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Hi,
Thank you for your advice. ?I have indeed already allocated as much memory as
possible to the VM. I did manage to finish recon-all for another subject
overnight, yet still not the subject that got terminated at this step.
I have now updated al
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Hi FreeSurfer experts,
Recently, I used Fresurfer's recon-all toprocess our own T1 MRI brain
volumes which is 0.7 m3 isotropic. For most young brain cases, FS performs
very well, the segmention is great. But for almost every elderly brain case,
Hi Rita - Can you share this volume with me? I haven't been able to replicate
your error message so far.
/home/rita/Desktop/test/diffusion_dcm/MRI_20160226_2_PHD003/MRI_20160226_2_PHD003_dwi.nii.gz
Thanks,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
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Dear Douglas,
Thank you very much for your suggestion.
Sincerely,
Tien Pham
On Tue, Mar 9, 2021 at 12:55 AM Douglas N. Greve
wrote:
> We have abandonded QDEC, so try using the command line stream
> http://secure-web.cisco.com/11tn2HXIVZKcF0Wonwwp-
Yes, I was just going to follow up with this disclaimer. It’s a slightly newer
version of nu_correct, so it’s possible the result will differ very slightly.
The problem is that the FS 5.3 version of MNI/nu_correct uses a perl version
that reached end-of-life in 2008! So it would be quite difficu
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The subcortical structures do look okay to me.
-Laurel
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, March 8, 2021 9:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re:
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Andrew,
That's a great suggestion, thanks.
Any idea whether using the MNI from FS6 has an impact on the results?
Cheers,
Malcolm
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoopes, Andrew
Sent: Monda
Hi Malcolm,
Yes, this is an unfortunate bug, but I've been playing around with a few
options and the following seems to be the best patch. This assumes you also
have FS v6 installed and, in this case, FS_53 and FS_60 point to the
respective freesurfer base directories:
rm -rf $FS_53/mni
cp -r
If you installed freesurfer with admin permissions, you should mv or cp the
file to the destination directory with `sudo` in front of your command to run
as root.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Donato Romano
Date: Monday, March 8, 2021 at 6:52 AM
To: freesur
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Hi Doug,
Any other suggestions I could try? It seems to be only an issue with the
non-pvc data.
Thanks
Julie
On Tue, 2 Feb 2021 at 11:10, Julie Ottoy wrote:
> Hi Doug,
>
> I tried these fixes but they still give me the error message below. I did
>
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I want to use the annotation file created by myself in fsaverage to
calculate the anatomical stats, but i dont know what is the best workflow.
1. Convert the annotation file to each subject space using mri_sur2surf and
using mri_anatomical_stats in eac
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Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on lying on
the cortical surface on a flat map and a spherical map.
I've run recon-all and cr
Look in the csdbase.y.ocn.dat
Run mri_glmfit-sim --help
for more info
On 3/3/2021 2:38 PM, Fang, Angela,Ph.D. wrote:
Hello Freesurfer community,
I would like to extract individual brain activation values in specific
clusters emerging from an FSFAST group analysis that tested a certain
contr
We have abandonded QDEC, so try using the command line stream
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
The only thing you'll have to figure out is what to use for --meas in
mris_preproc
On 3/3/2021 4:09 AM, Tien Pham wrote:
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Dear F
You can also use tksurferfv, which is a frontend for freeview that takes
the tksurfer options
On 3/2/2021 1:41 PM, Wang, Ruopeng wrote:
Hi,
Tksurfer has been replaced by freeview. You can load an overlay file
with the following freeview command:
freeview -f lh.inflated:overlay=xxx.mgh
Best
I don't know entirely what that refers to. I found this page
https://adni.bitbucket.io/reference/ucberkeleyav1451.html
Looks like someone is doing an analysis outside of freesurfer, and this
is the uptake in the "unknown" region of cortex (ie, a part that is not
labeled, probably in the medial w
Sorry made a mistake: it is CFT= 4
freeview -f
$SUBJECTS_DIR/fsaverage/surf/rh.inflated:overlay=cache.th40.pos.sig.cluster.mgh
Thank you
Akila
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, March 8, 2021 10:45 AM
To:
Hard to say from a description. If you look at the subcortical
structures, do they look like they are accurate?
On 3/1/2021 4:36 PM, Laurel Quinlan wrote:
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Hi Freesurfer Team,
I am checking over the aseg on one of my subjects and notice that
there are lar
This is a bug. You can try this
cd /lab-share/Psych-Glahn-e2/Public/UKB_4844/FS_MRI/6026423/surf/
ln -s lh.sphere.reg lh.fsaverage5.sphere.reg
Then re-run
On 3/1/2021 4:14 PM, Amanda Rodrigue wrote:
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Hello,
I am attempting to run mris_preproc with a single
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All,
We're setting up a new cluster (based on CentOS 8) but have many users that
still want to run older versions of FreeSurfer (5.3 and 5.3-HCP).
We're hitting a perl error which appears to be a known issue with newer
versions of Perl:
[mtobias@log
Can you send your full mri_glmfit-sim command line? It looks like you
used a cluster forming threshold (CFT) of 1.3. If so, when you look at
the uncorrected sig.mgh files and threshold at 1.3, do you see the same
thing? Also, what is the threshold for the image below
On 3/1/2021 1:35 PM, Weera
Hi Raquel
The log says:
Command terminated by signal 9
Which is a message from the Linux scheduler, and usually means you ran out of
ram. It looks like you have 5G on that machine and some of it was in use at the
time. Can you find a machine with more ram to try it on? Or free up the memory
b
Hi Alberto
1. And 4. Are not properties of single surfaces – they are computed from the
white and the pial. For 2 and 3 that is really up to you
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Alberto Del Cerro Leon
Sent: Monday, March 8, 2021 7:02 AM
To: Freesurfer
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Hello Freesurfer team, I am using an annotation file that i've created
previously to obtain the measures of some ROIs. To do that i am using de
commands mri_surf2surf and mri_segstats. I want to obtain the following
measures:
1. Gray and White Matter Vo
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Hello FreeSurfer Developers,
I have a problem with the license.txt file. I installed freesurfer
https://secure-web.cisco.com/1kr9diGzYY_KvBEtklD2GLjlt2rQ-By6uhuAuJRXSN2879KFTSeYZav73HMpBhcTE0d8WNcIjIe8X4-vOrM_6fCmgI45J-_6TNefbMPRLQFZfOsFiRaZQOrN4clNbaf
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