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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"). Howev
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:
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Hi,
I am referring to the anatomical region of interest - the surfac
what version of freesurfer are you running?
On 7/17/2020 2:24 PM, Bahrani, Ahmed A. wrote:
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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 recon-all
On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:
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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 RO
We don't have recommendations on this, sorry
On 7/21/2020 12:18 PM, Zeng, Qi wrote:
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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 rem
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:
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Hello Freesurfer Experts,
I think I may already know the answer to this, but just wanted
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 7/22/20
Do you not see ?lh.pial.avg.area.mgh in
$FREESURFER/subjects/fsaverage/surf ?
On 7/21/2020 3:11 PM, Xiaojiang Yang wrote:
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Dear FS developers,
I have noticed that for each subject, there are ?h.area and
?h.area.pial files under the $SUBJECT_DIR/$subject/s
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:
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Thanks
I found a new b
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:
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Dear experts,
I am running mri_aparc2aseg and, based on the output, it seems to run
through suc
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:
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Dear experts,
I am running mri_aparc2aseg and, based on the output, it seems to run
through successfully until the v
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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
>
>
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:
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Hi Douglas,
mri_segstats wouldn't generate binary ROI masks, so I tried using
*mri_binarize* and *mri_
700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=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:
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Dear FS developers,
I have noticed t
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:
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Yes, exactly, I am running it from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0.
(using a virtual machine, but ran
http://freesurfer.net/fswiki/ThalamicNuclei
On 7/23/2020 11:04 AM, Al Qadi, Ameen wrote:
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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>> wrot
com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20200723>
On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:
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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 point
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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
s N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=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&q=date:20200723>
On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:
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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 Dougla
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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
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