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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.apa
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-boun...@nmr.mgh.harvard.edu
On Behalf Of Luke K Harper
Sent: Fri
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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_lg
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I have noticed a change made in the release of FSL 6.0.6 that may affect
FreeSurfer. FSL executables now lie in ${FSLDIR}/share/fsl/bin not
${FSLDIR}/bin. The Freesurfer set up script adds ${FSLDIR}/bin to the PATH.
Not sure if this causes any trouble.
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
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.c
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Thanks!
As the subject ID in my example is A152 should this be replaced by $subj in the
label section too? Each individual has a label created via label2label from a
label on fsaverage or does this not matter?
Best,
Luke
> On 2 Dec 2022, at 16:46
Yes, replace A152 in your example with $subj. I’m assuming there are
label/rh.c1.label and surf/rh.pial_lgi in each individual subjects.
Not sure I understand your second question.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Luke K Harper
Sent: Friday, December 2
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Perfect that has worked.
Thank you so much for your help!
Have a great weekend,
Luke
> On 2 Dec 2022, at 16:57, Luke K Harper wrote:
>
> Thanks!
>
> As the subject ID in my example is A152 should this be replaced by $subj in
> the label section
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HI,
we have run a cohort of 200 subjects through FS6.0 (including tracula) with
good results.
Is it possible to use the FS6.0 outputs (aparc+aseg, etc.) to run these data
though only the updated tracula pipeline in 7.2?
Jim
Dear FreeSurfer team,
1. We're trying to focus our cortical analysis following suggestions here
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html. The
FS ROI tutorial page mentions that labels should be drawn or registered on the
fsaverage template; could we then bre
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Dear Sir/Madam,
I am Eric Naab, a Ph.D. student at the University of Ghana, and currently
doing my research at the University of Ghana MRI Medical Center. The title
of my research is "Optimization of Pulse Sequence Protocols for Magnetic
Resonance Imag
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