How much space would I need to run this? Thanks, Mona
On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: Any chance you're low on disk space? ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Nasiriavanaki, Zahra,M.D. <znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>> Sent: Tuesday, December 14, 2021 12:18 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula error Yes. dmri.bedpostX has these files in it: diff_slices empty xfms empty bvals bvecs monitor nodiff_brain_mask.nii.gz logs: monitor empty bedpostx_pre.e9769 bedpostx_pre.e47281 bedpostx_pre.o9769 bedpostx_pre.o47281 Hard to tell from the two lines. Did any files get created in bedpostX output directory? ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Nasiriavanaki, Zahra,M.D. <znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>> Sent: Tuesday, December 14, 2021 11:40 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula error Hello, I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is. Thanks, Mona ----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed bedpostx_pre.e9769: /usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77: 9819 Illegal instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data /usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78: 9837 Illegal instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere In your case you'd replace /path/to/file with $ANTSPATH. Anastasia. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Nasiriavanaki, Zahra,M.D. <znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula error Hi Anastasia, I did add the ANTs to my path, but am still getting that same error. I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the .csh file which has all the TRACULA configuration info, and also to the bash script that I’m running the trac-all from: export ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin Is there anything else I should do? Thanks, Mona On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: Hi Mona - You need to add the location of the ANTs executables to your path. Best, Anastasia. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Nasiriavanaki, Zahra,M.D. <znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>> Sent: Sunday, December 5, 2021 12:21 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Tracula error Hello, I’ve been running the trac-all -prep step and I faced this error: ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu/> 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021 Could you please let me know what the problem is? I’m running it in dev environment. Thanks, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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