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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
| February 11, 2020 02:16PM | |
Registered: 4 years ago Posts: 48 |
Im trying to run the SSwarp in my T1 data but I don’t understand what ishappening with the SkullStrip step. It is giving me a very ugly results
I will be gratefull if you help me with this, Im sorry if is a dump question, Im kind of new with this program
Here is also my output of the sswarper
+ Based on input, the output directory will be:
/Users/lbohorquez/Desktop/example/307_122117/anat
++ 3dUnifize: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
+ Pre-processing: ADV.............UWGm
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/anatU.ssWarp.nii
++ ===== CPU time = 137.7 sec Elapsed = 19.8
++ Notice SUMA_BrainWrap_ParseInput (SUMA_3dSkullStrip.c:1219 @08:58:33):
Setting fill_hole to 10
++ Notice 3dSkullStrip (SUMA_3dSkullStrip.c:1529 @08:58:33):
Loading dset, performing Spatial Normalization
3dSkullStrip:
Original resolution -0.937500, -0.937500, 1.000000
SpatNorm resolution 0.937500, 0.937500, 1.000000
++mri_brainormalize: normalizing
++mri_brainormalize: Rescaling.
++mri_brainormalize: Eroding, clustering ...
+ Eroded 642134 voxels
+ Restored 587395 eroded voxels
+ Clustering voxels ...
+ Largest cluster has 4457392 voxels
+ Clustering voxels ...
+ Largest cluster has 1687639 voxels
++mri_brainormalize: Clipping extreme values.
+ scaling by fac=0.035397
3dSkullStrip: -spatnorm: Expecting 6195700 voxels in in_vol dset (167 212 175)
3dSkullStrip: Edge threshold set to 41.218464. (minimum acceptable was 24.292912)
(92.000000 percentile =41.218464, 99.999001 percentile = 242.929123)
3dSkullStrip: Prepping volume...
SUMA_LoadPrepInVol: Volume 4500527.000000, radius 102.421638
++ Notice SUMA_LoadPrepInVol (SUMA_BrainWrap.c:183 @08:58:37):
Radius estimated at 102.421638 is large.
Setting back to 100.0
3dSkullStrip: Beginning brain extraction...
3dSkullStrip: Have surface, OK for 1st entry.
3dSkullStrip: Stretching to avoid ventricles.
SO->Center is [-0.203728 11.719861 1.268312]
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: pastarea = 66015.661895
SUMA_StretchToFitLeCerveau:
Stage1: MaxExp = 0.567497, darea = 0.000000, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 5887 troubled nodes, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.443859 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.082773 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.010989 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.040741 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.021762 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: -0.009329 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Stage converged. Moving to new Stage or Type.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
Stage 3, type 2: 1.000000 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
3dSkullStrip: Checking for self intersection...
3dSkullStrip: No intersections found.
3dSkullStrip: Final smoothing of 72
3dSkullStrip: Touchup correction, pass 1 ...
3dSkullStrip: The beauty treatment smoothing.
3dSkullStrip: Locating voxels inside surface ...
3dSkullStrip: Setting output to orig_vol (iset = 0x7fee81804c00) (osnd = 0x7fee4100f200)...
3dSkullStrip: Coercing...
3dSkullStrip: Writing masked volume ...
