ (initial) Slice spacing ordered (x,y,z) is: 275 347 245
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
------------------- end of optionizing -------------------
-- trying to start Xvfb :527
[1] 24715
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=3 mont=1x1:275:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=3 mont=1x1:347:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=3 mont=1x1:245:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 0 -com SET_FUNC_RANGE 208.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 0 0 0 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com QUITT ./__tmp_chauf_2sjmch3CY7E
+/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/QC/__workdir_olap_Cz0OKk26mCn/__tmp_chauf_2sjmch3CY7E++ Writing one 550x694 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.axi.jpg'
++ Writing one 694x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.sag.jpg'
++ Writing one 550x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.cor.jpg'
AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_2sjmch3CY7E'.
[1] + Done Xvfb :527 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 550x694) into a 3x1 matrix.
+++ Transforming all input to rgb for a good reason
+++ Writing image to ../init_qc_02_inpaff_base.jpg
You can view image ../init_qc_02_inpaff_base.jpg with:
aiv ../init_qc_02_inpaff_base.jpg
+* Removing temporary workdir 'QC/__workdir_olap_Cz0OKk26mCn*'
++ DONE! Image output:
QC/init_qc_02_inpaff_base
#++ auto_warp.py version: 0.06
-- clearing AFNI_COMPRESSOR ...
# Output directory /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/awpy_center_aligned_T1_pshft/
#Script is running (command trimmed):
mkdir ./awpy_center_aligned_T1_pshft/
cd /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/awpy_center_aligned_T1_pshft/
#Script is running (command trimmed):
3dcopy /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_shft_aff.nii.gz ./anat.nii
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
+ Pre-processing: ADVUWm
++ Output dataset ./anat.un.nii
++ ===== Elapsed = 17.7 sec
#Script is running (command trimmed):
3dcopy /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz ./base.nii
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#Script is running (command trimmed):
3dAttribute DELTA ./anat.un.nii
#Script is running (command trimmed):
3dAttribute DELTA ./base.nii
0.250000 0.250000
#Script is running (command trimmed):
3dinfo -same_grid ./anat.un.nii ./base.nii
#++ Aligning /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/awpy_center_aligned_T1_pshft/base.nii data to /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/awpy_center_aligned_T1_pshft/anat.un.nii data
#Script is running (command trimmed):
3dQwarp -prefix ./anat.un.qw.nii -blur -3 -3 -workhard:0:2 -iwarp \
-maxlev 09 -base ./base.nii -source ./anat.un.nii
++ OpenMP thread count = 4
++ 3dQwarp: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
** FATAL ERROR: 3dQwarp fails :: source image has 0 nonzero voxels (< 100)
** Program compile date = Sep 27 2021
#**ERROR Failed in warping step
** ERROR - script failed
3dcopy: No match.
3dcopy: No match.
