which version of FS are you using?
On 11/5/2020 11:29 AM, Chan, Shi Yu wrote:
Hi,
Yes, sorry! I copied the error message from terminal, but copied the
command from my script so I copied the error message for the wrong
hemisphere. I apologise for the confusion.
I've attached the terminal output (I've put ##### at the lines above
the error message) and the script I use in this email.
Thank you for all your help!
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Thursday, November 5, 2020 9:44 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mris_anatomical_stats error: stating file
Is that the right error msg? It says it can't find the RH, but you are
running it with LH. Can you post the entire terminal output?
On 11/3/2020 2:00 PM, Chan, Shi Yu wrote:
Hi FreeSurferDevelopers,
I'm trying to calculate cortical thickness statistics from the Yeo 17
Network cortical parcellation and have used mri_surf2surf to get the
.annot files for each subject.
However, when I run mris_anatomical_stats, I get an error:
ERROR: stating file
subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot
It seems like the "sub-001/label" portion is repeated.
The command I use for mris_anatomical_stats is:
mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label
-f sub-001/stats/lh.Yeo_17Networks.stats -b -a
sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white
The command still runs despite the error, and outputs the stats files
accordingly, so I'm not sure how important this error is, but I can't
figure out how to fix it.
This is a similar issue to:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67595.html
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67595.html> but
I've checked $SUBJECTS_DIR, and it is correct. If I run ls
$SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in
sub-001 (mri stats labels etc)
Any help would be much appreciated! Thank you!
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