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Subject:

TBSS error

From:

Alina Dinu <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 12 Oct 2016 17:52:54 +0100

Content-Type:

text/plain

Parts/Attachments:
Parts/Attachments

text/plain (32 lines) 

Hello,

I am trying to run a GBSS pipeline and I am getting erros at the first steps of TBSS step. I am getting this enrmous error and then there are many more to come. Could you please help me? 

Thank you very much!
ANTS Method=1
Template File: /data/standard/MNI152_T1_1mm.nii.gz
MRF=0.3
Output directory: directory
mkdir: cannot create directory ‘directory/tmpspace’: File exists
Starting TBSS preproc to discard the high intensity rim of the FA files...
Now running "slicesdir" to generate report of all input images
Finished. To view, point your web browser at
file:/home/brain/GBSS/NODDI/directory/FA/FA/slicesdir/index.html
+ echo 'GM/WM PVE estimation/Creating PseudoT1 Images...'
GM/WM PVE estimation/Creating PseudoT1 Images...
+ cd directory/FA/FA
./gbss_1_reg.sh: line 155: cd: directory/FA/FA: No such file or directory
+ for a in '*_FA.nii.gz'
++ echo antsApplyTransforms.e1364 antsApplyTransforms.e1384 antsApplyTransforms.e1404 antsApplyTransforms.e1424 antsApplyTransforms.e1444 antsApplyTransforms.e1783 antsApplyTransforms.e1803 antsApplyTransforms.e1823 antsApplyTransforms.e1843 antsApplyTransforms.e1863 antsApplyTransforms.e2255 antsApplyTransforms.e2275 antsApplyTransforms.e2295 antsApplyTransforms.e2315 antsApplyTransforms.e2335 antsApplyTransforms.e2675 antsApplyTransforms.e2695 antsApplyTransforms.e2715 antsApplyTransforms.e2735 antsApplyTransforms.e2755 antsApplyTransforms.e2957 antsApplyTransforms.e2977 antsApplyTransforms.e2997 antsApplyTransforms.e3017 antsApplyTransforms.e3037 antsApplyTransforms.e3605 antsApplyTransforms.e3625 antsApplyTransforms.e3645 antsApplyTransforms.e3665 antsApplyTransforms.e3685 antsApplyTransforms.e4215 antsApplyTransforms.e4235 antsApplyTransforms.e4255 antsApplyTransforms.e4275 antsApplyTransforms.e4295 antsApplyTransforms.e4634 antsApplyTransforms.e4654 antsApplyTransforms.e4674 antsApplyTransforms.e4694 antsApplyTransforms.e4714 antsApplyTransforms.e5212 antsApplyTransforms.e5232 antsApplyTransforms.e5252 antsApplyTransforms.e5272 antsApplyTransforms.e5292 antsApplyTransforms.e6149 antsApplyTransforms.e6169 antsApplyTransforms.e6189 antsApplyTransforms.e6209 antsApplyTransforms.e6229 antsApplyTransforms.e6571 antsApplyTransforms.e6591 antsApplyTransforms.e6611 antsApplyTransforms.e6631 antsApplyTransforms.e6651 antsApplyTransforms.o1364 antsApplyTransforms.o1384 antsApplyTransforms.o1404 antsApplyTransforms.o1424 antsApplyTransforms.o1444 antsApplyTransforms.o1783 antsApplyTransforms.o1803 antsApplyTransforms.o1823 antsApplyTransforms.o1843 antsApplyTransforms.o1863 antsApplyTransforms.o2255 antsApplyTransforms.o2275 antsApplyTransforms.o2295 antsApplyTransforms.o2315 antsApplyTransforms.o2335 antsApplyTransforms.o2675 antsApplyTransforms.o2695 antsApplyTransforms.o2715 antsApplyTransforms.o2735 antsApplyTransforms.o2755 antsApplyTransforms.o2957 antsApplyTransforms.o2977 antsApplyTransforms.o2997 antsApplyTransforms.o3017 