3dSkullStrip: Applying a bit of erosion and dilatation
++ OpenMP thread count = 15
++ 3dQwarp: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Starting 3dAllineate (affine register) command:
3dAllineate -base /Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz[1] -source /Users/lbohorquez/Desktop/example/307_122117/anat/anatU.ssWarp.nii -prefix AFN_6dV8ibQNvXSA7A38zvsJiQ.nii -1Dmatrix_save AFN_6dV8ibQNvXSA7A38zvsJiQ -cmass -final wsinc5 -float -master BASE -twobest 7 -zclip -fineblur 4.44
++ ###########################################################
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/lbohorquez/Desktop/example/307_122117/anat/anatU.ssWarp.nii
++ Base dataset: /Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz
++ Loading datasets
++ 6608697 voxels in source_automask+0
++ Zero-pad: ybot=0 ytop=1
++ Computing -autobox
++ 8007930 voxels [93.5%] in weight mask
++ Number of points for matching = 3763727
++ OpenMP thread count = 15
++ ======= Allineation of 1 sub-bricks using Hellinger metric =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift= -9.8505 y-shift=-30.2513 z-shift= 7.7683
z-angle= 29.9972 x-angle= -0.9430 y-angle= 0.2854
x-scale= 1.0294 y-scale= 1.1859 z-scale= 0.9280
y/x-shear= -0.0524 z/x-shear= -0.0080 z/y-shear= -0.0153
++ Output dataset ./AFN_6dV8ibQNvXSA7A38zvsJiQ.nii
++ Wrote -1Dmatrix_save AFN_6dV8ibQNvXSA7A38zvsJiQ.aff12.1D
++ 3dAllineate: total CPU time = 774.0 sec Elapsed = 282.5
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ 3dQwarp: replacing source dataset with 3dAllineate result /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_Allin.nii
+ 3dAllineate output files have been renamed
# mat44 3dAllineate matrix:
0.891573 0.514593 -0.005128 -9.850480
-0.639590 0.999954 -0.019249 -30.251301
-0.001752 -0.004263 0.928154 7.768310
++ Dataset zero-pad: xbot=34 xtop=33 ybot=28 ytop=37 zbot=34 ztop=28 voxels
++ +++++++++++ Begin warp optimization: base=/Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz source=/Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_Allin.nii
++ AFNI warpomatic: 260 x 294 x 255 volume ; autobbox = 40..219 41..253 40..214 [clock= 4m 44s 595ms]
lev=0 18..241 15..279 19..235: [first cost=-0.00967] .. done [cost:-0.00967==>-0.13139]
lev=1 patch=195x221x191 [clock= 6m 3s 372ms]..... done [cost:-0.13139==>-0.20469 ; 5 patches optimized, 3 skipped]
lev=2 patch=147x165x143 [clock= 7m 6s 560ms]..... done [cost:-0.20469==>-0.24007 ; 5 patches optimized, 7 skipped]
lev=3 patch=111x125x107 [clock= 7m 43s 286ms]..... done [cost:-0.24007==>1.73064 ; 19 patches optimized, 8 skipped]
lev=4 patch=83x93x81 [clock= 10m 3s 137ms]........... done [cost:1.73064==>0.67559 ; 54 patches optimized, 26 skipped]
lev=5 patch=61x71x61 [clock= 12m 54s 371ms]......... done [cost:0.67559==>0.17896 ; 135 patches optimized, 81 skipped]
++ ========== total number of parameters 'optimized' = 5337
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_AWARP.nii
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5.nii
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_WARP.nii
++ Inverting warp *********...............:..
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_WARPINV.nii
++ ===== CPU time = 5034.5 sec clock time = 16m 45s 17ms
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 1 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2000189 survived, 6529832 were zero
++ writing result junk.SSwarper.qYoxXgLeCSu_MASK.nii...
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_MASK.nii
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5mm.nii
++ 3dNwarpApply: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is '/Users/lbohorquez/Desktop/example/307_122117/anat/anatS.ssWarp.nii'
** AFNI converts NIFTI_datatype=2 (UINT8) in file /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5mm.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ opened source dataset '/Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5mm.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5ww.nii
++ total CPU time = 86.7 sec Elapsed = 8.8
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 2 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2117569 survived, 6412452 were zero
++ writing result junk.SSwarper.qYoxXgLeCSu_MASK.nii...
