Hi Vasudev
those areas are definied in the aseg.mgz (and the wmparc.mgz), so you
should be able to get them from either of those volumes.
cheers
Bruce
On Thu, 25 Aug
2016, Dev vasu wrote:
Dear all,
After running through recon-all ,I have obtained wmparc parcellation file (see
the at
Hi Vasudev - These regions are part of the subcortical segmentation (aseg)
volume:
http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
a.y
On Thu, 25 Aug 2016, Dev vasu wrote:
Dear all,
After running through recon-al
Dear all,
After running through recon-all ,I have obtained wmparc parcellation file
(see the attached figure ). I would like to obtain parcellation at specific
regions of interest for my study i.e Brain stem region and Thalamus
region, could you please let me know how i could perform parcellati
you can also use
mri_binarize --i wmparc.nii --match 1006 --o lh_entorhinal.nii
On 05/13/2016 06:12 PM, Pradeep wrote:
> Hi,
>
> This task will be a bit easy using fslmaths
>
> - convert mgz file to nii using mri_convert
> -then use fslmaths -thr -uthr
>
>
> example:
> fslmaths wmparc.nii -t
Hi,
This task will be a bit easy using fslmaths
- convert mgz file to nii using mri_convert
-then use fslmaths -thr -uthr
example:
fslmaths wmparc.nii -thr 1006 -uthr 1006 lh_entorhinal.nii
On Thu, May 12, 2016 at 9:12 AM Douglas N Greve
wrote:
> What version of FS are you using? You may
What version of FS are you using? You may need a newer version of
mri_aparc2aseg. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg
On 05/12/2016 06:53 AM, Caroline Beelen wrote:
>
> If we changed the command –-ribbon to –- no ribbon, the script ran,
> bu
Dear FS team,
We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran
the following command:
mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown --ribbon --o
mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz ( was replaced by
our subject)
We get the following er
Thank you Doug.
On Mon, Sep 28, 2015 at 11:32 AM, Douglas Greve
wrote:
>
> I made one and put it here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/wmparc.mgz
>
> Note that this should not be used for anything other than visualization,
> ie, it has little or no scientific val
I made one and put it here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/wmparc.mgz
Note that this should not be used for anything other than visualization,
ie, it has little or no scientific value
On 9/24/15 6:25 PM, Mohammed Goryawala wrote:
Hello FreeSurfer Experts,
Hello FreeSurfer Experts,
This question has been asked before by someone and I am looking to do
something similar.
*If this isn't possible, could we obtain this from fsaverage? I noticed **that
$FREESURFER_HOME/subjects/fsaverage does have an aparc+aseg.mgz *
*is there also a way to get wmparc.
Hi Sujith, sorry for the delay. The rule is that the voxel has to be
within 5mm of the label. The unsegmented is the WM that is not within
5mm of any cortical label.
Here is the ref
https://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2008.pdf
doug
On 02/07/2014 04:53 PM, sujith vijayan wrot
Hi All,
I have a few questions about wmparc:
What rule is used to determine what grey matter structure corresponds to a
white matter point?
What exactly has to be the case when UnsegmentedWhiteMatter is reported?
Is there a reference you could point me to?
Thanks,
Sujith
__
Hi All,
I have a couple of question about wmparc:
What rule is used to determine what grey matter structure is reported for a
point in the white matter?
What exactly has to be the case when UnsegmentedWhiteMatter is reported?
Is there a reference you could point me to?
Thanks,
Sujith
I'm running FSv5.1.0 on RHEL6.
1) My goal is to run a glm-fit on White Matter aparc regions for a
"between group" surf-based analysis and evaluate spatial maps of significant
differences.
2) I noticed that fsaverage does not have a wmparc.mgz file, so I'm
currently working with bert
How much is the dilation (perpendicular to the cortical surface) for
the creation of the white matter ROIs? Is there a citation for this?
Chris Bell
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Hi Jose,
I believe we just got rid of redundant information. The subcortical
structures are in the aseg.stats and don't need to be in the wmparc.stats.
