Oh, yes. I used mriconvert.

Sure! So ill convert it again (using mriconvert?), and run preproc-sess and send you the terminal output.

P.S. I can still view the file after conversion normally.

Thank you,

DWY

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, April 4, 2018 3:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]

but using what program? mri_convert? Can you try converting it again and sending me the terminal output?

On 4/3/18 11:38 PM, Dave Yas wrote:

By hand. I followed the FSFAST hierarchy and just simply created the files and named them.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@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-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.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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