Hi Paul,
So, I ran this 2 ways and I'm including the diary file from both. First, I ran @SSwarper -input ant+orig -base MNI152_2009_template_SSW.nii.gz -subid anat_warp -odir "$rootdir"/FACES_DATA/"$i". Based on some of the warnings, I then ran 3dwarp -deoblique first and re-ran things with that input.
thanks and let me know where to upload raw data if that will help.
thanks,
Stu
diary with anat input:
/Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111
++ Starting: @SSwarper v2.33
++ Default OMP_NUM_THREADS is 4
++ Prepare for running @djunct_overlap_check (ver = 0.2)
++ Just copy olay, bc ulay will get regridded
++ 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 4 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -set_dicom_xyz 0 0 0
\n------------------ start of optionizing ------------------\n
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: ./__tmp_chauf_th4Xoh7Cmt6
++ 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, 703.000000]
++ For olay, the 98%ile value leads to
--> upper range value: 1151.000000
++ Dimensions (xyzt): 280 320 208 1
++ (initial) Slice spacing ordered (x,y,z) is: 208 280 320
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :537
[1] 2821
Precompiled binary macos_10.12_local: Dec 7 2020 (Version AFNI_20.3.03 'Vespasian')
+++ Command Echo:
afni -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=1x1:208:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=1x1:280:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=1x1:320:1: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 703.000000 -com SET_FUNC_RANGE 1151.000000 -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_DICOM_XYZ 0 0 0 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com QUITT ./__tmp_chauf_th4Xoh7Cmt6
....\n+* Removing temporary image directory './__tmp_chauf_th4Xoh7Cmt6'.\n
[1] Done Xvfb :537 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 416x560) into a 3x1 matrix.
You can view image ../init_qc_00_overlap_usrc_obase.jpg with:
aiv ../init_qc_00_overlap_usrc_obase.jpg
++ And as a bonus, we have datasets with obliquity!
We will make an image of them with '3dWarp -deobliqu ..'
applied to each
++ My command:
@chauffeur_afni -obliquify ALL -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 4 -zerocolor black -prefix img01_DEOB -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -set_dicom_xyz 0 0 0
\n------------------ start of optionizing ------------------\n
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: ./__tmp_chauf_ZLdvAqIVAau
++ Apply obliquity to: ALL
# mat44 Obliquity Transformation ::
0.996664 -0.010595 0.080919 -8.025101
0.019156 0.994206 -0.105770 8.679749
-0.079330 0.106967 0.991093 10.631966
# mat44 Obliquity Transformation ::
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
++ 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, 657.000000]
++ For olay, the 98%ile value leads to
--> upper range value: 1151.000000
++ Dimensions (xyzt): 237 317 364 1
++ (initial) Slice spacing ordered (x,y,z) is: 237 317 364
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :312
[1] 2925
Precompiled binary macos_10.12_local: Dec 7 2020 (Version AFNI_20.3.03 'Vespasian')
+++ Command Echo:
afni -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=1x1:237:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=1x1:317:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=1x1:364:1: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 657.000000 -com SET_FUNC_RANGE 1151.000000 -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_DICOM_XYZ 0 0 0 -com SAVE_JPEG sagittalimage ./img01_DEOB.sag blowup=2 -com SAVE_JPEG coronalimage ./img01_DEOB.cor blowup=2 -com SAVE_JPEG axialimage ./img01_DEOB.axi blowup=2 -com QUITT ./__tmp_chauf_ZLdvAqIVAau
....\n+* Removing temporary image directory './__tmp_chauf_ZLdvAqIVAau'.\n
[1] + Done Xvfb :312 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img01_DEOB*
+++ Arranging 3 images (each 474x634) into a 3x1 matrix.
