Re: [Freesurfer] mris_anatomical_stats error: stating file

2020-11-11 Thread Chan, Shi Yu 
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-boun...@nmr.mgh.harvard.edu 

Date: Wednesday, November 11, 2020 at 12:44 PM
To: 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, November 11, 2020 11:07 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto: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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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 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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Re: [Freesurfer] mris_anatomical_stats error: stating file

2020-11-11 Thread Douglas N. Greve 

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 
 on behalf of Douglas N. Greve 


*Sent:* Wednesday, November 11, 2020 11:07 AM
*To:* 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> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas 
N. Greve  <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> 
 <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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>



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Re: [Freesurfer] mris_anatomical_stats error: stating file

2020-11-11 Thread Chan, Shi Yu 
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 
 on behalf of Douglas N. Greve 

Sent: Wednesday, November 11, 2020 11:07 AM
To: 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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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 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.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
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PHS009090:recon_unedited pnlmcleaneeg$ export 
FREESURFER_HOME=/Applications/freesurfer
PHS009090:recon_unedited pnlmcleaneeg$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/fr

Re: [Freesurfer] mris_anatomical_stats error: stating file

2020-11-11 Thread Douglas N. Greve 
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 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, November 5, 2020 9:44 AM
*To:* 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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>



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Re: [Freesurfer] mris_anatomical_stats error: stating file

2020-11-06 Thread Chan, Shi Yu 
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:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Friday, November 6, 2020 at 10:11 AM
To: "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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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 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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




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


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Re: [Freesurfer] mris_anatomical_stats error: stating file

2020-11-06 Thread Douglas N. Greve 

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 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, November 5, 2020 9:44 AM
*To:* 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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>



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Re: [Freesurfer] mris_anatomical_stats error: stating file

2020-11-05 Thread Chan, Shi Yu 
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 
 on behalf of Douglas N. Greve 

Sent: Thursday, November 5, 2020 9:44 AM
To: 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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PHS009090:freesurfer pnlmcleaneeg$ bash extractYeo17.sh
/Volumes/SY_MRI/freesurfer/recon_unedited
sub-001_ses-01
Setting mapmethod to nnf

7.1.1

setenv SUBJECTS_DIR /Volumes/SY_MRI/freesurfer/recon_unedited
cd /Volumes/SY_MRI/freesurfer/recon_unedited
mri_surf2surf --srcsubject fsaverage5 --trgsubject sub-001_ses-01 --hemi lh 
--sval-annot fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
 

sysname  Darwin
hostname PHS009090
machine  x86_64
user pnlmcleaneeg
srcsubject = fsaverage5
srcval = (null)
srctype= 
trgsubject = sub-001_ses-01
trgval = 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
trgtype= 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/lh.sphere.reg
Loading source data
Reading surface file 
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/lh.orig
reading colortable from annotation file...
colortable with 18 entries read (originally MyColorLUT)
Reading target surface reg 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.sphere.reg
Done
Using surf2surf_nnfr()
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (134953)

Surf2Surf: Dividing by number of hits (134953)
INFO: nSrcLost = 0
nTrg121 = 134953, nTrgMulti = 0, MnTrgMultiHits = 0
nSrc121 = 1, nSrcLost = 0, nSrcMulti = 10241, MnSrcMultiHits = 13.1776
Saving target data
Converting to target annot
Saving to target annot 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
Setting mapmethod to nnf

7.1.1

setenv SUBJECTS_DIR /Volumes/SY_MRI/freesurfer/recon_unedited
cd /Volumes/SY_MRI/freesurfer/recon_unedited
mri_surf2surf --srcsubject fsaverage5 --trgsubject sub-001_ses-01 --hemi lh 
--sval-annot 
fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot
 

sysname  Darwin
hostname PHS009090
machine  x86_64
user pnlmcleaneeg
srcsubject = fsaverage5
srcval = (null)
srctype= 
trgsubject = sub-001_ses-01
trgval = 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot
trgtype= 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg

Re: [Freesurfer] mris_anatomical_stats error: stating file

2020-11-05 Thread Douglas N. Greve 


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 
 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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Re: [Freesurfer] mris_anatomical_stats error: missing ", " in "Measure Cortex, CortexVol Total cortical gray matter volume, ..."

2017-09-05 Thread Douglas N Greve 
what is this causing an error in?