+++ Command Echo:
3dNwarpCat -warp1 center_aligned_T1_shft_WARP.nii.gz -warp2 intermediate/center_aligned_T1_shft_al2std_mat.aff12.1D -prefix intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz
++ 3dNwarpCat: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Warper
** ERROR: Can't open dataset from file 'center_aligned_T1_shft_WARP.nii.gz'
** ERROR: Failed to read 3D warp from 'center_aligned_T1_shft_WARP.nii.gz'
** ERROR: Can't compute nonlinear warp from string 'center_aligned_T1_shft_WARP.nii.gz intermediate/center_aligned_T1_shft_al2std_mat.aff12.1D '
** ERROR: EDIT_dset_items[1]: invalid input dataset
** ERROR: Cannot write dataset: it is invalid
Fatal Signal 11 (SIGSEGV) received
3dNwarpCat
Bottom of Debug Stack
** Command line was:
3dNwarpCat -warp1 center_aligned_T1_shft_WARP.nii.gz -warp2 intermediate/center_aligned_T1_shft_al2std_mat.aff12.1D -prefix intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz
** AFNI version = AFNI_21.2.09 Compile date = Sep 27 2021
** [[Precompiled binary linux_openmp_64: Sep 27 2021]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/c1639425/.afni.crashlog
+++ Command Echo:
3dNwarpCat -warp1 intermediate/center_aligned_T1_shft_inv_al2std_mat.aff12.1D -warp2 center_aligned_T1_shft_WARPINV.nii.gz -space NO-DSET -prefix intermediate/center_aligned_T1_shft_base2osh_WARP.nii.gz
++ 3dNwarpCat: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Warper
** ERROR: Can't open dataset from file 'center_aligned_T1_shft_WARPINV.nii.gz'
** ERROR: Failed to read 3D warp from 'center_aligned_T1_shft_WARPINV.nii.gz'
** ERROR: Can't compute nonlinear warp from string 'intermediate/center_aligned_T1_shft_inv_al2std_mat.aff12.1D center_aligned_T1_shft_WARPINV.nii.gz '
Fatal Signal 11 (SIGSEGV) received
3dNwarpCat
Bottom of Debug Stack
** Command line was:
3dNwarpCat -warp1 intermediate/center_aligned_T1_shft_inv_al2std_mat.aff12.1D -warp2 center_aligned_T1_shft_WARPINV.nii.gz -space NO-DSET -prefix intermediate/center_aligned_T1_shft_base2osh_WARP.nii.gz
** AFNI version = AFNI_21.2.09 Compile date = Sep 27 2021
** [[Precompiled binary linux_openmp_64: Sep 27 2021]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/c1639425/.afni.crashlog
++ 3dNwarpApply: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Warped
++ opened source dataset 'intermediate/center_aligned_T1_shft.nii.gz'
++ -master dataset is '/cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz'
++ Processing -nwarp ** ERROR: Can't open dataset from file 'intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz'
** ERROR: Can't open 3D warp dataset 'intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz'
** FATAL ERROR: Cannot process warp string 'intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz '
** Program compile date = Sep 27 2021
** ERROR: program failed (3dNwarpApply, osh2base)
The outputs (with some trimming) and QC images are below.
Many thanks!
Sam
@animal_warper -input center_aligned_T1.nii -base /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz -atlas /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_atlas_v2.0.nii.gz
++ Start @animal_warper, ver = 3.39
++ Prepare for running @djunct_overlap_check (ver = 0.42)
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aw_results/QC/__workdir_olap_BF2DtBfz9Vc/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./aw_results/QC/__workdir_olap_BF2DtBfz9Vc/olapch_1_cp_olay.nii
++ Quietly run: 3drefit -space D99_Macaque olapch_0_cp_ulay.nii
++ olay_alpha has known value: No
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 3 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -set_dicom_xyz 0 0 0
++ Using AFNI ver : AFNI_21.2.09
++ chauffeur ver : 6.29
------------------ start of optionizing ------------------
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 3
++ Making temporary work directory to copy vis files: ./__tmp_chauf_5DPqsY1gM2c
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 2265.500000]
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_5DPqsY1gM2c/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_5DPqsY1gM2c/tmp_olay.nii
++ For olay, the 98%ile value leads to
--> upper range value: 208.000000
++ Dimensions (xyzt): 275 347 245 1
++ (initial) Slice spacing ordered (x,y,z) is: 275 347 245
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
------------------- end of optionizing -------------------
-- trying to start Xvfb :822
[1] 23135
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=3 mont=1x1:275:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=3 mont=1x1:347:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=3 mont=1x1:245:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 2265.500000 -com SET_FUNC_RANGE 208.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 0 0 0 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com QUITT ./__tmp_chauf_5DPqsY1gM2c
+/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/QC/__workdir_olap_BF2DtBfz9Vc/__tmp_chauf_5DPqsY1gM2c++ Writing one 550x694 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.axi.jpg'
++ Writing one 694x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.sag.jpg'
++ Writing one 550x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.cor.jpg'
AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_5DPqsY1gM2c'.
[1] + Done Xvfb :822 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 550x694) into a 3x1 matrix.
