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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
person to whom it is
addressed. If you believe this e-mail was sent to you
in error and the e-mail
contains patient information, please contact the
Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail
was sent to you in error
but does not contain patient information, please
contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