antsApplyTransforms.o3037 antsApplyTransforms.o3605 antsApplyTransforms.o3625 antsApplyTransforms.o3645 antsApplyTransforms.o3665 antsApplyTransforms.o3685 antsApplyTransforms.o4215 antsApplyTransforms.o4235 antsApplyTransforms.o4255 antsApplyTransforms.o4275 antsApplyTransforms.o4295 antsApplyTransforms.o4634 antsApplyTransforms.o4654 antsApplyTransforms.o4674 antsApplyTransforms.o4694 antsApplyTransforms.o4714 antsApplyTransforms.o5212 antsApplyTransforms.o5232 antsApplyTransforms.o5252 antsApplyTransforms.o5272 antsApplyTransforms.o5292 antsApplyTransforms.o6149 antsApplyTransforms.o6169 antsApplyTransforms.o6189 antsApplyTransforms.o6209 antsApplyTransforms.o6229 antsApplyTransforms.o6571 antsApplyTransforms.o6591 antsApplyTransforms.o6611 antsApplyTransforms.o6631 antsApplyTransforms.o6651 FA origdata
+ subname='antsApplyTransforms.e1364 antsApplyTransforms.e1384 antsApplyTransforms.e1404 antsApplyTransforms.e1424 antsApplyTransforms.e1444 antsApplyTransforms.e1783 antsApplyTransforms.e1803 antsApplyTransforms.e1823 antsApplyTransforms.e1843 antsApplyTransforms.e1863 antsApplyTransforms.e2255 antsApplyTransforms.e2275 antsApplyTransforms.e2295 antsApplyTransforms.e2315 antsApplyTransforms.e2335 antsApplyTransforms.e2675 antsApplyTransforms.e2695 antsApplyTransforms.e2715 antsApplyTransforms.e2735 antsApplyTransforms.e2755 antsApplyTransforms.e2957 antsApplyTransforms.e2977 antsApplyTransforms.e2997 antsApplyTransforms.e3017 antsApplyTransforms.e3037 antsApplyTransforms.e3605 antsApplyTransforms.e3625 antsApplyTransforms.e3645 antsApplyTransforms.e3665 antsApplyTransforms.e3685 antsApplyTransforms.e4215 antsApplyTransforms.e4235 antsApplyTransforms.e4255 antsApplyTransforms.e4275 antsApplyTransforms.e4295 antsApplyTransforms.e4634 antsApplyTransforms.e4654 antsApplyTransforms.e4674 antsApplyTransforms.e4694 antsApplyTransforms.e4714 antsApplyTransforms.e5212 antsApplyTransforms.e5232 antsApplyTransforms.e5252 antsApplyTransforms.e5272 antsApplyTransforms.e5292 antsApplyTransforms.e6149 antsApplyTransforms.e6169 antsApplyTransforms.e6189 antsApplyTransforms.e6209 antsApplyTransforms.e6229 antsApplyTransforms.e6571 antsApplyTransforms.e6591 antsApplyTransforms.e6611 antsApplyTransforms.e6631 antsApplyTransforms.e6651 antsApplyTransforms.o1364 antsApplyTransforms.o1384 antsApplyTransforms.o1404 antsApplyTransforms.o1424 antsApplyTransforms.o1444 antsApplyTransforms.o1783 antsApplyTransforms.o1803 antsApplyTransforms.o1823 antsApplyTransforms.o1843 antsApplyTransforms.o1863 antsApplyTransforms.o2255 antsApplyTransforms.o2275 antsApplyTransforms.o2295 antsApplyTransforms.o2315 antsApplyTransforms.o2335 antsApplyTransforms.o2675 antsApplyTransforms.o2695 antsApplyTransforms.o2715 antsApplyTransforms.o2735 antsApplyTransforms.o2755 antsApplyTransforms.o2957 antsApplyTransforms.o2977 antsApplyTransforms.o2997 antsApplyTransforms.o3017 antsApplyTransforms.o3037 antsApplyTransforms.o3605 antsApplyTransforms.o3625 antsApplyTransforms.o3645 antsApplyTransforms.o3665 antsApplyTransforms.o3685 antsApplyTransforms.o4215 antsApplyTransforms.o4235 antsApplyTransforms.o4255 antsApplyTransforms.o4275 antsApplyTransforms.o4295 antsApplyTransforms.o4634 