Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that accounts for anything here).
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Tuesday, April 3, 2018 11:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Freesurfer/FSFAST]
Is the disk full?
On 4/3/18 6:48 PM, Dave Yas wrote:
Yes, the file exists!
Here is the full output:
-------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.sess01.log -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ Davey setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 /Users/Studies/Directory/Study_Directory /Applications/freesurfer/fsfast/bin/preproc-sess -fsd bold -per-run -s sess01 -fwhm 5 Tue Apr 3 10:11:25 JST 2018 instem f mc 1 f fmcpr stc 0 fmcpr sm 1 fmcpr fmcpr.sm5 mask 1 brain sess01 Template ----------------------------- mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory -fsd bold -update
Session: /Users/Studies/Directory/Study_Directory/sess01 ---------------- Tue Apr 3 10:11:25 JST 2018 Detected input format at nii /Users/Studies/Directory/Study_Directory mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii /Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0 mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii /Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0 INFO: using NIfTI-1 qform
Error: niiRead(): error reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...
After that nothing happens..
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Tuesday, April 3, 2018 1:17 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Freesurfer/FSFAST]
does that file exist? CAn you send the full terminal output?
On 4/2/18 9:53 PM, Dave Yas wrote:
Hi,
I am running preproc-sess on one subject.
I got the following error after running preproc-sess:
Error: niiRead(): error reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii
My PWD: /Users/Studies/Directory/Study_Directory
My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects
My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5
My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & subjectname.text/001/f.nii & paradigm file (.par) ~/002/f.nii & paradigm file
~/003/f.nii & paradigm file
Any help on the above?
I searched the previous mailing list and found someone who had the same problem but didn't reach a solution!
Thank you in advance,
DWY
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