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_MASK.nii
++ 3dNwarpApply: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is '/Users/lbohorquez/Desktop/example/307_122117/anat/anatS.ssWarp.nii'
++ opened source dataset '/Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_MASK.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_MASKO.nii
++ total CPU time = 68.5 sec Elapsed = 7.0
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/anatSS.ssWarp.nii
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Registrator
** AFNI converts NIFTI_datatype=2 (UINT8) in file /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5mm.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Source dataset: /Users/lbohorquez/Desktop/example/307_122117/anat/anatSS.ssWarp.nii
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 15
++ ========== 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 /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_AffSS.nii
++ 3dAllineate: total CPU time = 17.5 sec Elapsed = 2.4
++ ###########################################################
++ OpenMP thread count = 15
++ 3dQwarp: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=34 xtop=33 ybot=28 ytop=37 zbot=34 ztop=28 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=/Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz source=/Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_AffSS.nii
++ AFNI warpomatic: 260 x 294 x 255 volume ; autobbox = 53..207 48..238 35..198 [clock= 5s 670ms]
lev=1 patch=195x221x191 [clock= 7s 801ms][first cost=-1.48624] . done [cost:-1.48624==>-1.56122 ; 1 patches optimized, 8 skipped]
lev=2 patch=147x165x143 [clock= 20s 855ms][first cost=-1.23232] . done [cost:-1.56122==>-1.27021 ; 1 patches optimized, 8 skipped]
lev=3 patch=111x125x107 [clock= 30s 474ms][first cost=0.85435] ........ done [cost:-1.27021==>-0.35103 ; 16 patches optimized, 11 skipped]
lev=4 patch=83x93x81 [clock= 2m 12s 653ms][first cost=-0.08011] ... done [cost:-0.35103==>-0.42353 ; 32 patches optimized, 32 skipped]
lev=5 patch=61x71x61 [clock= 3m 45s 63ms][first cost=-0.24244] ..........:[cost=-0.43276]:......... done [cost:-0.42353==>-0.49690 ; 153 patches optimized, 97 skipped]
lev=6 patch=47x53x45 [clock= 7m 7s 520ms][first cost=-0.38270] .......:[cost=-0.45075]:....... done [cost:-0.49690==>-0.47322 ; 408 patches optimized, 278 skipped]
lev=7 patch=35x39x35 [clock= 10m 58s 828ms][first cost=-0.39106] ............:[cost=-0.43503]:...... done [cost:-0.47322==>-0.43361 ; 991 patches optimized, 809 skipped]
lev=8 patch=27x29x25 [clock= 15m 7s 250ms][first cost=-0.38754] ...........................:[cost=-0.41560]:.................... done [cost:-0.43361==>-0.40339 ; 2437 patches optimized, 2267 skipped]
lev=9 patch=19x23x19 [clock= 20m 40s 942ms][first cost=-0.38713] ...................................... done [cost:-0.40339==>-0.40732 ; 2779 patches optimized, 2423 skipped]
lev=10 patch=15x17x15 [clock= 24m 47s 347ms][first cost=-0.37899] ............................................................ done [cost:-0.40732==>-0.35802 ; 6104 patches optimized, 6040 skipped]
lev=11 patch=11x11x11 [clock= 32m 8s 674ms][first cost=-0.37682] ..................................................................................................................................... done [cost:-0.35802==>-0.39537 ; 18406 patches optimized, 20468 skipped]
++ ========== total number of parameters 'optimized' = 751872
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/anatQQ.ssWarp.nii
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/anatQQ.ssWarp_WARP.nii
++ ===== CPU time = 12916.6 sec clock time = 51m 42s 978ms
Illegal variable name.
-- trying to start Xvfb :302
[1] 21375
++ 3dAutobox: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Auto bbox: x=8..184 y=8..221 z=-13..176
++ 3dAutobox: output dataset = ./zzerm.X302-330924.acrop.nii
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 15
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset ./zzerm.X302-330924.epiR.nii
++ 3dAllineate: total CPU time = 0.5 sec Elapsed = 0.4
++ ###########################################################
++ 3dMedianFilter: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Output dataset ./zzerm.X302-330924.epiRS.nii
++ 3dedge3: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ 3dAutomask: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Emperor Zhark
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./zzerm.X302-330924.epiEM.nii
Precompiled binary macosx_10.7_local: Aug 28 2018 (Version AFNI_18.2.15)
Thanks go to J Rajendra for great efforts
Initializing: X11[The X.Org Foundation v 11804000].. Widgets...... Input files:
session # 1 = fromCLI ==> 2 datasets
dataset count = 2
Time series = 1 files read
Plugins = 0 libraries read
++ Writing one 1284x380 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X302-330924.sag.jpg'
++ Writing one 1062x380 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X302-330924.cor.jpg'
++ Writing one 1062x428 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X302-330924.axi.jpg'
AFNI QUITTs!
@snapshot_volreg output image = /Users/lbohorquez/Desktop/example/307_122117/anat/AMssWarp.jpg
Illegal variable name.
