Luke

On 2 Dec 2022, at 16:46, Huang, Yujing <YHUANG43@MGH.HARVARD.EDU> wrote:

Sorry, ‘Done’ should be in all lower case.

for subj in `ls -1`
do
echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
#mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
done

1. remove the commented out line # first to verify echo printout
2. add back the line w/o the # sign

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing
Sent: Friday, December 2, 2022 10:34 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] LGI label statistics

Hi Luke,

I don’t know any bash script available to perform the batch job.

You can enter it in a for loop at prompt. From your $SUBJECTS_DIR,

for subj in `ls -1`
do
echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
#mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
Done

I commented out the command submitting mri_segstat. I always verify the printout from the echo first before submitting the jobs.

Hope this helps.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 10:08 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] LGI label statistics

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Hi Yujing

Ah great, Thank you so much for your help! That was the answer. I have been able to extract the stats now using the following script:

mri_segstats --slabel A152 rh $SUBJECTS_DIR/A152/label/rh.c1.label --i $SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum $SUBJECTS_DIR/A152/stats/rh.c1.pial_lgi.stats

I have 186 individuals and have been trying to extract each individuals statistics individually, do you know if there is a bash shell script available to perform this process on all individuals in my study at once?

Best,
Luke

On 2 Dec 2022, at 15:28, Huang, Yujing <YHUANG43@MGH.HARVARD.EDU> wrote:

Hi Luke,

Can you try to pass the full path to your label file? Instead of ‘rh.c1.label’, pass ‘/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label’ to mri_segstats.

I think that should work.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 5:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] LGI label statistics

External Email - Use Caution
Dear freesurfer,

I am attempting to extract LGI statistical data from a label running the mri_segstats command

Here is the script I am attempting to run:

mri_segstats --slabel A152 rh rh.c1.label --i $SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats

This returns an error: error: mri_segstats: could not open label file rh.c1.label

I created the label using freeview - make closed path - then filling the closed path. The label projects on pial and inflated surfaces
Furthermore the label is able to be identified and used in the following command

mris_anatomical_stats \
-l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
-f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
A152 \
rh

Please could you advise me on where I am going wrong here?

Many thanks,

Luke
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