antsApplyTransforms.o4654 antsApplyTransforms.o4674 antsApplyTransforms.o4694 antsApplyTransforms.o4714 antsApplyTransforms.o5212 antsApplyTransforms.o5232 antsApplyTransforms.o5252 antsApplyTransforms.o5272 antsApplyTransforms.o5292 antsApplyTransforms.o6149 antsApplyTransforms.o6169 antsApplyTransforms.o6189 antsApplyTransforms.o6209 antsApplyTransforms.o6229 antsApplyTransforms.o6571 antsApplyTransforms.o6591 antsApplyTransforms.o6611 antsApplyTransforms.o6631 antsApplyTransforms.o6651 FA origdata'
+ fsl5.0-fslmaths '*_FA.nii.gz' -bin antsApplyTransforms.e1364 antsApplyTransforms.e1384 antsApplyTransforms.e1404 antsApplyTransforms.e1424 antsApplyTransforms.e1444 antsApplyTransforms.e1783 antsApplyTransforms.e1803 antsApplyTransforms.e1823 antsApplyTransforms.e1843 antsApplyTransforms.e1863 antsApplyTransforms.e2255 antsApplyTransforms.e2275 antsApplyTransforms.e2295 antsApplyTransforms.e2315 antsApplyTransforms.e2335 antsApplyTransforms.e2675 antsApplyTransforms.e2695 antsApplyTransforms.e2715 antsApplyTransforms.e2735 antsApplyTransforms.e2755 antsApplyTransforms.e2957 antsApplyTransforms.e2977 antsApplyTransforms.e2997 antsApplyTransforms.e3017 antsApplyTransforms.e3037 antsApplyTransforms.e3605 antsApplyTransforms.e3625 antsApplyTransforms.e3645 antsApplyTransforms.e3665 antsApplyTransforms.e3685 antsApplyTransforms.e4215 antsApplyTransforms.e4235 antsApplyTransforms.e4255 antsApplyTransforms.e4275 antsApplyTransforms.e4295 antsApplyTransforms.e4634 antsApplyTransforms.e4654 antsApplyTransforms.e4674 antsApplyTransforms.e4694 antsApplyTransforms.e4714 antsApplyTransforms.e5212 antsApplyTransforms.e5232 antsApplyTransforms.e5252 antsApplyTransforms.e5272 antsApplyTransforms.e5292 antsApplyTransforms.e6149 antsApplyTransforms.e6169 antsApplyTransforms.e6189 antsApplyTransforms.e6209 antsApplyTransforms.e6229 antsApplyTransforms.e6571 antsApplyTransforms.e6591 antsApplyTransforms.e6611 antsApplyTransforms.e6631 antsApplyTransforms.e6651 antsApplyTransforms.o1364 antsApplyTransforms.o1384 antsApplyTransforms.o1404 antsApplyTransforms.o1424 antsApplyTransforms.o1444 antsApplyTransforms.o1783 antsApplyTransforms.o1803 antsApplyTransforms.o1823 antsApplyTransforms.o1843 antsApplyTransforms.o1863 antsApplyTransforms.o2255 antsApplyTransforms.o2275 antsApplyTransforms.o2295 antsApplyTransforms.o2315 antsApplyTransforms.o2335 antsApplyTransforms.o2675 antsApplyTransforms.o2695 antsApplyTransforms.o2715 antsApplyTransforms.o2735 antsApplyTransforms.o2755 antsApplyTransforms.o2957 antsApplyTransforms.o2977 antsApplyTransforms.o2997 antsApplyTransforms.o3017 antsApplyTransforms.o3037 antsApplyTransforms.o3605 antsApplyTransforms.o3625 antsApplyTransforms.o3645 antsApplyTransforms.o3665 antsApplyTransforms.o3685 antsApplyTransforms.o4215 antsApplyTransforms.o4235 antsApplyTransforms.o4255 antsApplyTransforms.o4275 antsApplyTransforms.o4295 antsApplyTransforms.o4634 antsApplyTransforms.o4654 antsApplyTransforms.o4674 antsApplyTransforms.o4694 antsApplyTransforms.o4714 antsApplyTransforms.o5212 antsApplyTransforms.o5232 antsApplyTransforms.o5252 antsApplyTransforms.o5272 antsApplyTransforms.o5292 antsApplyTransforms.o6149 antsApplyTransforms.o6169 antsApplyTransforms.o6189 antsApplyTransforms.o6209 antsApplyTransforms.o6229 antsApplyTransforms.o6571 antsApplyTransforms.o6591 antsApplyTransforms.o6611 antsApplyTransforms.o6631 antsApplyTransforms.o6651 FA origdata_mask