+++ Transforming all input to rgb for a good reason
+++ Writing image to ../init_qc_00_inp_base.jpg
You can view image ../init_qc_00_inp_base.jpg with:
aiv ../init_qc_00_inp_base.jpg
+* Removing temporary workdir 'aw_results/QC/__workdir_olap_BF2DtBfz9Vc*'
++ DONE! Image output:
aw_results/QC/init_qc_00_inp_base
++ Making 'base' abbrev:
... D99_Macaque
--> D99_Macaque
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Making list of 'atlas_follower' abbrevs:
... D99_atlas_v2.0 --> D99_atlas_v2.0
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ 3drefit: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./intermediate/center_aligned_T1_pshft.nii.gz
+ deoblique
+ loading and re-writing dataset ./intermediate/center_aligned_T1_pshft.nii.gz (/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_pshft.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ Prepare for running @djunct_overlap_check (ver = 0.42)
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__workdir_olap_V6nDvfjZlLN/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__workdir_olap_V6nDvfjZlLN/olapch_1_cp_olay.nii
++ Quietly run: 3drefit -space D99_Macaque olapch_0_cp_ulay.nii
++ olay_alpha has known value: No
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 3 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -set_dicom_xyz 0 0 0
++ Using AFNI ver : AFNI_21.2.09
++ chauffeur ver : 6.29
------------------ start of optionizing ------------------
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 3
++ Making temporary work directory to copy vis files: ./__tmp_chauf_2MFLsOmdtou
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 2265.500000]
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_2MFLsOmdtou/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_2MFLsOmdtou/tmp_olay.nii
++ For olay, the 98%ile value leads to
--> upper range value: 208.000000
++ Dimensions (xyzt): 275 347 245 1
++ (initial) Slice spacing ordered (x,y,z) is: 275 347 245
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
------------------- end of optionizing -------------------
-- trying to start Xvfb :300
[1] 23550
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=3 mont=1x1:275:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=3 mont=1x1:347:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=3 mont=1x1:245:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 2265.500000 -com SET_FUNC_RANGE 208.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 0 0 0 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com QUITT ./__tmp_chauf_2MFLsOmdtou
+/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/QC/__workdir_olap_V6nDvfjZlLN/__tmp_chauf_2MFLsOmdtou++ Writing one 550x694 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.axi.jpg'
++ Writing one 694x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.sag.jpg'
++ Writing one 550x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.cor.jpg'
AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_2MFLsOmdtou'.
[1] + Done Xvfb :300 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 550x694) into a 3x1 matrix.
+++ Transforming all input to rgb for a good reason
+++ Writing image to ../init_qc_01_inpsh_base.jpg
You can view image ../init_qc_01_inpsh_base.jpg with:
aiv ../init_qc_01_inpsh_base.jpg
+* Removing temporary workdir 'QC/__workdir_olap_V6nDvfjZlLN*'
++ DONE! Image output:
QC/init_qc_01_inpsh_base
#++ align_epi_anat version: 1.62
#++ turning off tshift, volume registration, resampling
#++ turning off tshift, volume registration, resampling
#Script is running (command trimmed):
3dAttribute DELTA ./intermediate/center_aligned_T1_pshft.nii.gz
#Script is running (command trimmed):
3dAttribute DELTA ./intermediate/center_aligned_T1_pshft.nii.gz
#Script is running:
3dAttribute DELTA /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz
#++ Multi-cost is lpa+ZZ
# User has selected a new output directory /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/
#Script is running (command trimmed):
