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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Thursday, November 5, 2020 9:44 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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 FreeSurfer Developers,
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 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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