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!
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!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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 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!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
Hi,
I’ve tried this script in both freesurfer6.0.0 and freesurfer7.1.1, and get the same error message in both. My subjects were processed through recon-all with freesurfer 6.0.0.
Thank you!
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, November 6, 2020 at 10:11 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file
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-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!
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
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!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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.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 N. Greve dgreve@mgh.harvard.edu mailto:dgreve@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!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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
Hi,
Thank you, that fixed the error! Also, I’m glad to say that the error didn’t make a difference in the output stats files.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Date: Wednesday, November 11, 2020 at 12:44 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file 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-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: Wednesday, November 11, 2020 11:07 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
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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