mkdir ./intermediate/
mkdir: cannot create directory ‘./intermediate/’: File exists
cd /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/
#++ Removing all the temporary files
#Script is running (command trimmed):
\rm -f ./__tt_center_aligned_T1_pshft*
#Script is running (command trimmed):
\rm -f ./__tt_D99_template*
#Script is running (command trimmed):
3dcopy /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz ./__tt_D99_template+orig
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#Script is running (command trimmed):
3dinfo ./__tt_D99_template+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/__tt_D99_template+orig is not oblique
#Script is running (command trimmed):
3dinfo ./center_aligned_T1_pshft.nii.gz | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_pshft.nii.gz is not oblique
#++ Copying NIFTI EPI input to AFNI format
#Script is running (command trimmed):
3dcopy ./center_aligned_T1_pshft.nii.gz ./__tt_center_aligned_T1_pshft+tlrc
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix ./__tt_center_aligned_T1_pshft_ts ./__tt_center_aligned_T1_pshft+tlrc'[0]'
++ 3dbucket: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#++ removing skull or area outside brain
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_center_aligned_T1_pshft_ts+tlrc
#++ Applying threshold of 2200.000000 on /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/__tt_center_aligned_T1_pshft_ts+tlrc
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_center_aligned_T1_pshft_ts_wt -a ./__tt_center_aligned_T1_pshft_ts+tlrc -expr 'min(1,(a/2200.000000))'
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
#++ Aligning dset1 data to dset2 data
#Script is running (command trimmed):
3dAllineate -lpa+ZZ -wtprefix ./__tt_D99_template_al2std_wtal -weight ./__tt_center_aligned_T1_pshft_ts_wt+tlrc -source ./__tt_D99_template+orig -prefix ./__tt_D99_template_al2std -base ./__tt_center_aligned_T1_pshft_ts+tlrc -cmass -1Dmatrix_save ./D99_template_al2std_mat.aff12.1D -master BASE -mast_dxyz 0.250000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -twoblur 1.000000 -blok "RHDD(0.500000)" -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 0.5 -source_automask+2
++ 3dAllineate: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ lpa+ parameters: hel=1.00 mi=0.00 nmi=0.20 crA=0.40 ov=0.00 [to be zeroed at Final iteration]
++ Option '-cmass' enables center-of-mass code = 7 = +xyz
*+ WARNING: Small value 0.25 after -mast_dxyz
++ Source dataset: ./__tt_D99_template+orig.HEAD
++ Base dataset: ./__tt_center_aligned_T1_pshft_ts+tlrc.HEAD
++ Loading datasets into memory
++ 7006921 voxels in -source_automask+2
++ Zero-pad: xbot=30 xtop=26
++ Zero-pad: ybot=16 ytop=43
++ Zero-pad: zbot=21 ztop=17
++ 7388107 voxels [19.4%] in weight mask
++ Number of points for matching = 7388107
++ Local correlation: blok type = 'RHDD(1.63065)'
++ lpa+ parameters: hel=1.00 mi=0.00 nmi=0.20 crA=0.40 ov=0.00 [to be zeroed at Final iteration]
++ base center of mass = 165.789 223.093 139.041 (index)
+ source center of mass = 136.500 147.653 125.509 (index)
+ source-target CM = 0.428 -2.186 1.867 (xyz)
+ estimated center of mass shifts = 0.428 -2.186 1.867
< parameter values removed>
# Finished alignment successfully
++ 3dAFNItoNIFTI: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ 3drefit: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset intermediate/center_aligned_T1_shft.nii.gz
+ deoblique
+ loading and re-writing dataset intermediate/center_aligned_T1_shft.nii.gz (/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_shft.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
++ 3dAllineate: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_shft.nii.gz
++ Base dataset: /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz
++ Loading datasets into memory
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be TERRIBLY large!