You can view image ../init_qc_00_overlap_usrc_obase_DEOB.jpg with:
aiv ../init_qc_00_overlap_usrc_obase_DEOB.jpg
\n+* Removing temporary workdir '/Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/__workdir_olap_0JcN9AmIuN0*'\n
++ DONE! Image output:
/Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/init_qc_00_overlap_usrc_obase
++ SSW Step 1
++ SSW Step 2
++ SSW Step 3
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[1] -lpa -warpscale 1 -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/anatUAC.anat_warp.nii -weight /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[2] -allineate -noneg -maxlev 5 -iwarp -awarp -wtgaus 4.5 -inedge -workhard:3:5 -nopenalty -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_TAL5.nii
# mat44 3dAllineate matrix:
0.870266 0.001529 0.010382 12.227700
-0.021335 0.907647 0.259981 -37.692600
-0.019619 -0.254539 0.793411 -15.753800
++ SSW Step 4
++ SSW Step 5
+++ Command Echo:
3dNwarpApply -nwarp /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_TAL5_WARPINV.nii -master /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/anatS.anat_warp.nii -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_TAL5mm.nii -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_TAL5ww.nii
+++ Command Echo:
3dmask_tool -input /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[3] -dilate_input 3 -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_MASK.nii
++ SSW Step 6
++ SSW Step 6 ... piece 0
++ SSW Step 6 ... piece 1
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[0] -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_AffSS.nii -iniwarp /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_TAL5_AWARP.nii -warpscale 1 -lpa -inilev 1 -maxlev 5 -wtgaus 4.5 -inedge -pblur -workhard:5:5 -nodset -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_QQ5.nii
++ SSW Step 6 ... piece 2
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[0] -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_AffSS.nii -iniwarp /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_QQ5_WARP.nii -warpscale 1 -pcl -inilev 6 -maxlev 7 -workhard:6:7 -wtgaus 4.5 -inedge -pblur -nodset -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_QQ7.nii
++ SSW Step 6 ... piece 3a
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[0] -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_AffSS.nii -iniwarp /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_QQ7_WARP.nii -warpscale 1 -pcl -inilev 8 -minpatch 17 -wtgaus 4.5 -inedge -pblur -nodset -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_DdgX81GF88L_QQ9.nii
** ERROR: program failed in Step 6.3b
*********************************************************************************************************************************************************************************
diary with output of 3dwarp -deoblique
/Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111
++ Starting: @SSwarper v2.33
++ Default OMP_NUM_THREADS is 4
++ Prepare for running @djunct_overlap_check (ver = 0.2)
++ Just copy olay, bc ulay will get regridded
++ 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 4 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -set_dicom_xyz 0 0 0
\n------------------ start of optionizing ------------------\n
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: ./__tmp_chauf_PmBYgkeaGhg
++ 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, 653.000000]
++ For olay, the 98%ile value leads to
--> upper range value: 1151.000000
++ Dimensions (xyzt): 237 317 364 1
++ (initial) Slice spacing ordered (x,y,z) is: 237 317 364
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :624
[1] 3650
Precompiled binary macos_10.12_local: Dec 7 2020 (Version AFNI_20.3.03 'Vespasian')
+++ Command Echo:
afni -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=1x1:237:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=1x1:317:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=1x1:364:1: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 653.000000 -com SET_FUNC_RANGE 1151.000000 -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_DICOM_XYZ 0 0 0 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com QUITT ./__tmp_chauf_PmBYgkeaGhg
....\n+* Removing temporary image directory './__tmp_chauf_PmBYgkeaGhg'.\n
[1] Done Xvfb :624 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 474x634) into a 3x1 matrix.
You can view image ../init_qc_00_overlap_usrc_obase.jpg with:
aiv ../init_qc_00_overlap_usrc_obase.jpg
\n+* Removing temporary workdir '/Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/__workdir_olap_JpZFjSfc0Jb*'\n
++ DONE! Image output:
/Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/init_qc_00_overlap_usrc_obase
++ SSW Step 1
++ SSW Step 2
++ SSW Step 3
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[1] -lpa -warpscale 1 -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/anatUAC.anat_warp.nii -weight /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[2] -allineate -noneg -maxlev 5 -iwarp -awarp -wtgaus 4.5 -inedge -workhard:3:5 -nopenalty -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_TAL5.nii
# mat44 3dAllineate matrix:
0.865222 -0.028987 0.072508 3.309490
-0.004089 0.928828 0.176186 -26.855400
-0.093809 -0.152533 0.813783 -10.068000
++ SSW Step 4
++ SSW Step 5
+++ Command Echo:
3dNwarpApply -nwarp /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_TAL5_WARPINV.nii -master /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/anatS.anat_warp.nii -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_TAL5mm.nii -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_TAL5ww.nii
+++ Command Echo:
3dmask_tool -input /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[3] -dilate_input 3 -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_MASK.nii
++ SSW Step 6
++ SSW Step 6 ... piece 0
++ SSW Step 6 ... piece 1
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[0] -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_AffSS.nii -iniwarp /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_TAL5_AWARP.nii -warpscale 1 -lpa -inilev 1 -maxlev 5 -wtgaus 4.5 -inedge -pblur -workhard:5:5 -nodset -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_QQ5.nii
++ SSW Step 6 ... piece 2
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[0] -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_AffSS.nii -iniwarp /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_QQ5_WARP.nii -warpscale 1 -pcl -inilev 6 -maxlev 7 -workhard:6:7 -wtgaus 4.5 -inedge -pblur -nodset -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_QQ7.nii
++ SSW Step 6 ... piece 3a
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[0] -source /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_AffSS.nii -iniwarp /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_QQ7_WARP.nii -warpscale 1 -pcl -inilev 8 -minpatch 17 -wtgaus 4.5 -inedge -pblur -nodset -prefix /Users/whistu/Desktop/fMRI/MILLER_wave2/FACES_DATA/111/junk.SSwarper_FO8ndMHh6MH_QQ9.nii
** ERROR: program failed in Step 6.3b
