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:

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

History of AFNI updates  

|
December 18, 2018 09:56AM
hi paul, i think the netpbm is already in my macos.
=====
bash-3.2$ brew install netpbm
Warning: netpbm 10.73.22 is already installed and up-to-date
To reinstall 10.73.22, run `brew reinstall netpbm`
=====
Here is the output in the command during running the
===============
"# I/O path, same as above; just need the "proc" dirs now
set path_P_ss = /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001

# reference anatomical volumes to which we axialize
set here = $PWD/fatcat_proc_mni_ref
set ref_t2w = $here/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz
set ref_t2w_wt = $here/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz

fat_proc_axialize_anat \
-inset $path_P_ss/anat_00/s005a1001.nii \
-prefix $path_P_ss/anat_01/t1w \
-mode_t1w \
-refset $ref_t2w \
-extra_al_wtmask $ref_t2w_wt \
-out_match_ref -extra_al_opts "-newgrid 1.0"
"
====================
CMac:scripts caroline$ tcsh dti_proc
++ Start script version: 4.2
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
118
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Found input file: /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_00/s005a1001.nii
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Found input file: /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Found input file: /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz

++ Based on prefix, the output directory will be:
/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01
++ Based on prefix, the output prefix will be:
t1w

+* WARNING: Somehow found a premade working directory (?):
/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w
NB: will *not* clean it afterwards.
\n-----> STARTING ---->
\n\nThis command:
fat_proc_axialize_anat -inset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_00/s005a1001.nii -prefix /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/t1w -mode_t1w -refset /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz -extra_al_wtmask /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz -out_match_ref -extra_al_opts -newgrid 1.0\n\n
++ Echoing the command to: /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/t1w_cmd.txt
\nThe reference template is: /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz

+++ Command Echo:
3dresample -orient AIL -prefix /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii -inset /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.gz -overwrite


+++ Command Echo:
3drefit -space ORIG -view orig /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii

++ 3drefit: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii
+ loading and re-writing dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii (/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF.nii in NIFTI storage)
++ 3drefit processed 1 datasets

+++ Command Echo:
3dresample -orient AIL -prefix /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii -inset /Users/caroline/CON_IA27/fatcat/scripts/fatcat_proc_mni_ref/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE_wtell.nii.gz -overwrite


+++ Command Echo:
3drefit -space ORIG -view orig /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii

++ 3drefit: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii
+ loading and re-writing dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii (/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/REF_WT.nii in NIFTI storage)
++ 3drefit processed 1 datasets

+++ Command Echo:
3dcalc -a /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_00/s005a1001.nii -expr a -prefix /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/tt_00.nii -float -overwrite

++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w/tt_00.nii
++ Distance between input's center of mass to (0,0,0) is 46.16598 mm.
-> if this is large, you might want to recenter with:
3dCM -set 0 0 0 FILE
or something (you could copy it first).
\n\n++ Threshold value at 90%: 476.000000\n

+++ Command Echo:
3dcalc -a tt_00.nii -expr maxbelow(476.000000,a) -prefix tt_01_thr.nii -overwrite

++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./tt_01_thr.nii
\n++ Doing unifizing.

+++ Command Echo:
3dUnifize -echo_edu -GM -prefix tt_02_uni.nii -input tt_01_thr.nii -overwrite


+++ Command Echo:
3dUnifize -echo_edu -GM -prefix tt_02_uni.nii -input tt_01_thr.nii -overwrite

++ 3dUnifize: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
+ Pre-processing: ADV...........UWGm
++ Output dataset ./tt_02_uni.nii
++ ===== CPU time = 99.3 sec Elapsed = 29.2
\n\n++ Percentile for thresholding: 1198.538086\n

+++ Command Echo:
3dcalc -a tt_02_uni.nii -expr maxbelow(1198.538086,a) -prefix tt_03_thr2.nii -overwrite

++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./tt_03_thr2.nii
++ processing tt_03_thr2.nii ...