*+ WARNING: - at least one is more than 50% of search range
+ -cmass x y z shifts = 9.290 39.922 54.804
+ shift search range is +/- = 21.989 27.767 19.581
+ 42.2% 143.8% 279.9%
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset intermediate/center_aligned_T1_shft_aff.nii.gz
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2.2
++ ###########################################################
+
++ ***********************************************************
*+ WARNING: -cmass was turned off, but might have been needed :(
+ Please check your results - PLEASE PLEASE PLEASE
++ ***********************************************************
++ Prepare for running @djunct_overlap_check (ver = 0.42)
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__workdir_olap_Cz0OKk26mCn/olapch_0_cp_ulay.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__workdir_olap_Cz0OKk26mCn/olapch_1_cp_olay.nii
++ Quietly run: 3drefit -space D99_Macaque olapch_0_cp_ulay.nii
++ olay_alpha has known value: No
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 3 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean -set_dicom_xyz 0 0 0
++ Using AFNI ver : AFNI_21.2.09
++ chauffeur ver : 6.29
------------------ start of optionizing ------------------
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 3
++ Making temporary work directory to copy vis files: ./__tmp_chauf_2sjmch3CY7E
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 0]
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_2sjmch3CY7E/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_2sjmch3CY7E/tmp_olay.nii
++ For olay, the 98%ile value leads to
--> upper range value: 208.000000
++ Dimensions (xyzt): 275 347 245 1
++ (initial) Slice spacing ordered (x,y,z) is: 275 347 245
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
------------------- end of optionizing -------------------
-- trying to start Xvfb :527
[1] 24715
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=3 mont=1x1:275:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=3 mont=1x1:347:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=3 mont=1x1:245:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 0 -com SET_FUNC_RANGE 208.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 0 0 0 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com QUITT ./__tmp_chauf_2sjmch3CY7E
+/cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/QC/__workdir_olap_Cz0OKk26mCn/__tmp_chauf_2sjmch3CY7E++ Writing one 550x694 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.axi.jpg'
++ Writing one 694x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.sag.jpg'
++ Writing one 550x490 image to filter '/cubric/software/afni.versions/21.2.09/cjpeg -quality 95 > ./img00.cor.jpg'
AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_2sjmch3CY7E'.
[1] + Done Xvfb :527 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 550x694) into a 3x1 matrix.
+++ Transforming all input to rgb for a good reason
+++ Writing image to ../init_qc_02_inpaff_base.jpg
You can view image ../init_qc_02_inpaff_base.jpg with:
aiv ../init_qc_02_inpaff_base.jpg
+* Removing temporary workdir 'QC/__workdir_olap_Cz0OKk26mCn*'
++ DONE! Image output:
QC/init_qc_02_inpaff_base
#++ auto_warp.py version: 0.06
-- clearing AFNI_COMPRESSOR ...
# Output directory /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/awpy_center_aligned_T1_pshft/
#Script is running (command trimmed):
mkdir ./awpy_center_aligned_T1_pshft/
cd /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/awpy_center_aligned_T1_pshft/
#Script is running (command trimmed):
3dcopy /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/intermediate/center_aligned_T1_shft_aff.nii.gz ./anat.nii
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
+ Pre-processing: ADVUWm
++ Output dataset ./anat.un.nii
++ ===== Elapsed = 17.7 sec
#Script is running (command trimmed):
3dcopy /cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz ./base.nii
++ 3dcopy: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
#Script is running (command trimmed):
3dAttribute DELTA ./anat.un.nii
#Script is running (command trimmed):
3dAttribute DELTA ./base.nii
0.250000 0.250000
#Script is running (command trimmed):
3dinfo -same_grid ./anat.un.nii ./base.nii
#++ Aligning /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/awpy_center_aligned_T1_pshft/base.nii data to /cubric/collab/505_subiculum/Monkey_brains/data/derivatives/sub-06/anat/animal_warper/aw_results/awpy_center_aligned_T1_pshft/anat.un.nii data
#Script is running (command trimmed):
3dQwarp -prefix ./anat.un.qw.nii -blur -3 -3 -workhard:0:2 -iwarp \
-maxlev 09 -base ./base.nii -source ./anat.un.nii
++ OpenMP thread count = 4
++ 3dQwarp: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
** FATAL ERROR: 3dQwarp fails :: source image has 0 nonzero voxels (< 100)
** Program compile date = Sep 27 2021
#**ERROR Failed in warping step
** ERROR - script failed
3dcopy: No match.
3dcopy: No match.
