Try
cd $SUBJECTS_DIR/subject/scripts
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.yeo.stats -b -a ../label/lh.yeo2011_17Networks_N1000.annot
-c ../label/aparc.annot.ctab subject lh white
On 10/2/15 12:19 PM, Ali Radaideh wrote:
I am trying to extract the cort
I am trying to extract the cortical volume, thickness, and area based on
these 17Networks cortical parcellation.
Thanks,
Ali
On Fri, Oct 2, 2015 at 6:23 PM, Douglas Greve
wrote:
> You should not use both --seg and --annot. What are you trying to
> accomplish?
>
> On 10/2/15 3:34 AM, Ali Radaide
You should not use both --seg and --annot. What are you trying to
accomplish?
On 10/2/15 3:34 AM, Ali Radaideh wrote:
Hi Bruce,
I have used the following command line:
mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh
lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum
and got the
Hi Bruce,
I have used the following command line:
mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh
lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum
and got the following:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName
1 0 15766121 15766121.0 Seg
2 2182848
sure, you can use mri_segstats to get stats from it
Bruce
On Thu, 1 Oct 2015, Ali
Radaideh wrote:
Can we get any stats from this type of parcellation? I only can see two
annotation files after running the mri_surf2surf command and these can be
loaded tksurfer as an overlay.
Thanks,
Ali
On T
Can we get any stats from this type of parcellation? I only can see two
annotation files after running the mri_surf2surf command and these can be
loaded tksurfer as an overlay.
Thanks,
Ali
On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl
wrote:
> that will generate a parcellation on the individua
that will generate a parcellation on the individual subject surface of
Thomas Yeo's 17-network clustering. It won't do anything with the thickness
though. What are you trying to do?
On Tue, 29 Sep 2015, Ali Radaideh wrote:
mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
--sv
mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
--sval-annot
$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot
--tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
scz10 is my subject name
On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve
wr
what is your surf2surf command?
On 9/28/15 5:11 PM, Ali Radaideh wrote:
Dear Douglas,
Thanks for your email. I meant to say that after running the
recon-all, i ran the sur2surf command to get the cortical parcellation
using Thomas Yeo Atlas.
I thought that the extracted cortical thickness a
Dear Douglas,
Thanks for your email. I meant to say that after running the recon-all, i
ran the sur2surf command to get the cortical parcellation using Thomas Yeo
Atlas.
I thought that the extracted cortical thickness after running the surf2surf
command will be different from the one extracted be
I can't understand what you are asking. Can you elaborate?
On 09/28/2015 01:51 PM, Ali Radaideh wrote:
> Thanks alot Douglas,
>
> Yes it is there but after checking it many time I found it corrupted
> for some subjects due to copying them many times between machines.
>
> But May I ask you some th
Hi Ali
using Thomas' parcellation won't change the vertex-wise thickness values,
but of course if you want to average within his ROIs you can generate stats
files with that information.
Sorry, does that answer you question?
cheers
Bruce
On Mon, 28 Sep 2015,
Ali Radaideh wrote:
Thanks a
Thanks alot Douglas,
Yes it is there but after checking it many time I found it corrupted for
some subjects due to copying them many times between machines.
But May I ask you some thing related. I have just posted a question
regarding getting the cortical thickness after running the surf2surf
com
does that file exist?
On 09/28/2015 01:05 PM, Ali Radaideh wrote:
> Dear FreeSurfer experts,
> After finishing the recon-all, I am trying to extract the cortical
> thickness for each subject and group them into one table but
> unfortunately i keep getting the following error:
>
> rh.aparc.DKTa
Dear FreeSurfer experts,
After finishing the recon-all, I am trying to extract the cortical
thickness for each subject and group them into one table but unfortunately
i keep getting the following error:
rh.aparc.DKTatlas40.stats is not found or is too small to be a valid
statsfile
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