On 08/29/2017 06:50 AM, Ernst Schwartz wrote:
> Hi!
>
> It seems that in FreeSurfer 6, the comma between “CortexVol” and 
> “Total cortical gray matter volume” is missing
>
> here’s the relevant part of one of my stats-files:
>
> # Table of FreeSurfer cortical parcellation anatomical statistics
> #
> # CreationTime 2017/08/23-20:19:44-GMT
> # generating_program 
> /software/easybuild/software/FreeSurfer/6.0.0-centos6_x86_64/bin/mris_anatomical_stats
> # cvs_version $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 
> greve Exp $
> # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 
> zkaufman Exp $
> # cmdline 
> /software/easybuild/software/FreeSurfer/6.0.0-centos6_x86_64/bin/mris_anatomical_stats
>  
> -mgz -cortex 
> /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.cortex.label 
> -a 
> /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.aparc.a2009s.annot
>  
> -b -f 
> /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/stats/lh.aparc.a2009s.pial.stats
>  
> sub-A00057725_ses-CLG2 lh pial
> # sysname  Linux
> # hostname cn4.cir.meduniwien.ac.at 
> # machine x86_64
> # user ernst
> #
> # SUBJECTS_DIR /data/datasets/pediatric/CLG/
> # anatomy_type surface
> # subjectname sub-A00057725_ses-CLG2
> # hemi lh
> # AnnotationFile 
> /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.aparc.a2009s.annot
> # AnnotationFileTimeStamp 2017/08/23 22:18:44
> # Measure Cortex, NumVert, Number of Vertices, 121790, unitless
> # Measure Cortex, PialSurfArea, Pial Surface Total Area, 105158, mm^2
> # Measure Cortex, MeanThickness, Mean Thickness, 2.80672, mm
> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 
> 1051285.00, mm^3
> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation 
> Volume Without Ventricles, 1040194.00, mm^3
> # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain 
> Segmentation Volume Without Ventricles from Surf, 1039128.584538, mm^3
> # Measure Cortex, *CortexVol Total* cortical gray matter volume, 
> 532907.136355, mm^3
> # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 
> 926570.584538, mm^3
> # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, 
> Supratentorial volume, 918874.584538, mm^3
> # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total 
> Intracranial Volume, 1254280.104289, mm^3
>
>
> cheers,
> Ernst
>
>
> ~
>
> Ernst Schwartz
> Computational Image Research (CIR) Lab
> Department of Biomedical Imaging and Image-guided Therapy
> Medical University Vienna, Austria
>
> --
>
>
>
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Re: [Freesurfer] mris_anatomical_stats error

2013-12-09 Thread Bruce Fischl 

Hi Krista

the optional last argument for mris_anatomical_stats is a surface name 
(not a scalar field over the surface, like the thickness file)


cheers
Bruce


On Mon, 9 Dec 2013, krista kelly wrote:


Hi,

I'm trying to run mris_anatomical_stats to get cortical thickness from
labels for each participant but I keep getting the following error:

MRISread: file '/Applications/freesurfer/subjects/MB19/surf/lh.thickness'
has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

Here is the command I'm using:

mris_anatomical_stats -l MB07/label/lh.V1.thresh.label -b -f
MB07/stats/lh.V1.thresh.thickness.stats MB07 lh thickness

I wasn't able to find a suitable solution from the archives. I used the same
command to get area.pial stats without any problems. Any help is
appreciated!

Krista 



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Re: [Freesurfer] mris_anatomical_stats error

2010-02-16 Thread Bruce Fischl 
hmmm, sounds like a bug. If you tar and gzip the subject and drop it on 
our site we'll take a look.
On Tue, 16 Feb 2010 yzha...@artsci.wustl.edu 
wrote:

 Dear experts,

 i try to run the command mris_anatomical_stats to get GrayVol, ThickAvg,
 etc from the left cortex as following:

 mris_anatomical_stats -l lh.cortex.label -f nmr033_2/stats/lh.cortex.stats
 nmr033_2 lh

 so the output is like following and did not generate any stats
 file(lh.cortex.stats) :

 limiting computations to label lh.cortex.label.
 reading volume /windata/yuning/freesurfer/nmr033_2/mri/wm.mgz...
 reading input surface /windata/yuning/freesurfer/nmr033_2/surf/lh.white...
 reading input pial surface
 /windata/yuning/freesurfer/nmr033_2/surf/lh.pial...
 reading input white surface
 /windata/yuning/freesurfer/nmr033_2/surf/lh.white...
 /windata/yuning/freesurfer/nmr033_2/label/lh.cortex.label
 /windata/yuning/freesurfer/nmr033_2/label/lh.cortex.label
 Segmentation fault

 could anyone tell me what's wrong with it and what segmentaion fault is ?

 thanks a lot
 yuning


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Re: [Freesurfer] mris_anatomical_stats error

2009-08-14 Thread Bruce Fischl 
sounds like the annotation file is corrupted. Can you load it in 
tksurfer?
On Fri, 14 Aug 2009, Rutvik Desai wrote:

 We get the following error on one subject when running
 mris_anatomical_stats. The same command workson other subjects who were
 generated the same way. Using
 freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5,
 also tried freesurfer-Linux-rh9-stable-pub-v3.0.5. No heavy processes were
 running on the machine
 that would prevent memory allocation.

 thanks,
 Rutvik

 -

 % mris_anatomical_stats -a ep.1071/label/lh.aparc.annot -b -i 0.5 8 -f
 ep.1071.lh.stats ep.1071 lh

 computing statistics for each annotation in ep.1071/label/lh.aparc.annot.

 only considering thicknesses in the range [0.5,8.0].

 reading volume /usr/home/possing/pub/Epilepsy/ep.1071/mri/wm.mgz...

  Talairach transform
 /home/mgolovin/fs_subjects/ep.1071/mri/transforms/talairach.xfm does not
 exist ...

