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mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --replaceonly 8204
--replaceonly 8205 --replaceonly 8206 --replaceonly 8217 --replaceonly 8218 --o
$SUBJECTS_DIR/R-Intralaminar.mgz
ERROR: Option 8205 unknown
mri_binarize --i
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mri_segstats --seg $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --ctab-default
--sum sum.dat --id 8130
Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt
$Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $
cwd
cmdline
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Thank you for the reply, I look forward to your email.
Perfectly valid point regarding the AUR post, I must not have read it closely
enough.
RE: CentOS8, we exclusively use Ubuntu on our lab processing servers
(compatibility reasons), however I
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Moreover, how can I merge, with mri_binarize, more thalamic regions?
e.g. 8204 8205 8206 8217 8218
> Il 13 maggio 2020 alle 23.03 "Douglas N. Greve" ha
> scritto:
>
> It problably means that seg 8130 does not exist in the input mgz. Can you
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Hello Tristan,
I can send you an email directly later today with some tests you can try for
freeview and some other commands If the test succeeds, then at least it
would mean your environment is good.
The original bug report on the Arch Linus page -
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Dear Freesurfer experts,
I am trying to run recon-all for a new subject, however I came across with
this error 'Talairach failed'. The error log is as following:
*talairach done\n cp transforms/talairach.auto.xfm
Hmmm, I don't know. Can you upload the data set? Follow these instructions
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name:
Someone just pointed out that I posted the wrong file. Here is the
correct one. Copy it to the same folder
https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m
On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
Download this file
Have you read this page? Just follow those steps
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
On 5/14/2020 9:28 AM, Peng Liu wrote:
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Dear Freesurfer experts,
I am trying to run recon-all for a new subject, however I came across
On 5/11/2020 5:53 PM, özenç taskin wrote:
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Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different
surfaces and I'd like a little bit of guidance as I am slightly
confused about some of the outputs of freesurfer.
I
Try running
mri_segstats --seg ThalamicNuclei.v10.T1.mgz --ctab-default --sum
sum.dat --id 8130
And send the contents of sum.dat
On 5/13/2020 7:37 PM, std...@virgilio.it wrote:
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In the FreeSurferColorLUT.txt 8130 is the left VM.
The volume is correctly
Just add more --replaceonly args
On 5/14/2020 10:38 AM, std...@virgilio.it wrote:
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Moreover, how can I merge, with mri_binarize, more thalamic regions?
e.g. 8204 8205 8206 8217 8218
Il 13 maggio 2020 alle 23.03 "Douglas N. Greve"
ha scritto:
It
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Hi FreeSurfer Experts,
I am trying to extract or calculate the adjusted values for each participant in
each cluster after accounting for covariates in my permutation analysis.
This is a 3 group analysis with 3 covariates (age, sex, and ICV).
That is how you would compute a partial model fit, though I'm not sure
which part of the model you are trying to fit. In what you have, it will
remove the main effect of group (but not interactions).
On 5/14/2020 1:30 PM, Hua, Jessica wrote:
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Hi
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