cd $SUBJECTS_DIR/$subject/mri
set hemi=lh
mri_label2vol --labe ${hemi}.perirhinal_exvivo.thresh.label \
--regheader \
../mri/norm.mgz \
--fill-ribbon \
--subject $subject \
--hemi $hemi \
--o ${hemi}.peri.nii.gz
should do the trick
cheers
Bruce
On Thu, 24 Sep 2015,
Priyanka Mehta wrote:
Hi again,
I do have the following files in the label directory:
lh.perirhinal_exvivo.label
lh.perirhinal_exvivo.thresh.label
rh.perirhinal_exvivo.label
rh.perirhinal_exvivo.thresh.label
I want to get the right perirhinal cortex in the .nii format for further
analysis. How can I get that?
Thanks,
Priyanka
On Thu, Sep 24, 2015 at 11:54 AM, Lee Tirrell <ltirr...@nmr.mgh.harvard.edu>
wrote:
Hi Priyanka,
I believe there should already be a perirhinal label created
(the ?h.BA_exvivo.annot is created by combining together a few
labels).
Try seeing if these files exist with this command (replacing
subject_name with your subject):
ls $SUBJECTS_DIR/subject_name/label/*perirhinal*.label
If no files exist, I can send you the command or files
necessary.
Best,
Lee
On Thu, 24 Sep 2015, Priyanka Mehta wrote:
Thank you for the response Lee!
I was able to locate all the files now. To extract
the perirhinal cortex from rh.BA_exvivo.annot, would
I just use mri_annotation2label command?
On Thu, Sep 17, 2015 at 3:43 PM, Lee Tirrell
<ltirr...@nmr.mgh.harvard.edu> wrote:
Hi Priyanka,
The cortical labels are exactly the same for
wmparc.mgz and the aparc+aseg.mgz, they just differ
in how they label the subcortical structures and
white matter. It should matter which you use for
masking the cortex.
The "_exvivo" in the label names is new to the
dev version of Freesurfer, I previously answered
your question based on the output from Freesurfer
5.3. I looked at a subject processed with dev, and
it seems there are are
?h.perirhinal_exvivo.label files in the label
directory and a ?h.BA_exvivo.stats file in the stats
directory. The perirhinal cortex should also be
included in the ?h.BA_exvivo.annot files.
If the stats file is missing, you can extact
them from the ?h.BA_exvivo.annot files using the
following commands:
cd $SUBJECTS_DIR/subject_name/label
mris_anatomical_stats -mgz -f
../stats/lh.BA_exvivo.stats -b -a
./lh.BA_exvivo.annot -c ./BA_exvivo.ctab
subject_name lh white
mris_anatomical_stats -mgz -f
../stats/rh.BA_exvivo.stats -b -a
./rh.BA_exvivo.annot -c ./BA_exvivo.ctab
subject_name rh white
Also, if this doesn't work, I can send you the
perirhinal label from fsaverage, and you can map
this to your subject using mri_label2label.
Best,
Lee
On Thu, 10 Sep 2015, Priyanka Mehta wrote:
Correction in the previous message: I
need to mask the functional images (EPI) for further
analysis.
On Wed, Sep 9, 2015 at 11:56 PM,
Priyanka Mehta <priyankamehta0...@gmail.com> wrote:
Thank you for the explanation Lee.
I need to use the cortical labels for
masking the T1 for further analysis. Which file
should I be using then - wmparc.mgz or
aparc+aseg.mgz?
For the perirhinal cortex, I do not have
the following files even after running recon-all
<subject>/label/lh.BA.annot
<subject>/label/rh.BA.annot
<subject>/stats/lh.BA.stats
<subject>/stats/rh.BA.stats
Instead I have these files (The .stats
files are missing):
<subject>/label/lh.BA_exvivo.annot
<subject>/label/rh.BA_exvivo.annot
Your help is greatly appreciated!
Priyanka Mehta
On Thu, Sep 3, 2015 at 12:22 PM, Lee
Tirrell <ltirr...@nmr.mgh.harvard.edu> wrote:
Hi Priyanka,
The cortical labels are the same
for wmparc.mgz and aparc+aseg.mgz (taken from the
?h.aparc.annot files), but they differ on the way
the white matter is labeled. The aparc+aseg uses the
white matter and
subcortical
labels from the aseg.mgz, while
the wmparc labels each point in the white matter as
the nearest cortical label to that point, as well as
the subcortical labels from the aseg.
The perirhinal cortex isn't
included in the aparc, so it isn't in either of
these mgz files. However, it is included in the
Brodmann area annotation files, and stats are
computed for this region
automatically when
you run recon-all:
<subject>/label/lh.BA.annot
<subject>/label/rh.BA.annot
<subject>/stats/lh.BA.stats
<subject>/stats/rh.BA.stats
To see this on the inflated left
hemisphere, for example, you can run:
freeview -f
subject/surf/lh.inflated:annot=subject/label/lh.BA.annot
Best,
Lee
On Thu, 20 Aug 2015, Priyanka
Mehta wrote:
Hi Lee
Thank you for your response.
I have a follow up question-
After running recon-all -all, I found the
parahippocampal cortex and entorhinal cortex under
two files- wmparc.mgz and aparc+ages.mgz. What is
the difference between
the two?
Also, I haven't been able to
find perirhinal cortex under any of the files. I
wonder why?
On Mon, Aug 3, 2015 at 5:22
PM, Lee Tirrell <ltirr...@nmr.mgh.harvard.edu>
wrote:
Hi Priyanka,
These are all
automatically created automatically by running
recon-all -all.
Best,
Lee
On Sat, 1 Aug 2015,
Priyanka Mehta wrote:
Hi
Please excuse my
extremely basic question.
I would like to
perform segmentation on my T1 image to obtain the
following:
a. Entorhinal
Cortex
b. Perirhinal
Cortex
c.
Parahippocampal Cortex
Is there a
specific command I should be using in the 6.0 dev
version? Or should I just be using recon-all -all ?
Best,
Priyanka Mehta
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