Hi Amy,
please send your questions to the freesurfer email list .
Try replacing ID with fsid , also you may need to fix the white spaces (replace
multiple spaces with a single space or tab).
Best, Martin
> On 9. Oct 2017, at 03:09, 田阿敏 <237416...@qq.com> wrote:
>
>
> Hi~
>
> I am Amy from
Dear FS developer,
I am a FS beginner and trying to make QDEC images of cortical thickness
difference (color-coded inflated brain) between groups.
No problem when fsid, diagnosis, age, and sex were only included in
qdec.table.dat file. However, adding any other factors such as hypertension,
dia
Hi all,
I would like to perform a fixed effects analysis on a small sample of
subjects with FS-fast -- where the time series from all subjects are
concatenated together and analysed in a large design matrix.
Is there an easy way to do this? I don't know if I'm looking in the wrong
place but I can
This issue is likely the newness of the OS you are running and the version of
glibc libs it has. The license code in the old versions of freesurfer simply
will not work with any license file with the newest glibc libs. There may be
a workaround by preloading an older libcrypt.so library. Can
Technically, it does not use an anatomical volume but rather the
surfaces derived from the conformed volume (so the registration will be
good for any conformed volume). No need to reorient the functionals as
long as the header info about the head orientation is correct.
On 10/6/17 5:29 PM, Ji
A quick question re: the hippocampus segmenation using FS 53.
Is the Fornix included as as part of the hippocampus segmentation/volume.
Looking at the aseg for "bert", it appears not to be included.
Jim
The materials in this message are private and may contain
Hi Eugenio,
I just wanted to follow up and see if you could tell anything about what
was going on from the response I got to running "mri_robust_register" as
you suggested.
-- Forwarded message --
From: Max Owens
Date: Wed, Sep 27, 2017 at 3:51 PM
Subject: Re: [Freesurfer] Problem
Not an easy way to do it. I guess you could create an FSFAST session for
it, eg, allconcat/bold/001/all.nii.gz, then run mkanalysis-sess with
-funcstem all
Alternatively, you have run the individual analyses, then
isxconcat-sess, then the FFX analysis in mri_glmfit with the --yffxvar
and --ff
I don't know what you are asking
On 10/6/17 9:24 AM, std...@virgilio.it wrote:
> 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) g
What is your command line and what is your terminal output?
On 10/6/17 9:57 AM, Patricia Stefancin wrote:
Hello,
I have been trying to flatten patches (the occipital cortex) in order
to create retinotopic maps. However, when I run mris_flatten, the
command window says it cannot read the patch
I have noticed it before. I don't think it is a problem, but it is on my
list of things to fix.
On 10/6/17 4:50 PM, Funk, Quentin wrote:
FS Experts,
There seems to be a hole in the lh.pial for fsaverage--see the
attached screenshot. It doesn't show up when checking the Euler
number, but i
what is the dimension of the rawavg.mgz? what is the dimension of the
output? What is the terminal output?
On 10/8/17 1:51 AM, Fereshte wrote:
Dear Experts,
I've run " mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o
aseg-in-rawavg.mgz --regheader aseg.mgz" as explained, however i can't
se
On 10/8/17 10:06 AM, Jonathan Bain wrote:
Dear FreeSurfer community,
For a template subject (Colin27), I have a volumetric atlas (nifti
file, where each brain region is numbered 1, 2, 3...). I am trying to
use FreeSurfer to get the volumetric atlas into volumetric subject
space (moving thro
You can't run it with missing variables
On 10/9/17 12:40 AM, 박경일 wrote:
Dear FS developer,
I am a FS beginner and trying to make QDEC images of cortical
thickness difference (color-coded inflated brain) between groups.
No problem when fsid, diagnosis, age, and sex were only included in
qdec.
no, it isn't
On Mon, 9 Oct 2017, Alexopoulos, Dimitrios wrote:
A quick question re: the hippocampus segmenation using FS 53.
Is the Fornix included as as part of the hippocampus segmentation/volume.
Looking at the aseg for “bert”, it appears not to be included.
Jim
_
Dear freesurfer experts,
I ran a spatial ICA in volume and would like to visualize the components in
surface in order to assess the overlap between the independent components
and my ROI (defined on surface). However after reading this paper,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/,
How did you get your ICA analysis into MNI305 (or MNI152) space? You're
ICA intergroup comparisons will only be as good as that space -- how you
get it onto the surface from there is not so important. You can run
recon-all on the MNI152, sample the ICA maps onto the surface, then use
the surf
I¹d note that you can run the group ICA on surface data in surface space
pretty easily using melodic, which would avoid the issue that Doug mentions.
Peace,
Matt.
From: on behalf of Douglas Greve
Reply-To: Freesurfer support list
Date: Monday, October 9, 2017 at 7:20 PM
To:
Subject: Re:
Hi Matt,
Thank you for your quick input ; I did not try yet to use melodic, it seems
indeed to be the most straightforward solution, I will try it, thank you
again!
Florence
Le lundi 9 octobre 2017, Matt Glasser > a écrit :
> I’d note that you can run the group ICA on surface data in surface sp
The latest version of melodic is compatible with CIFTI data (e.g. From the
HCP).
Peace,
Matt.
From: on behalf of Florence
Campana
Reply-To: Freesurfer support list
Date: Monday, October 9, 2017 at 9:25 PM
To: Freesurfer support list
Subject: [Freesurfer] Transformation between spaces
H
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