Try giving it a full path the the annot, eg,
-a $SUBJECTS_DIR/sub-230_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
On 11/11/2020 12:09 PM, Chan, Shi Yu wrote:
Hi,
Sure, I've attached 2 txt files:
fs_terminal_output.txt - I pasted the lines from the script into the
command line for sub-230_ses-01
fs_terminal_output_short.txt - I just ran mris_anatomical_stats on the
left hemisphere alone for sub-230_ses-01
I get the same error in both cases.
I've tested this on multiple subjects using both the script and
mris_anatomical_stats directly on the command line, using different
freesurfer versions, and have also tried using different folders as
the subject directory, and always get the same error. Since it seems
like the "sub-230_ses-01/label" part is repeated in the error, I've
also tried writing out the full path to each file in the
mris_anatomical_stats command, and still get the same error. If I try
removing the sub-230_ses-01 part and starting with /label or
"../label" (for e.g. mris_anatomical_stats -th3 -mgz -cortex
../label/lh.cortex.label -a ../label/lh.Yeo2011_17Networks_N1000.annot
-f ../stats/lh.Yeo_17Networks.stats -b -c
../label/lh.Yeo_17Networks.annot.ctab sub-230_ses-01 lh white) I will
get a different error where freesurfer is unable to find the files
(i.e. error: no such file or directory).
mris_anatomical_stats still continues running despite the error, and
still produces stat output files with the script, so would this error
(error: stating file) affect the stats output?
Thank you for all your help with this!
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Wednesday, November 11, 2020 11:07 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mris_anatomical_stats error: stating file
Can you send the exact command line that generated the terminal output
you sent? The line below has a different subject name. Run that
command from the shell (rather than from your script) to verify that
it creates an error
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
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Thursday, November 5, 2020 9:44 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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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