+++ Command Echo:
3dAllineate -1Dmatrix_save _map_lr6 -warp shift_rotate -prefix tt_05_LR6.nii -base tt_04_LRflip.nii -twopass -cost nmi -source tt_03_thr2.nii -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_03_thr2.nii
++ Base dataset: ./tt_04_LRflip.nii
++ Loading datasets
++ 4614769 voxels in source_automask+0
++ Zero-pad: xbot=3 xtop=0
++ Zero-pad: ybot=4 ytop=0
++ Zero-pad: zbot=4 ztop=4
++ Computing -autobox
++ 8887424 voxels [81.8%] in weight mask
++ Number of points for matching = 4177089
++ master dataset for output = base
++ OpenMP thread count = 6
++ ======= Allineation of 1 sub-bricks using Normalized MI [H(b,s)/(H(b)+H(s))] =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift= 3.0378 y-shift= 0.2042 z-shift= 0.4294
z-angle= 4.5462 x-angle= -0.3741 y-angle= -8.8608
++ Output dataset ./tt_05_LR6.nii
++ Wrote -1Dmatrix_save _map_lr6.aff12.1D
++ 3dAllineate: total CPU time = 468.7 sec Elapsed = 217.0
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################

+++ Command Echo:
3dAllineate -1Dmatrix_apply _map_lr_half.aff12.1D -prefix tt_06_LRmid.nii -source tt_03_thr2.nii -final wsinc5 -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_03_thr2.nii
++ Base dataset: (not given)
++ You might want to use '-master' when using '-1D*_apply'
++ Loading datasets
++ master dataset for output = source
++ OpenMP thread count = 6
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./tt_06_LRmid.nii
++ 3dAllineate: total CPU time = 22.6 sec Elapsed = 4.6
++ ###########################################################
++ New inp0 = tt_07_origLR.nii

+++ Command Echo:
3dAllineate -1Dmatrix_apply _map_lr_half.aff12.1D -prefix tt_07_origLR.nii -source tt_00.nii -final wsinc5 -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_00.nii
++ Base dataset: (not given)
++ You might want to use '-master' when using '-1D*_apply'
++ Loading datasets
++ master dataset for output = source
++ OpenMP thread count = 6
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./tt_07_origLR.nii
++ 3dAllineate: total CPU time = 22.5 sec Elapsed = 4.5
++ ###########################################################
++ Aligning center of inset -> refset.
*+ WARNING: Over-writing dataset ./tt_06_LRmid.nii
++ Wrote new dataset: ./tt_06_LRmid.nii
base: 0.507591 20.3921 11.2511
dset: 3.76337 -21.7929 -48.2708
delta: -3.255779 42.185000 59.521900
42.185000 59.521900 3.255779
++ 3drefit: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./tt_07_origLR.nii
+ deoblique
+ loading and re-writing dataset ./tt_07_origLR.nii (./tt_07_origLR.nii in NIFTI storage)
++ 3drefit processed 1 datasets

+++ Command Echo:
3dAllineate -1Dparam_save _map_9dof -warp shift_rotate_scale -prefix tt_08_alnd.nii -base REF.nii -twopass -source_automask -weight REF_WT.nii -wtprefix tt_08_wtmask.nii -cost lpa -source tt_06_LRmid.nii -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_06_LRmid.nii
++ Base dataset: ./REF.nii
++ Loading datasets
++ 4456775 voxels in -source_automask
++ Zero-pad: ybot=3 ytop=0
++ 2227632 voxels [28.1%] in weight mask
++ Output dataset ./tt_08_wtmask.nii
++ Number of points for matching = 1046987
++ Local correlation: blok type = 'RHDD(6.54321)'
++ master dataset for output = base
++ OpenMP thread count = 6
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Abs =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift= -0.1258 y-shift= 11.0985 z-shift= 35.4955
z-angle= -0.5371 x-angle= 6.5675 y-angle= -0.1284
x-scale= 1.0493 y-scale= 0.9702 z-scale= 0.9082
++ Output dataset ./tt_08_alnd.nii
++ Wrote -1Dparam_save _map_9dof.param.1D
++ 3dAllineate: total CPU time = 146.2 sec Elapsed = 50.6
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ # '-autoweight' is recommended when using -lpc or -lpa #
++ # If your results are not good, please try again. #
++ ###########################################################