-- trying to start Xvfb :257
[1] 21466
++ 3dAutobox: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Auto bbox: x=8..185 y=8..222 z=-10..177
++ 3dAutobox: output dataset = ./zzerm.X257-917921.acrop.nii
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/lbohorquez/Desktop/example/307_122117/anat/anatQQ.ssWarp.nii
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 15
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset ./zzerm.X257-917921.epiR.nii
++ 3dAllineate: total CPU time = 0.4 sec Elapsed = 0.4
++ ###########################################################
++ 3dMedianFilter: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Output dataset ./zzerm.X257-917921.epiRS.nii
++ 3dedge3: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ 3dAutomask: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Emperor Zhark
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./zzerm.X257-917921.epiEM.nii
Precompiled binary macosx_10.7_local: Aug 28 2018 (Version AFNI_18.2.15)
Thanks go to SM Laconte for inspiration
Initializing: X11[The X.Org Foundation v 11804000].. Widgets...... Input files:
session # 1 = fromCLI ==> 2 datasets
dataset count = 2
Time series = 1 files read
Plugins = 0 libraries read
++ Writing one 1290x376 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X257-917921.sag.jpg'
++ Writing one 1068x376 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X257-917921.cor.jpg'
++ Writing one 1068x430 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X257-917921.axi.jpg'
AFNI QUITTs!
@snapshot_volreg output image = /Users/lbohorquez/Desktop/example/307_122117/anat/MAssWarp.jpg
##Here is my script
#!/bin/bash
subject="$1"
export SUBJECTS_DIR=/Users/lbohorquez/Desktop/"$subject"/
#Run SSwarp
cd /Users/lbohorquez/Desktop/example/307_122117/anat
@SSwarper -input /Users/lbohorquez/Desktop/example/307_122117/anat/307_Ax_FSPGR_3D_GR.nii.gz -base MNI152_2009_template_SSW.nii.gz -subid ssWarp
I will be gratefull if you help me with this, Im sorry if is a dump question, Im kind of new with this program
Here is also my output of the sswarper
+ Based on input, the output directory will be:
/Users/lbohorquez/Desktop/example/307_122117/anat
++ 3dUnifize: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
+ Pre-processing: ADV.............UWGm
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/anatU.ssWarp.nii
++ ===== CPU time = 137.7 sec Elapsed = 19.8
++ Notice SUMA_BrainWrap_ParseInput (SUMA_3dSkullStrip.c:1219 @08:58:33):
Setting fill_hole to 10
++ Notice 3dSkullStrip (SUMA_3dSkullStrip.c:1529 @08:58:33):
Loading dset, performing Spatial Normalization
3dSkullStrip:
Original resolution -0.937500, -0.937500, 1.000000
SpatNorm resolution 0.937500, 0.937500, 1.000000
++mri_brainormalize: normalizing
++mri_brainormalize: Rescaling.
++mri_brainormalize: Eroding, clustering ...
+ Eroded 642134 voxels
+ Restored 587395 eroded voxels
+ Clustering voxels ...
+ Largest cluster has 4457392 voxels
+ Clustering voxels ...
+ Largest cluster has 1687639 voxels
++mri_brainormalize: Clipping extreme values.
+ scaling by fac=0.035397
3dSkullStrip: -spatnorm: Expecting 6195700 voxels in in_vol dset (167 212 175)
3dSkullStrip: Edge threshold set to 41.218464. (minimum acceptable was 24.292912)
(92.000000 percentile =41.218464, 99.999001 percentile = 242.929123)
3dSkullStrip: Prepping volume...
SUMA_LoadPrepInVol: Volume 4500527.000000, radius 102.421638
++ Notice SUMA_LoadPrepInVol (SUMA_BrainWrap.c:183 @08:58:37):
Radius estimated at 102.421638 is large.
Setting back to 100.0
3dSkullStrip: Beginning brain extraction...
3dSkullStrip: Have surface, OK for 1st entry.
3dSkullStrip: Stretching to avoid ventricles.
SO->Center is [-0.203728 11.719861 1.268312]
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: pastarea = 66015.661895
SUMA_StretchToFitLeCerveau:
Stage1: MaxExp = 0.567497, darea = 0.000000, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 5887 troubled nodes, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.443859 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.082773 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.010989 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.040741 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.021762 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: -0.009329 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Stage converged. Moving to new Stage or Type.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
Stage 3, type 2: 1.000000 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
3dSkullStrip: Checking for self intersection...
