Sorry, ‘Done’ should be in all lower case.
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
1. remove the commented out line # first to verify echo printout
2. add back the line w/o the # sign
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,
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
I commented out the command submitting mri_segstat. I always verify the printout from the echo first before submitting the jobs.
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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?
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.
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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
-l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
-f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
Please could you advise me on where I am going wrong here?
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