+++ Command Echo:
3dAllineate -1Dparam_apply map_fake12dof.param.1D -prefix tt_09_alnd0.nii -source tt_07_origLR.nii -final wsinc5 -newgrid 1.0 -master REF.nii -overwrite

++ 3dAllineate: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./tt_07_origLR.nii
++ Base dataset: (not given)
++ Loading datasets
++ changing output grid spacing to 1.0000 mm
++ OpenMP thread count = 6
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./tt_09_alnd0.nii
++ 3dAllineate: total CPU time = 15.1 sec Elapsed = 3.2
++ ###########################################################

+++ Command Echo:
3dcalc -overwrite -a tt_09_alnd0.nii -expr a -prefix ../t1w.nii.gz

++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../t1w.nii.gz
++ Making QC images.
++ QC image 00 (final output ulay): t1w_qc_xlzd
++ My command:
@chauffeur_afni -ulay ../t1w.nii.gz -prefix ../QC/t1w_qc_xlzd -montx 3 -monty 3 -set_xhairs MULTI -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
+* Noting: you did NOT provide an overlay, and yet
you did NOT turn off the overlay with '-olay_off'
--> so I assume you just want to view the underlay.
++ Using blowup factor: 2
++ Using opacity: 6
++ Making temporary work directory to copy vis files: ../QC/__tmp_chauf_J2dMGFqIb7v
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 570.249207]
++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../QC/__tmp_chauf_J2dMGFqIb7v/tmp_ulay.nii
++ No overlay viewing
++ Dimensions (xyzt): 236 172 192 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 26 19
++ 3dmaskdump: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ 7793664 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 117 85 95
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :81
[1] 65074
Precompiled binary macos_10.12_local: Dec 5 2018 (Version AFNI_18.3.15 'Augustus')

+++ Command Echo:
afni -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_ulay.nii -com SEE_OVERLAY - -com SET_PBAR_ALL -99 1 Plasma -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 570.249207 -com SET_FUNC_RANGE 0 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS MULTI -com OPEN_WINDOW sagittalimage opacity=6 mont=3x3:21 crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=3x3:26 crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=3x3:19 crop=0:0,0:0 -com SET_IJK 117 85 95 -com SAVE_PNG sagittalimage ../QC/t1w_qc_xlzd.sag blowup=2 -com SAVE_PNG coronalimage ../QC/t1w_qc_xlzd.cor blowup=2 -com SAVE_PNG axialimage ../QC/t1w_qc_xlzd.axi blowup=2 -com QUITT ../QC/__tmp_chauf_J2dMGFqIb7v


Thanks go to KR Hammett for great efforts

Initializing: X11[The X.Org Foundation v 11804000].
*** can't get X11 colormap entry for overlay color ###
*** can't get X11 colormap entry for overlay color for
*** can't get X11 colormap entry for overlay color underlay
*** can't get X11 colormap entry for overlay color AFNI_GLOBAL_SESSION. Widgets...... Input files:
session # 1 = QC/__tmp_chauf_J2dMGFqIb7v/ ==> 1 dataset
dataset count = 1
Time series = 5 files read
Plugins = 0 libraries read
++ Writing one 1416x1032 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_xlzd.sag.png'
++ Writing one 1152x1032 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_xlzd.cor.png'
++ Writing one 1152x1416 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_xlzd.axi.png'

