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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<dgr...@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-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
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