Cannot open volume *_FA for reading!
+ '[' 1 -eq 1 ']'
+ echo 'Using FA images to estimate WM PVE'
Using FA images to estimate WM PVE
+ Atropos -d 3 -a '*_FA.nii.gz' -x antsApplyTransforms.e1364 antsApplyTransforms.e1384 antsApplyTransforms.e1404 antsApplyTransforms.e1424 antsApplyTransforms.e1444 antsApplyTransforms.e1783 antsApplyTransforms.e1803 antsApplyTransforms.e1823 antsApplyTransforms.e1843 antsApplyTransforms.e1863 antsApplyTransforms.e2255 antsApplyTransforms.e2275 antsApplyTransforms.e2295 antsApplyTransforms.e2315 antsApplyTransforms.e2335 antsApplyTransforms.e2675 antsApplyTransforms.e2695 antsApplyTransforms.e2715 antsApplyTransforms.e2735 antsApplyTransforms.e2755 antsApplyTransforms.e2957 antsApplyTransforms.e2977 antsApplyTransforms.e2997 antsApplyTransforms.e3017 antsApplyTransforms.e3037 antsApplyTransforms.e3605 antsApplyTransforms.e3625 antsApplyTransforms.e3645 antsApplyTransforms.e3665 antsApplyTransforms.e3685 antsApplyTransforms.e4215 antsApplyTransforms.e4235 antsApplyTransforms.e4255 antsApplyTransforms.e4275 antsApplyTransforms.e4295 antsApplyTransforms.e4634 antsApplyTransforms.e4654 antsApplyTransforms.e4674 antsApplyTransforms.e4694 antsApplyTransforms.e4714 antsApplyTransforms.e5212 antsApplyTransforms.e5232 antsApplyTransforms.e5252 antsApplyTransforms.e5272 antsApplyTransforms.e5292 antsApplyTransforms.e6149 antsApplyTransforms.e6169 antsApplyTransforms.e6189 antsApplyTransforms.e6209 antsApplyTransforms.e6229 antsApplyTransforms.e6571 antsApplyTransforms.e6591 antsApplyTransforms.e6611 antsApplyTransforms.e6631 antsApplyTransforms.e6651 antsApplyTransforms.o1364 antsApplyTransforms.o1384 antsApplyTransforms.o1404 antsApplyTransforms.o1424 antsApplyTransforms.o1444 antsApplyTransforms.o1783 antsApplyTransforms.o1803 antsApplyTransforms.o1823 antsApplyTransforms.o1843 antsApplyTransforms.o1863 antsApplyTransforms.o2255 antsApplyTransforms.o2275 antsApplyTransforms.o2295 antsApplyTransforms.o2315 antsApplyTransforms.o2335 antsApplyTransforms.o2675 antsApplyTransforms.o2695 antsApplyTransforms.o2715 antsApplyTransforms.o2735 antsApplyTransforms.o2755 antsApplyTransforms.o2957 antsApplyTransforms.o2977 antsApplyTransforms.o2997 antsApplyTransforms.o3017 antsApplyTransforms.o3037 antsApplyTransforms.o3605 antsApplyTransforms.o3625 antsApplyTransforms.o3645 antsApplyTransforms.o3665 antsApplyTransforms.o3685 antsApplyTransforms.o4215 antsApplyTransforms.o4235 antsApplyTransforms.o4255 antsApplyTransforms.o4275 antsApplyTransforms.o4295 antsApplyTransforms.o4634 antsApplyTransforms.o4654 antsApplyTransforms.o4674 antsApplyTransforms.o4694 antsApplyTransforms.o4714 antsApplyTransforms.o5212 antsApplyTransforms.o5232 antsApplyTransforms.o5252 antsApplyTransforms.o5272 antsApplyTransforms.o5292 antsApplyTransforms.o6149 antsApplyTransforms.o6169 antsApplyTransforms.o6189 antsApplyTransforms.o6209 antsApplyTransforms.o6229 antsApplyTransforms.o6571 antsApplyTransforms.o6591 antsApplyTransforms.o6611 