3dSkullStrip: No intersections found.
3dSkullStrip: Final smoothing of 72
3dSkullStrip: Touchup correction, pass 1 ...
3dSkullStrip: The beauty treatment smoothing.
3dSkullStrip: Locating voxels inside surface ...
3dSkullStrip: Setting output to orig_vol (iset = 0x7fee81804c00) (osnd = 0x7fee4100f200)...
3dSkullStrip: Coercing...
3dSkullStrip: Writing masked volume ...
3dSkullStrip: Applying a bit of erosion and dilatation
++ OpenMP thread count = 15
++ 3dQwarp: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Starting 3dAllineate (affine register) command:
3dAllineate -base /Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz[1] -source /Users/lbohorquez/Desktop/example/307_122117/anat/anatU.ssWarp.nii -prefix AFN_6dV8ibQNvXSA7A38zvsJiQ.nii -1Dmatrix_save AFN_6dV8ibQNvXSA7A38zvsJiQ -cmass -final wsinc5 -float -master BASE -twobest 7 -zclip -fineblur 4.44
++ ###########################################################
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/lbohorquez/Desktop/example/307_122117/anat/anatU.ssWarp.nii
++ Base dataset: /Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz
++ Loading datasets
++ 6608697 voxels in source_automask+0
++ Zero-pad: ybot=0 ytop=1
++ Computing -autobox
++ 8007930 voxels [93.5%] in weight mask
++ Number of points for matching = 3763727
++ OpenMP thread count = 15
++ ======= Allineation of 1 sub-bricks using Hellinger metric =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift= -9.8505 y-shift=-30.2513 z-shift= 7.7683
z-angle= 29.9972 x-angle= -0.9430 y-angle= 0.2854
x-scale= 1.0294 y-scale= 1.1859 z-scale= 0.9280
y/x-shear= -0.0524 z/x-shear= -0.0080 z/y-shear= -0.0153
++ Output dataset ./AFN_6dV8ibQNvXSA7A38zvsJiQ.nii
++ Wrote -1Dmatrix_save AFN_6dV8ibQNvXSA7A38zvsJiQ.aff12.1D
++ 3dAllineate: total CPU time = 774.0 sec Elapsed = 282.5
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ 3dQwarp: replacing source dataset with 3dAllineate result /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_Allin.nii
+ 3dAllineate output files have been renamed
# mat44 3dAllineate matrix:
0.891573 0.514593 -0.005128 -9.850480
-0.639590 0.999954 -0.019249 -30.251301
-0.001752 -0.004263 0.928154 7.768310
++ Dataset zero-pad: xbot=34 xtop=33 ybot=28 ytop=37 zbot=34 ztop=28 voxels
++ +++++++++++ Begin warp optimization: base=/Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz source=/Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_Allin.nii
++ AFNI warpomatic: 260 x 294 x 255 volume ; autobbox = 40..219 41..253 40..214 [clock= 4m 44s 595ms]
lev=0 18..241 15..279 19..235: [first cost=-0.00967] .. done [cost:-0.00967==>-0.13139]
lev=1 patch=195x221x191 [clock= 6m 3s 372ms]..... done [cost:-0.13139==>-0.20469 ; 5 patches optimized, 3 skipped]
lev=2 patch=147x165x143 [clock= 7m 6s 560ms]..... done [cost:-0.20469==>-0.24007 ; 5 patches optimized, 7 skipped]
lev=3 patch=111x125x107 [clock= 7m 43s 286ms]..... done [cost:-0.24007==>1.73064 ; 19 patches optimized, 8 skipped]
lev=4 patch=83x93x81 [clock= 10m 3s 137ms]........... done [cost:1.73064==>0.67559 ; 54 patches optimized, 26 skipped]
lev=5 patch=61x71x61 [clock= 12m 54s 371ms]......... done [cost:0.67559==>0.17896 ; 135 patches optimized, 81 skipped]
++ ========== total number of parameters 'optimized' = 5337
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_AWARP.nii
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5.nii
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_WARP.nii
++ Inverting warp *********...............:..
