External Email - Use Caution
Hi Freesurfer experts,
I am trying to extract only the cerebellum and then save it to nii file. How
can I do it with freesurfer ?
Thanks a lot and have a nice day,
Aldo
___
Freesurfer mailing list
External Email - Use Caution
Hi Doug,
Yes that's the area. Thank you for your help!
Angel Hammond
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
s N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>Thu,
23 Jul 2020 07:37:13 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200723>
On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:
External Email - Use Caution
Hi Douglas,
For the container, I am using version 6.0.0-min
The freesurfer on my computer is
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Thanks,
Ahmed
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
search?l=freesurfer@nmr.mgh.harvard.edu=date:20200723>
On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:
External Email - Use Caution
Hi Doug,
For your questions:
1. "Not sure what you mean by in the ROI. Are you trying to permute
across space?
That generally does not work because the points are no
http://freesurfer.net/fswiki/ThalamicNuclei
On 7/23/2020 11:04 AM, Al Qadi, Ameen wrote:
External Email - Use Caution
Thank you. How do I generate this image? It wasn't generated using
recon-all.
On Thu, Jul 23, 2020 at 10:55 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
does the mri folder exist? do you have write permission to it? is the
disk out of space?
On 7/23/2020 11:04 AM, Ellen Ji wrote:
External Email - Use Caution
Yes, exactly, I am running it from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0.
(using a virtual machine, but
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200723>
Do you not see ?lh.pial.avg.area.mgh in $FREESURFER/subjects/fsaverage/surf
?
On 7/21/2020 3:11 PM, Xiaojiang Yang wrote:
External Email - Use Caution
Dear FS developers,
I have noticed that for
aparc+aseg does not have the thalamic nuclei. You need to run it on
ThalamicNuclei.v10.T1.FSvoxelSpace.mgz
On 7/22/2020 6:26 PM, Al Qadi, Ameen wrote:
External Email - Use Caution
Hi Douglas,
mri_segstats wouldn't generate binary ROI masks, so I tried using
*mri_binarize* and
External Email - Use Caution
Thank you. How do I generate this image? It wasn't generated using
recon-all.
On Thu, Jul 23, 2020 at 10:55 AM Douglas N. Greve
wrote:
> aparc+aseg does not have the thalamic nuclei. You need to run it on
> ThalamicNuclei.v10.T1.FSvoxelSpace.mgz
>
>
Sorry, it should be from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0
(without the /mri)
On 7/23/2020 8:37 AM, Ellen Ji wrote:
External Email - Use Caution
Dear experts,
I am running mri_aparc2aseg and, based on the output, it seems to run
through successfully until the
Where are you running the program from? Make sure it is from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/mri
On 7/23/2020 8:37 AM, Ellen Ji wrote:
External Email - Use Caution
Dear experts,
I am running mri_aparc2aseg and, based on the output, it seems to run
through
I could not reproduce that bug, but I did find another one. I created a
new version longmc in the same location. I used it yesterday and it ran
all the way through, so please git it a try
On 7/22/2020 2:28 PM, Knut J Bjuland wrote:
External Email - Use Caution
Thanks
I found a new
Do you not see ?lh.pial.avg.area.mgh in
$FREESURFER/subjects/fsaverage/surf ?
On 7/21/2020 3:11 PM, Xiaojiang Yang wrote:
External Email - Use Caution
Dear FS developers,
I have noticed that for each subject, there are ?h.area and
?h.area.pial files under the
You can binarize the final cluster map (mri_binarize --i clustermap.mgz
--min 0.5 --o bin.clustermap.mgz)
Then run mri_segstats --annot fsaverage lh aparc --i bin.clustermap.mgz
The mean value will be the fraction of the vertices in the ROI that
belongs to (any) significant cluster
On
do you mean where the cursor is? That's in hippocampus or amygdala, so
it is fine that the pial surfaces cuts through them
On 7/21/2020 1:44 PM, Angel Hammond wrote:
External Email - Use Caution
Hello Freesurfer Experts,
I think I may already know the answer to this, but just wanted
We don't have recommendations on this, sorry
On 7/21/2020 12:18 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi,
I have a question about how to handle outliers in aparc, aseg and
tracula results? Usually, each subject has one result regarding one
measurement and I detect and
On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:
External Email - Use Caution
Hi Doug,
For your questions:
1. "Not sure what you mean by in the ROI. Are you trying to permute across
space? That generally does not work because the points are not
exchangeable across space."
By "In the
what version of freesurfer are you running?
On 7/17/2020 2:24 PM, Bahrani, Ahmed A. wrote:
External Email - Use Caution
Hi Douglas,
I am using the following:
Linux Redhat version 7.9
Singularity version 3.6.0
Freesurefer version 6.0.0-min (for containers)
I checked all the
we don't have a specific label for that, though if you can find a set of
labels that meet your requirements, then you can merge them together
On 7/17/2020 1:48 PM, Anja Samardzija wrote:
External Email - Use Caution
Hi,
I am referring to the anatomical region of interest - the
External Email - Use Caution
Dear experts,
I am running mri_aparc2aseg and, based on the output, it seems to run
through successfully until the very end where it does not actually write
the file (I receive "error: niiWrite(): error opening file
mri/aparc.500+2mm.nii.gz").
21 matches
Mail list logo