antsApplyTransforms.o6631 antsApplyTransforms.o6651 FA origdata_mask.nii.gz -i 'Kmeans[2]' -m '[0.3,1x1x1]' -o '[segmentation.nii.gz,antsApplyTransforms.e1364' antsApplyTransforms.e1384 antsApplyTransforms.e1404 antsApplyTransforms.e1424 antsApplyTransforms.e1444 antsApplyTransforms.e1783 antsApplyTransforms.e1803 antsApplyTransforms.e1823 antsApplyTransforms.e1843 antsApplyTransforms.e1863 antsApplyTransforms.e2255 antsApplyTransforms.e2275 antsApplyTransforms.e2295 antsApplyTransforms.e2315 antsApplyTransforms.e2335 antsApplyTransforms.e2675 antsApplyTransforms.e2695 antsApplyTransforms.e2715 antsApplyTransforms.e2735 antsApplyTransforms.e2755 antsApplyTransforms.e2957 antsApplyTransforms.e2977 antsApplyTransforms.e2997 antsApplyTransforms.e3017 antsApplyTransforms.e3037 antsApplyTransforms.e3605 antsApplyTransforms.e3625 antsApplyTransforms.e3645 antsApplyTransforms.e3665 antsApplyTransforms.e3685 antsApplyTransforms.e4215 antsApplyTransforms.e4235 antsApplyTransforms.e4255 antsApplyTransforms.e4275 antsApplyTransforms.e4295 antsApplyTransforms.e4634 antsApplyTransforms.e4654 antsApplyTransforms.e4674 antsApplyTransforms.e4694 antsApplyTransforms.e4714 antsApplyTransforms.e5212 antsApplyTransforms.e5232 antsApplyTransforms.e5252 antsApplyTransforms.e5272 antsApplyTransforms.e5292 antsApplyTransforms.e6149 antsApplyTransforms.e6169 antsApplyTransforms.e6189 antsApplyTransforms.e6209 antsApplyTransforms.e6229 antsApplyTransforms.e6571 antsApplyTransforms.e6591 antsApplyTransforms.e6611 antsApplyTransforms.e6631 antsApplyTransforms.e6651 antsApplyTransforms.o1364 antsApplyTransforms.o1384 antsApplyTransforms.o1404 antsApplyTransforms.o1424 antsApplyTransforms.o1444 antsApplyTransforms.o1783 antsApplyTransforms.o1803 antsApplyTransforms.o1823 antsApplyTransforms.o1843 antsApplyTransforms.o1863 antsApplyTransforms.o2255 antsApplyTransforms.o2275 antsApplyTransforms.o2295 antsApplyTransforms.o2315 antsApplyTransforms.o2335 antsApplyTransforms.o2675 antsApplyTransforms.o2695 antsApplyTransforms.o2715 antsApplyTransforms.o2735 antsApplyTransforms.o2755 antsApplyTransforms.o2957 antsApplyTransforms.o2977 antsApplyTransforms.o2997 antsApplyTransforms.o3017 antsApplyTransforms.o3037 antsApplyTransforms.o3605 antsApplyTransforms.o3625 antsApplyTransforms.o3645 antsApplyTransforms.o3665 antsApplyTransforms.o3685 antsApplyTransforms.o4215 antsApplyTransforms.o4235 antsApplyTransforms.o4255 antsApplyTransforms.o4275 antsApplyTransforms.o4295 antsApplyTransforms.o4634 antsApplyTransforms.o4654 antsApplyTransforms.o4674 antsApplyTransforms.o4694 antsApplyTransforms.o4714 antsApplyTransforms.o5212 antsApplyTransforms.o5232 antsApplyTransforms.o5252 antsApplyTransforms.o5272 antsApplyTransforms.o5292 antsApplyTransforms.o6149 antsApplyTransforms.o6169 antsApplyTransforms.o6189 antsApplyTransforms.o6209 antsApplyTransforms.o6229 antsApplyTransforms.o6571 antsApplyTransforms.o6591 antsApplyTransforms.o6611 antsApplyTransforms.o6631 antsApplyTransforms.o6651 FA 'origdata_%02d.nii.gz]'

Running Atropos for 3-dimensional images.
 file origdata_mask.nii.gz does not exist . 
 file *_FA.nii.gz does not exist .

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