External Email - Use Caution
I have made manual edits to a subject that was initially run with the -FLAIR
and -FLAIRpial input flags. When I want to rerun freesurfer to
implement these edits should I add these flags again, or is it sufficient to
run recon-all -all?
request
Sure. We’ll add those in.
Best,
Ruopeng
On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS
mailto:vincent.koppelm...@utah.edu>> wrote:
External Email - Use Caution
Dear FreeSurfer team,
I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39
Would it be po
External Email - Use Caution
Dear FreeSurfer team,
I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39
Would it be possible to add the following features as command line flags to
FreeView?
1) Set opacity for a surface
It is currently only possible via CLI to
eg and rerun autorecon2-wm and autorecon3 I believe.
For the medial ttemporal lobe issue is that really cortex? I can't really tell
from the single coronal slice. I'll cc Jean Augustinack to see if she has an
opinion.
cheers
Bruce
On Fri, 30 Jun 2017, Vincent Koppelmans wrote:
Hi all,
I was wonderin
Hi all,
I was wondering how to fix the following issues:
1) The cortical ribbon extends into the gray matter of the putamen (see
the top row of this image:
https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0).
2) Cortical gray matter is missing in the medial temporal lobes (see the
bottom
of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert
Hello Freesurfer experts,
I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems
about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop
Hello Freesurfer experts,
I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:
#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
Hello Freesurfer developers,
I am looking for a version of Freeview that recognizes the -noquit flag.
V 1.0 Build Aug 24 2015 14:50:08 allows this, but is no longer available from
"ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev
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Hello Freesurfer experts,
I would like to display stats images that are in MNI space on an MNI surface
volume.
I found this thread on the mailing list that explains how to use mri_vol2surf
to convert volumetric images to a surface:
Dear FreeSurfer experts,
I have some experience with FSL and SPM, but not a lot with FreeSurfer, so
please bear with me.
When I observe FreeSurfer segmentations, I see that images are binary (either a
voxel belongs to a tissue class, or it does not) and not probabilistic. I want
to obtain
Hi all,
I am trying to convert Brodmann area 4a and 4p to .nii file format in native
space. I have used to following syntax:
tkregister2 --mov ${SUBJECTS_DIR}/mri/rawavg.mgz --noedit --s [SUBJECT_ID]
--regheader --reg ./register.dat
mri_label2vol --label [PATH-TO-LABEL-FILE] --temp
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