By hand. I followed the FSFAST hierarchy and just simply created the files and named them.
________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> Sent: Wednesday, April 4, 2018 3:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Freesurfer/FSFAST] The version should not matter here. How did you create /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii ? On 4/3/18 7:51 PM, Dave Yas wrote: Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that accounts for anything here). ________________________________ 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 Douglas Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Tuesday, April 3, 2018 11:42 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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-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 Douglas Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Tuesday, April 3, 2018 1:17 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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 _______________________________________________ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