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5_WARPINV.nii
++ ===== CPU time = 5034.5 sec clock time = 16m 45s 17ms
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 1 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2000189 survived, 6529832 were zero
++ writing result junk.SSwarper.qYoxXgLeCSu_MASK.nii...
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_MASK.nii
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5mm.nii
++ 3dNwarpApply: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is '/Users/lbohorquez/Desktop/example/307_122117/anat/anatS.ssWarp.nii'
** AFNI converts NIFTI_datatype=2 (UINT8) in file /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5mm.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ opened source dataset '/Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5mm.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5ww.nii
++ total CPU time = 86.7 sec Elapsed = 8.8
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 2 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2117569 survived, 6412452 were zero
++ writing result junk.SSwarper.qYoxXgLeCSu_MASK.nii...
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_MASK.nii
++ 3dNwarpApply: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is '/Users/lbohorquez/Desktop/example/307_122117/anat/anatS.ssWarp.nii'
++ opened source dataset '/Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_MASK.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_MASKO.nii
++ total CPU time = 68.5 sec Elapsed = 7.0
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/anatSS.ssWarp.nii
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Registrator
** AFNI converts NIFTI_datatype=2 (UINT8) in file /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_TAL5mm.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Source dataset: /Users/lbohorquez/Desktop/example/307_122117/anat/anatSS.ssWarp.nii
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 15
++ ========== 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 /Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_AffSS.nii
++ 3dAllineate: total CPU time = 17.5 sec Elapsed = 2.4
++ ###########################################################
++ OpenMP thread count = 15
++ 3dQwarp: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=34 xtop=33 ybot=28 ytop=37 zbot=34 ztop=28 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=/Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz source=/Users/lbohorquez/Desktop/example/307_122117/anat/junk.SSwarper.qYoxXgLeCSu_AffSS.nii
++ AFNI warpomatic: 260 x 294 x 255 volume ; autobbox = 53..207 48..238 35..198 [clock= 5s 670ms]
lev=1 patch=195x221x191 [clock= 7s 801ms][first cost=-1.48624] . done [cost:-1.48624==>-1.56122 ; 1 patches optimized, 8 skipped]
lev=2 patch=147x165x143 [clock= 20s 855ms][first cost=-1.23232] . done [cost:-1.56122==>-1.27021 ; 1 patches optimized, 8 skipped]
lev=3 patch=111x125x107 [clock= 30s 474ms][first cost=0.85435] ........ done [cost:-1.27021==>-0.35103 ; 16 patches optimized, 11 skipped]
lev=4 patch=83x93x81 [clock= 2m 12s 653ms][first cost=-0.08011] ... done [cost:-0.35103==>-0.42353 ; 32 patches optimized, 32 skipped]
lev=5 patch=61x71x61 [clock= 3m 45s 63ms][first cost=-0.24244] ..........:[cost=-0.43276]:......... done [cost:-0.42353==>-0.49690 ; 153 patches optimized, 97 skipped]
lev=6 patch=47x53x45 [clock= 7m 7s 520ms][first cost=-0.38270] .......:[cost=-0.45075]:....... done [cost:-0.49690==>-0.47322 ; 408 patches optimized, 278 skipped]
lev=7 patch=35x39x35 [clock= 10m 58s 828ms][first cost=-0.39106] ............:[cost=-0.43503]:...... done [cost:-0.47322==>-0.43361 ; 991 patches optimized, 809 skipped]
lev=8 patch=27x29x25 [clock= 15m 7s 250ms][first cost=-0.38754] ...........................:[cost=-0.41560]:.................... done [cost:-0.43361==>-0.40339 ; 2437 patches optimized, 2267 skipped]
lev=9 patch=19x23x19 [clock= 20m 40s 942ms][first cost=-0.38713] ...................................... done [cost:-0.40339==>-0.40732 ; 2779 patches optimized, 2423 skipped]
lev=10 patch=15x17x15 [clock= 24m 47s 347ms][first cost=-0.37899] ............................................................ done [cost:-0.40732==>-0.35802 ; 6104 patches optimized, 6040 skipped]
lev=11 patch=11x11x11 [clock= 32m 8s 674ms][first cost=-0.37682] ..................................................................................................................................... done [cost:-0.35802==>-0.39537 ; 18406 patches optimized, 20468 skipped]
++ ========== total number of parameters 'optimized' = 751872
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/anatQQ.ssWarp.nii
++ Output dataset /Users/lbohorquez/Desktop/example/307_122117/anat/anatQQ.ssWarp_WARP.nii
++ ===== CPU time = 12916.6 sec clock time = 51m 42s 978ms
Illegal variable name.
