Respected Sir,
I meant to ask that if i want to separate for example hippocampus and view
as a separate volume what code should i implement?
On Mon, Oct 2, 2017 at 6:44 PM, Bruce Fischl
wrote:
> what do you mean by separate? Extract into a separate volume? If so, you
> can use mri_extract_label
Hi Vidhu,
You could use mri_vol2label or mri_binarize ( check freesurfer site or help
in terminal for details )
Cheers
On Tue, Oct 3, 2017 at 11:05 AM Vidhu Agrawal
wrote:
> Respected Sir,
>
> I meant to ask that if i want to separate for example hippocampus and view
> as a separate volume what c
Respected sir,
I have run the code:
mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg
register.dat --fillthresh .5 --o cent-lh.nii.gz
it is giving error:
Loading registration from register.dat
regio_read_register(): No such file or directory
Could not open register.dat
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Respected Sir,
A segment.dat file is formed and when i am running:
mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg
segment.dat --fillthresh .5 --o cent-lh.nii.gz
Then error is coming:
Error reading betplaneres from segment.dat
On Tue, Oct 3, 2017 at 4:13 PM, Vidhu Agraw
use, for example,
mri_binarize --i aseg.mgz --match 17 --o left-hippo.mgz
The 17 is the index for left hippo as found in
$FREESURFER_HOME/FreeSurferColorsLUT.txt
On 10/3/17 6:48 AM, Vidhu Agrawal wrote:
Respected Sir,
A segment.dat file is formed and when i am running:
mri_label2vol --la
cortex is always GM
On 10/3/17 2:19 AM, Fereshte wrote:
Dear Experts,
How to figure out if a cortical parcellation is Considered as a part
of gray matter or white matter ?
Thank you!
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yes, you can do that with either of the binaries I mentioned
cheers
Bruce
On Tue, 3 Oct
2017, Vidhu Agrawal wrote:
> Respected Sir,
>
> I meant to ask that if i want to separate for example hippocampus and view as
> a separate volume what
> code should i implement?
>
> On Mon, Oct 2, 2017 at
Hi Fereshte
all cortical parcels are gray matter. Maybe I'm not understanding your
question?
Bruce
On Tue, 3 Oct 2017, Fereshte wrote:
Dear Experts,How to figure out if a cortical parcellation is Considered as a
part of gray matter or
white matter ?
Thank you!
__
Many thank for your response.
Claryfing my question on point 3,
When I look in group.effect.slope, the map show the group difference removing
the effect of the covariate.
Conversely, I would to obtain the map reporting only the effect of covariate
on dependent variable (functional connectivity).
probably you want 0 0 0 0 .25 .25 .25 .25
On 10/3/17 10:10 AM, std...@virgilio.it wrote:
> Many thank for your response.
> Claryfing my question on point 3,
> When I look in group.effect.slope, the map show the group difference removing
> the effect of the covariate.
> Conversely, I would to obt
Thank you very much.
Where I should put 0 0 0 0 .25 .25 .25 .25?
Which are the contrast reported below that I should modify?
C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
C5) gr1-gr4_intercept 1
Hi,
I was wondering if there is a way to convert an asc file to fsaverage.
I have a list of vertex values and I want to convert them to a thickness
format. I know how to use mri_convert to go form thickness to ascii and I
was hoping there is a way to go in the other direction.
Thanks!
Ali
__
Hi Sol,
I don't recognize this error, but will look into it. Have you set up the
required system libraries and library dependencies described in
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page ?
Andrew
On Oct 2, 2017, at 5:55 PM, Sol Jerome
mailto:s...@utdallas.edu
Postdoctoral Fellow in Affective, Cognitive, and Aging Neuroscience
Degree and area of specialization:
Ph.D. in Neuroscience or Psychology
Experience in neuroimaging research in emotion, cognition, and/or aging
preferred.
Minimum number of years and type of relevant work experience:
* Demon
I think so. I am actually attempting to build an RPM. Here is my spec
file:
Name: freesurfer
Version:6.0.0
Release:1%{?dist}
Summary:FreeSurfer Software Suite
License:Proprietary
URL:https://surfer.nmr.mgh.harvard.edu/
Source0:
https:
Dear freesurfers,
I contact you since I ran a PCA with mri_glmfit. I do not manage to load
the output v.mgh as an overlay as suggested in the documentation, which
makes me wonder what is wrong. The output file or me loading it?
For clarification, I ran the command: mri_glmfit --surf fsaverage lh
Hi there
If I wanted to compare some spatial probability maps of some sulci of
interest with the Juelich Data provided by FreeSurfer, would it make more
sense to use the unthresholded Brodmann areas or the .thresh ones? Based on
my understanding of how the .thresh was created (by creating a surfac
I would use the versions where the group size approximately matched the
individual size.
Peace,
Matt.
From: on behalf of Trisanna
Sprung-Much
Reply-To: Freesurfer support list
Date: Tuesday, October 3, 2017 at 7:36 PM
To: Freesurfer support list
Subject: [Freesurfer] Brodmann areas -
yes, I agree with Matt. You need different thresholds for different areas
(e.g. V1 vs. BA44) and picking one that on average gives you the right
sized label seems reasonable
Bruce
On Tue, 3 Oct 2017, Matt Glasser wrote:
I would use the versions where the group size approximately matched the
Thanks for the speedy reply, Matt and Bruce! In that case I'll go with the
.thresh for each Brodmann area.
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Tue, Oct 3, 2017 at 8:32 PM, Bruce Fischl
wrote:
> yes, I agree with Matt. You need differ
If you cd into BUILD/freesurfer-6.0.0/lta_convert, does the file
lta_convert.help.xml.h exist?
Also, run ‘make' while in the lta_convert directory to see if the error output
provides more details. If not, can you send me the contents of
BUILD/freesurfer-6.0.0/lta_convert/Makefile?
thanks
Andrew
Sorry i meant brain parcellation ( aseg.mgz )
On Tue, Oct 3, 2017 at 5:33 PM Bruce Fischl
wrote:
> Hi Fereshte
>
> all cortical parcels are gray matter. Maybe I'm not understanding your
> question?
> Bruce
>
>
> On Tue, 3 Oct 2017, Fereshte wrote:
>
> > Dear Experts,How to figure out if a cortica
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