+++ Command Echo:
3dNwarpCat -warp1 center_aligned_T1_shft_WARP.nii.gz -warp2 intermediate/center_aligned_T1_shft_al2std_mat.aff12.1D -prefix intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz
++ 3dNwarpCat: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Warper
** ERROR: Can't open dataset from file 'center_aligned_T1_shft_WARP.nii.gz'
** ERROR: Failed to read 3D warp from 'center_aligned_T1_shft_WARP.nii.gz'
** ERROR: Can't compute nonlinear warp from string 'center_aligned_T1_shft_WARP.nii.gz intermediate/center_aligned_T1_shft_al2std_mat.aff12.1D '
** ERROR: EDIT_dset_items[1]: invalid input dataset
** ERROR: Cannot write dataset: it is invalid
Fatal Signal 11 (SIGSEGV) received
3dNwarpCat
Bottom of Debug Stack
** Command line was:
3dNwarpCat -warp1 center_aligned_T1_shft_WARP.nii.gz -warp2 intermediate/center_aligned_T1_shft_al2std_mat.aff12.1D -prefix intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz
** AFNI version = AFNI_21.2.09 Compile date = Sep 27 2021
** [[Precompiled binary linux_openmp_64: Sep 27 2021]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/c1639425/.afni.crashlog
+++ Command Echo:
3dNwarpCat -warp1 intermediate/center_aligned_T1_shft_inv_al2std_mat.aff12.1D -warp2 center_aligned_T1_shft_WARPINV.nii.gz -space NO-DSET -prefix intermediate/center_aligned_T1_shft_base2osh_WARP.nii.gz
++ 3dNwarpCat: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Warper
** ERROR: Can't open dataset from file 'center_aligned_T1_shft_WARPINV.nii.gz'
** ERROR: Failed to read 3D warp from 'center_aligned_T1_shft_WARPINV.nii.gz'
** ERROR: Can't compute nonlinear warp from string 'intermediate/center_aligned_T1_shft_inv_al2std_mat.aff12.1D center_aligned_T1_shft_WARPINV.nii.gz '
Fatal Signal 11 (SIGSEGV) received
3dNwarpCat
Bottom of Debug Stack
** Command line was:
3dNwarpCat -warp1 intermediate/center_aligned_T1_shft_inv_al2std_mat.aff12.1D -warp2 center_aligned_T1_shft_WARPINV.nii.gz -space NO-DSET -prefix intermediate/center_aligned_T1_shft_base2osh_WARP.nii.gz
** AFNI version = AFNI_21.2.09 Compile date = Sep 27 2021
** [[Precompiled binary linux_openmp_64: Sep 27 2021]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/c1639425/.afni.crashlog
++ 3dNwarpApply: AFNI version=AFNI_21.2.09 (Sep 27 2021) [64-bit]
++ Authored by: Zhark the Warped
++ opened source dataset 'intermediate/center_aligned_T1_shft.nii.gz'
++ -master dataset is '/cubric/collab/505_subiculum/Monkey_brains/D99_v2.0_dist/D99_template.nii.gz'
++ Processing -nwarp ** ERROR: Can't open dataset from file 'intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz'
** ERROR: Can't open 3D warp dataset 'intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz'
** FATAL ERROR: Cannot process warp string 'intermediate/center_aligned_T1_shft_osh2base_WARP.nii.gz '
** Program compile date = Sep 27 2021
** ERROR: program failed (3dNwarpApply, osh2base)
| Subject | Author | Posted |
|---|---|---|
|
El_suri | February 28, 2023 07:16AM |
|
ptaylor | February 28, 2023 08:46AM |
|
El_suri | February 28, 2023 09:50AM |
|
ptaylor | February 28, 2023 10:38AM |
|
El_suri | February 28, 2023 11:16AM |
|
ptaylor | February 28, 2023 11:35AM |
|
El_suri | March 03, 2023 07:03AM |
|
ptaylor | March 03, 2023 12:19PM |
|
El_suri | March 07, 2023 08:24AM |
|
ptaylor | March 07, 2023 03:12PM |