-- trying to start Xvfb :302
[1] 21375
++ 3dAutobox: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Auto bbox: x=8..184 y=8..221 z=-13..176
++ 3dAutobox: output dataset = ./zzerm.X302-330924.acrop.nii
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/lbohorquez/abin/MNI152_2009_template_SSW.nii.gz
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 15
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset ./zzerm.X302-330924.epiR.nii
++ 3dAllineate: total CPU time = 0.5 sec Elapsed = 0.4
++ ###########################################################
++ 3dMedianFilter: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Output dataset ./zzerm.X302-330924.epiRS.nii
++ 3dedge3: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ 3dAutomask: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Emperor Zhark
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./zzerm.X302-330924.epiEM.nii
Precompiled binary macosx_10.7_local: Aug 28 2018 (Version AFNI_18.2.15)
Thanks go to J Rajendra for great efforts
Initializing: X11[The X.Org Foundation v 11804000].. Widgets...... Input files:
session # 1 = fromCLI ==> 2 datasets
dataset count = 2
Time series = 1 files read
Plugins = 0 libraries read
++ Writing one 1284x380 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X302-330924.sag.jpg'
++ Writing one 1062x380 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X302-330924.cor.jpg'
++ Writing one 1062x428 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X302-330924.axi.jpg'
AFNI QUITTs!
@snapshot_volreg output image = /Users/lbohorquez/Desktop/example/307_122117/anat/AMssWarp.jpg
Illegal variable name.
-- trying to start Xvfb :257
[1] 21466
++ 3dAutobox: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Auto bbox: x=8..185 y=8..222 z=-10..177
++ 3dAutobox: output dataset = ./zzerm.X257-917921.acrop.nii
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/lbohorquez/Desktop/example/307_122117/anat/anatQQ.ssWarp.nii
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 15
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset ./zzerm.X257-917921.epiR.nii
++ 3dAllineate: total CPU time = 0.4 sec Elapsed = 0.4
++ ###########################################################
++ 3dMedianFilter: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Output dataset ./zzerm.X257-917921.epiRS.nii
++ 3dedge3: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ 3dAutomask: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Emperor Zhark
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./zzerm.X257-917921.epiEM.nii
Precompiled binary macosx_10.7_local: Aug 28 2018 (Version AFNI_18.2.15)
Thanks go to SM Laconte for inspiration
Initializing: X11[The X.Org Foundation v 11804000].. Widgets...... Input files:
session # 1 = fromCLI ==> 2 datasets
dataset count = 2
Time series = 1 files read
Plugins = 0 libraries read
++ Writing one 1290x376 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X257-917921.sag.jpg'
++ Writing one 1068x376 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X257-917921.cor.jpg'
++ Writing one 1068x430 image to filter '/usr/local/bin/cjpeg -quality 95 > zzerm.X257-917921.axi.jpg'
AFNI QUITTs!
@snapshot_volreg output image = /Users/lbohorquez/Desktop/example/307_122117/anat/MAssWarp.jpg
##Here is my script
#!/bin/bash
subject="$1"
export SUBJECTS_DIR=/Users/lbohorquez/Desktop/"$subject"/
#Run SSwarp
cd /Users/lbohorquez/Desktop/example/307_122117/anat
@SSwarper -input /Users/lbohorquez/Desktop/example/307_122117/anat/307_Ax_FSPGR_3D_GR.nii.gz -base MNI152_2009_template_SSW.nii.gz -subid ssWarp
| Subject | Author | Posted |
|---|---|---|
|
LuisaBoh | February 11, 2020 02:16PM |
|
ptaylor | February 11, 2020 02:23PM |
|
LuisaBoh | February 13, 2020 09:24AM |
|
ptaylor | February 14, 2020 12:20PM |
