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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 1:17 PM
To: 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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