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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