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FSGD file error

Surface label to volume and then...

Dave Yas

2 Apr 2018 2 Apr '18

9:53 p.m.

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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Douglas Greve

3 Apr 3 Apr

9:17 a.m.

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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Dave Yas

6:48 p.m.

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Douglas Greve

7:42 p.m.

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

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

Dave Yas

7:47 p.m.

Only ~80%, but there is space for this run..

________________________________ 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:

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.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu mailto: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

Dave Yas

7:51 p.m.

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:

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..

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

Douglas Greve

11:34 p.m.

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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu mailto:dgreve@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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Dave Yas

11:38 p.m.

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu Sent: Tuesday, April 3, 2018 11:42 PM To: freesurfer@nmr.mgh.harvard.edumailto: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:

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..

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

Douglas Greve

11:49 p.m.

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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu mailto:dgreve@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu mailto:dgreve@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

Dave Yas

11:53 p.m.

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu Sent: Wednesday, April 4, 2018 3:34 AM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu Sent: Tuesday, April 3, 2018 11:42 PM To: freesurfer@nmr.mgh.harvard.edumailto: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:

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..

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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Dave Yas
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