On Wed, 6 Apr 2011, Jose Soares wrote:
> Hi all,
>
> I am working with FS 4.5 and 5.0 and I have noticed that in wmparc.stats in
> 5.0 there ar
Hi all,
I am working with FS 4.5 and 5.0 and I have noticed that in wmparc.stats in 5.0
there are volumes (segmentations) that do not appear in the wmparc.stats file
(and appear in 4.5 version), for instance the subcortical structures,
ventricles, cerebellum. In wmparc V 4.5 I have 1189 rows wi
also be sure to add the flag --a2009s to the end of the mri_aparc2aseg
command shown below (i forgot to mention this the first time aroun).
this will fix the problem where you were not seeing the correct labels
(you should now see the Destrieux labels when viewing in tkmedit).
per the Segmentation
We don't usually use the Destrieux atlas for this as the wmparc was
oritinally intended to measure gyral white matter. However, you can
still run the commands, something like
cd $SUBJECTS_DIR/subject
mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
--volmask --annot aparc.a2009
aparc2aseg using Destrieux atlas now seems to run OK for a different subject
anyway - and I managed to get the same image as you did. But there are two
problems:
1. when I do tkmedit subjid T1.mgz -segmentation wmparc.a2009s.mgz with
color LUT, it still shows Killiany/Desikan conventions for wm par
To get the Destrieux atlas parcellations in the wmparc, first have a
look at the -wmparc section of the recon-all table:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
those last two commands would be modified like this:
mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown
--ribbo
Hi all
Could anyone help me with extracting the wmparc volume stats in accordance
with Destrieux atlas?
As it stands now the segmentations corresponding to whitematter beneath
Destrieux 2009 parcellations are returned empty when called for
Many thanks
Lena
\_
Le
I want to extract wm volumes using wmparc for parcellations contained in
Destrieux 2009 atlas but when I inspect my wmparc stats file, most of the
volumes that I am interested in are reported as zero. What should I do to
read these volumes?
Many thanks
Lena
__
Does the "mri" dir exist in the directory that you are running it from?
joel bruss wrote:
Hello-
I ran recon-all and it reported that everything ran with no errors
but, when I go into mri, there is no wmparc.mgz file. I tried running:
mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --ri
I'll try this again as I'm stuck and in need of help.
I ran recon-all and it reported that everything ran with no errors but, when
I go into mri, there is no wmparc.mgz file. I tried running:
mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon
--o mri/wmparc.mgz --ctxseg
Hello-
I ran recon-all and it reported that everything ran with no errors but, when
I go into mri, there is no wmparc.mgz file. I tried running:
mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon
--o mri/wmparc.mgz --ctxseg aparc+aseg.mgz
and all was running well until it
Hi Doug,
The white matter in aseg seems to follow the same pattern as the white
matter in wmparc...it goes into the ribbon (through the white matter
surface into gray matter).
-Ryan
On Dec 7 2007, Doug Greve wrote:
Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they
lo
Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they
look in that area?
Ryan Muetzel wrote:
Hi Doug,
The images are attached. Thanks again for your help!
-Ryan
On Dec 6 2007, Doug Greve wrote:
Can you send a pic?
Ryan Muetzel wrote:
Hello,
We are running Freesurf
Can you send a pic?
Ryan Muetzel wrote:
Hello,
We are running Freesurfer version 4.0.1 and seem to be having problems
with the white matter/gray matter parcellation borders. When viewing
the pial and the main white surfaces in tkmedit, everything looks good
against the t1 brain. However, wh
Hello,
We are running Freesurfer version 4.0.1 and seem to be having problems with
the white matter/gray matter parcellation borders. When viewing the pial
and the main white surfaces in tkmedit, everything looks good against the
t1 brain. However, when the wmparc is loaded on, we are seeing t
recon-all -wmparc -s subject
Amy DeLuca wrote:
could someone send me the command line for the last step in recon3 stream.
The new version differs from the wiki table and I need to run just that
last WMParc step.
Thanks
Amy
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could someone send me the command line for the last step in recon3 stream.
The new version differs from the wiki table and I need to run just that
last WMParc step.
Thanks
Amy
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Freesurfer@nmr.mgh.harvard.edu
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