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Dear all,
Have I understood correctly that the slice delay of each slice is not
needed when performing slice time correction with preprocess-sess?
I am processing an open OASIS fMRI dataset. The dataset has fMRI data in
nifti format and JSON files
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Instructions about how to setup a VM running Ubuntu 22.04 LTS Linux have
been updated on the wiki page,
I can't tell from those pics what is happening. Does it look like an
imaging artifact? You can try putting control points
On 2/26/2024 12:58 PM, lejia2011411409 wrote:
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Hi，
I used command: recon-all -s subject1 -i subject1.nii -all -sd
/home/t1. I
That is weird -- ft_read_mri is not one of our files. Can you send the
command line and the *full* terminal output? The lGI stuff is pretty old
and does not have a maintainer.
On 2/26/2024 1:40 PM, Michael Ruvalcaba wrote:
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Hi Douglas,
Yes I can
Hi Philip,
The deformable template was most beneficial when differences between time
points (TPs) were largest. While this is perhaps not surprising, it meant that
the long registration time of 8h/TP in the abstract was not time well spent
since we were already certain of group differences.
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Hi，
I used command: recon-all -s subject1 -i subject1.nii -all -sd
/home/t1. I think it is FrreSurfer default method to segementation.
Lejia
At 2024-02-27 01:24:00, "Douglas N. Greve" wrote:
what did you use the do the
what did you use the do the segmentation? Include command line and
terminal output
On 2/26/2024 10:46 AM, lejia2011411409 wrote:
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Dear freesurfer experts,
A large amount of subjects got segmentation white matter bad (some
dark white matter cannot be
You need to specify a format for the output (eg, ...thickness.mgz)
On 2/26/2024 10:31 AM, Asuka Toyofuku wrote:
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Hi, many thanks for your reply.
Here's the terminal output;
asuka@rigi:/media/.../FS7_Teen$ for d in Teen* EPK* epk*
> do mris_preproc
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Hi!
Thanks for getting back to me. I'm running it on CentOS Linux 7 in a
singularity container. What I did is to pull the freesurfer container from
the DockerHub
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Hi, many thanks for your reply.
Here's the terminal output;
asuka@rigi:/media/.../FS7_Teen$ for d in Teen* EPK* epk*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi
> lh --out
Dear Katharina,
First of all, and to avoid any confusion, the bug only affected the script to
gather the volumes from different subjects (“quantifyThalamicNuclei.sh”), and
not the segmentations themselves.
Would you mind sharing some images, showing how/where the LGN is oversegmented,
please?
Your mris_convert command looks correct. I'm able to do the conversion like
this with dev version:
mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot
I'm wondering which Freesurfer you are running. If you do 'mris_info surf.gii',
what does it report?
Best,
Yujing
It looks like the volume has very poor contrast. What volume are you
displaying it on? Can you take a pic on the nu.mgz?
On 2/26/2024 2:53 AM, Luisa Klahn wrote:
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Dear Douglas,
Please find attached the pictures for the following issue:
I am processing
Can you be even more specific? Operationally, what does it entail? Are
you just trying to correlate, say, cognitive deficits to, say, thickenss?
On 2/25/2024 9:12 PM, Martin Juneja wrote:
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Hi Doug,
Sorry for not elaborating in my previous email.
Voxel
Dear List,
We are using the thalamic segmentation and have encountered too large nuclei
volumes. We are aware of the bug in previous Freesurfer versions reported
here
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