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Hello Olga,
I have not tried the FS 5.3 binaries on an Ubuntu 20 system, but I suspect some
shared library references won’t be resolved there. Even if the FS 5.3
source were to compile on Ubuntu 20, you would likely get some discrepancy in
numeric o
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Dear Doug,
I have the same issue as the people below. I was wondering if this was
solved in the meantime.
I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and
got the following error in only one of my subjects. When I ran the same
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Hi all,
I'm encountering an issue with surface reconstruction quality in
ventromedial prefrontal cortex, using relatively high resolution (.8mm) T1-
and T2-weighted input data to recon-all. I'm using the following command,
with Freesurfer 7.1.1 running
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Dear FreeSurfer Developers,
I would like to run the Hippocampus subfields segmentation on Freesurfer 7.1.1.
I am working on a HCP cluster with CentOS 7 (Core). Before running the
segmentation on my data, I first tried to run the segmentation on your
Hi Alberto,
My name is Devani Cordero, I'm a research technician for the FreeSurfer lab.
You can absolutely use asegstats2table. First, what kind of labels did you
create? Did you make them based off of a volume such as T1.mgz or did you
create them on a surface?
Let me know!
Devani
Devani C
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Dear All,
Hope everyone is safe and well.
Did anyone you have MNI152 TEMPLATE mainly required for Alzheimer's
Diagnosis.
Also can anyone help in recommending any tool other than FREESURFER for
preprocessing of sMRI scans for Alzheimer's disease but the
Dear Alessio,
You need to request approximately 16GB of RAM when you submit your jobs to the
cluster.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of
"alessiopropos...@libero.it"
Reply-To: Free
Hi FreeSurfer Developers,
I am trying to process a few MPRAGE sequences (different sessions), so I can
edit the scans. And I am having trouble reconning the .mgz files.
I have looked into why my job terminated early and I have attached the message
below. The error states that 'input(s) cannot
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Dear colleagues,
I am looking for information about installing FS on Ubuntu 20.04.
One concern is that we might need to be able to use an older version of FS
(e.g. FS 5.3), and from what we can tell that won't even be compatible with
Ubuntu 18.0
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Hi Douglas,
Thanks a lot for your kind explanation!
With regards
Vittal
On Thu, Dec 17, 2020 at 8:12 PM
wrote:
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wi
Sorry, I'm not sure what you mean when you say the volume map is uncorrected
On 12/14/2020 10:02 AM, Sara Lyn wrote:
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And also i'm trying to extract these values from the uncorrected maps not
corrected. Is there a way for that? Thank you
On Mon, Dec 14, 202
If you want to apply etiv correction when extracting the cortical volume with
mris_preproc, just add --etiv to the command
On 12/14/2020 9:59 AM, Sara Lyn wrote:
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Hi
Thank you for your response. How do I correct this extracted volume for
intracranial volume
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Hi Doug,
it turns out part of the v5.3 installation had been accidentally deleted.
After restoring the file, it works fine, and I am happy to report the the
GPU versions work (with CUDA 5).
Thanks!
Caspar
Am Do., 17. Dez. 2020 um 15:37 Uhr schrieb Gre
The GPU stuff may or may not work. It was hard to maintain because the GPUs
kept changing so much, and it would not surprise me that the code from 5.3 is
incompatable with GPUs today. But it looks like the error is that it could not
find a file. Does that file actually exist?
On 12/12/2020 3:04
Are there presentations that are simultaneous?
On 12/12/2020 3:19 AM, Nina Khatibi wrote:
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Hi,
I'm using a functional analyse with selxavg3-sess, i have 25 subjects and each
subject contains 15 runs, I've done plenty of analyses with different paradigm
files
Sorry, I can't tell from your email what the problem is. Can you elaborate?
On 12/9/2020 2:30 PM, najme soleimani wrote:
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Dear FreeSurfer Developers,
I downloaded the HCP_1200 subjects' structural extended data. I am attempting
to have equal sized parcellatio
It depends on the order that you specified them. You will have four groups
SczUrban
SczRural
HVUrban
HVRural
The interaction will be of the form
(SczUrban-SczRural)-(HVUrban-HVRural)
Look in the y.fsgd to see what the order of the classes is. You can then look
in the contrast folder at C.dat to
Essentailly, this is a skull strip error, so you may need to remove the skull
(ie, non-brain) manually
On 12/9/2020 6:25 AM, Elisa Rehbein wrote:
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Dear Freesurfer experts,
we are currently running recon-all for our MP2RAGE images, using Freesurfer 7.
Howe
I don't know, that msg probably comes from the gifti code we link to. It looks
like it is just a warning. Do the output waveforms look ok?
On 12/9/2020 6:05 AM, Mason Wells wrote:
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Hi Experts,
I have pre-processed some resting-state date using fMRI prep. I h
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Any tools other than Freesurfer for preprocessing Nifti sMRI scans. Only
requirement is it should work on windows.
On Thu, 17 Dec 2020, 4:22 pm Laura f, wrote:
> Dear Sir or Madam,
> I am not longer working with FreeSurfer so I would like to remove m
Dear Sir or Madam,
I am not longer working with FreeSurfer so I would like to remove my
subscription to the mailing list.
Thank you,
Laura
smime.p7s
Description: S/MIME cryptographic signature
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Freesurfer m
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I need to use freesurfer brain_anat.nii T1 and path.pd.nii (CST WM tract )
in the navigator for neurosurgery. It is necessary to merge the two volume
images and to transform it in dicom.Exist a command for that or a procedure in
Fressurfer? Or sam
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