 Loading tal xfm file
 /usr/home/possing/pub/Epilepsy/ep.1071/mri/transforms/talairach.xfm

 reading input surface
 /usr/home/possing/pub/Epilepsy/ep.1071/surf/lh.white...

 reading input surface /usr/home/possing/pub/Epilepsy/ep.1071/surf/lh.pial...

 reading input surface
 /usr/home/possing/pub/Epilepsy/ep.1071/surf/lh.white...

 done.

 computing second fundamental form...reading colortable from annotation
 file...

 CTABreadFrom: could not allocate -2 bin table

 Cannot allocate memory

 Segmentation fault (core dumped)

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Re: [Freesurfer] mris_anatomical_stats error

2009-08-14 Thread Rutvik Desai 
I get the same error when trying to load it in tksurfer.

-
reading colortable from annotation file...
CTABreadFrom: could not allocate -2 bin table
Cannot allocate memory
Bus error
-

On Aug 14, 2009, at 4:31 PM, Bruce Fischl wrote:

 sounds like the annotation file is corrupted. Can you load it in
 tksurfer?
 On Fri, 14 Aug 2009, Rutvik Desai wrote:

 We get the following error on one subject when running
 mris_anatomical_stats. The same command workson other subjects who  
 were
 generated the same way. Using
 freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5,
 also tried freesurfer-Linux-rh9-stable-pub-v3.0.5. No heavy  
 processes were
 running on the machine
 that would prevent memory allocation.

 thanks,
 Rutvik

 -

 % mris_anatomical_stats -a ep.1071/label/lh.aparc.annot -b -i 0.5 8  
 -f
 ep.1071.lh.stats ep.1071 lh

 computing statistics for each annotation in ep.1071/label/ 
 lh.aparc.annot.

 only considering thicknesses in the range [0.5,8.0].

 reading volume /usr/home/possing/pub/Epilepsy/ep.1071/mri/wm.mgz...

 Talairach transform
 /home/mgolovin/fs_subjects/ep.1071/mri/transforms/talairach.xfm  
 does not
 exist ...

 Loading tal xfm file
 /usr/home/possing/pub/Epilepsy/ep.1071/mri/transforms/talairach.xfm

 reading input surface
 /usr/home/possing/pub/Epilepsy/ep.1071/surf/lh.white...

 reading input surface /usr/home/possing/pub/Epilepsy/ep.1071/surf/ 
 lh.pial...

 reading input surface
 /usr/home/possing/pub/Epilepsy/ep.1071/surf/lh.white...

 done.

 computing second fundamental form...reading colortable from  
 annotation
 file...

 CTABreadFrom: could not allocate -2 bin table

 Cannot allocate memory

 Segmentation fault (core dumped)


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Re: [Freesurfer] mris_anatomical_stats error

2006-11-01 Thread Johannes Klein 

Sure, my command would look something like this:
mris_anatomical_stats -b average_subject lh white -l lh.mylabel
Works on individual subjects, but not on the averaged one.
The latter was created with
make_average_subject --subjects STRU_1 STRU_2 [...] --out average_subject
Thanks for your help,
Johannes

Doug Greve schrieb:


The problem is that this is being done an the average subject, which 
does not have a wm.mgz file. Should be easy to fix. Johannes, can you 
send your cmd line?


doug





Nick Schmansky wrote:


Johannes,

wm.mgz is produced in the -autorecon2 stage of recon-all.  


A handy table to consult is:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

or

http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm

Nick  


On Tue, 2006-10-31 at 11:49 +, Johannes Klein wrote:
 


Hi everyone,
I'm trying to calculate surface areas for some labels I've drawn on an 
averaged subject created with mrake_average_surface, and 
mris_anatomical_stats seems the way to go.
Unfortunately, it needs a file called wm.mgz, which doesn't exist for my 
averaged subject. The mri subdir contains T1, brain, mni305.cor and 
orig.mgz, but no wm.mgz. Is there a way to create this file from the 
data I've got?

Thanks for your help,
Johannes
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Re: [Freesurfer] mris_anatomical_stats error

2006-10-31 Thread Doug Greve 





The problem is that this is being done an the average subject, which
does not have a wm.mgz file. Should be easy to fix. Johannes, can you
send your cmd line? 

doug





Nick Schmansky wrote:

  Johannes,

wm.mgz is produced in the -autorecon2 stage of recon-all.  

A handy table to consult is:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

or

http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm

Nick  

On Tue, 2006-10-31 at 11:49 +, Johannes Klein wrote:
  
  
Hi everyone,
I'm trying to calculate surface areas for some labels I've drawn on an 
averaged subject created with mrake_average_surface, and 
mris_anatomical_stats seems the way to go.
Unfortunately, it needs a file called wm.mgz, which doesn't exist for my 
averaged subject. The mri subdir contains T1, brain, mni305.cor and 
orig.mgz, but no wm.mgz. Is there a way to create this file from the 
data I've got?
Thanks for your help,
Johannes
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Phone Number: 617-724-2358 
Fax: 617-726-7422

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surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




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