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
External Email - Use Caution 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.EDUmailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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,
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