AFNI QUITTs!
\n+* Removing temporary image directory '../QC/__tmp_chauf_J2dMGFqIb7v'.\n
[1] Done Xvfb :81 -screen 0 1024x768x24
++ QC image 01 (earlier allin olaying ref ulay): t1w_qc_ref_in
++ 3dedge3: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ My command:
@chauffeur_afni -ulay REF.nii -ulay_range 2% 98% -olay ./tt_alnd_edges.nii -func_range_perc_nz 50 -pbar_posonly -cbar red_monochrome -opacity 6 -prefix ../QC/t1w_qc_ref_in -montx 3 -monty 3 -set_xhairs MULTI -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Using blowup factor: 2
++ Using opacity: 6
++ Making temporary work directory to copy vis files: ../QC/__tmp_chauf_aOV7ti8h37D
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[2%, 98%] -> [0.000000, 84.141731]
++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../QC/__tmp_chauf_aOV7ti8h37D/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../QC/__tmp_chauf_aOV7ti8h37D/tmp_olay.nii
++ For olay, the 50%ile value leads to
--> upper range value: 360.823853
++ Dimensions (xyzt): 236 172 192 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 26 19
++ 3dmaskdump: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
++ 7793664 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 117 85 95
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :393
[1] 65206
Precompiled binary macos_10.12_local: Dec 5 2018 (Version AFNI_18.3.15 'Augustus')

+++ Command Echo:
afni -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com SET_PBAR_ALL +99 1 red_monochrome -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 84.141731 -com SET_FUNC_RANGE 360.823853 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS MULTI -com OPEN_WINDOW sagittalimage opacity=6 mont=3x3:21 crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=3x3:26 crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=3x3:19 crop=0:0,0:0 -com SET_IJK 117 85 95 -com SAVE_PNG sagittalimage ../QC/t1w_qc_ref_in.sag blowup=2 -com SAVE_PNG coronalimage ../QC/t1w_qc_ref_in.cor blowup=2 -com SAVE_PNG axialimage ../QC/t1w_qc_ref_in.axi blowup=2 -com QUITT ../QC/__tmp_chauf_aOV7ti8h37D


Thanks go to JA Butman for many suggestions

Initializing: X11[The X.Org Foundation v 11804000].
*** can't get X11 colormap entry for overlay color ###
*** can't get X11 colormap entry for overlay color for
*** can't get X11 colormap entry for overlay color underlay
*** can't get X11 colormap entry for overlay color AFNI_GLOBAL_SESSION. Widgets...... Input files:
session # 1 = QC/__tmp_chauf_aOV7ti8h37D/ ==> 2 datasets
dataset count = 2
Time series = 5 files read
Plugins = 0 libraries read
++ Writing one 1416x1032 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_ref_in.sag.png'
++ Writing one 1152x1032 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_ref_in.cor.png'
++ Writing one 1152x1416 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../QC/t1w_qc_ref_in.axi.png'

AFNI QUITTs!
\n+* Removing temporary image directory '../QC/__tmp_chauf_aOV7ti8h37D'.\n
[1] + Done Xvfb :393 -screen 0 1024x768x24
\n++ NOT removing temporary axialization working dir: '/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/__WORKING_axialize_anat_t1w'\n

++ DONE! View the finished, axialized product:
/Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001/anat_01/t1w.nii.gz
Subject Author Posted

no png after fat_proc_axialize_anat

charujing123 December 17, 2018 10:00AM

Re: no png after fat_proc_axialize_anat

ptaylor December 17, 2018 10:07AM

Re: no png after fat_proc_axialize_anat

charujing123 December 17, 2018 07:01PM

Re: no png after fat_proc_axialize_anat

ptaylor December 18, 2018 09:25AM

Re: no png after fat_proc_axialize_anat

charujing123 December 18, 2018 09:56AM

Re: no png after fat_proc_axialize_anat

ptaylor December 18, 2018 10:41AM

Re: no png after fat_proc_axialize_anat

charujing123 December 20, 2018 12:03AM