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POST-DOCTORAL RESEARCH FELLOW CENTER FOR NEUROBIOLOGY OF STRESS AND RESILIENCE
UNIVERSITY OF CALIFORNIA LOS ANGELES
Background:
The Center for Neurobiology of Stress and Resilience in the Division of
Digestive Diseases at the University of Californi
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Right!
Thank you so much!
Best,
Laura.
De: Douglas N. Greve
Enviado: sábado, 19 de fevereiro de 2022 18:37
Para: Laura Willers de Souza
Cc: freesurfer@nmr.mgh.harvard.edu
Assunto: Re: [Freesurfer] Question glm analy
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Hello FreeSurfer Developers,
I would like to know if it is correct to perform volume and surface area
analysis using freesurfer's GLM!?
In several mailing list questions I have already seen instructions for
performing these types of analysis. But I
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I am trying to extract mean intensity in my PET data for every ROI. Doug said
to run mri_segstats passing the PET with --i and using --seg to spec the
segmentation. I would like to confirm that I am using this properly.
mri_segstats --i $PET_DIR/$ID/
Hi Edan
Control points might be helpful in both cases, but you are right it is more
often the case when the wm is too dark. Another thing you can try is using
expert options for mri_segment to constrain the intensity ranges of wm/gm. Or
you could try using the samseg stream (someone else will h
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Hi all,
Quick question on a puzzling error with bbregister version 7.1.1. When I run:
bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg
7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1
I get the error:
ERROR: must spec a subject
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Hi Dylan,
I call bbregister with --s in the same place you have it. Is it possible there
is something wrong with $SUBJECTS_DIR when you are calling bbregister?
Matt.
On 2/21/22, 2:43 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Tisdall
Is there a blank subject line in the lta file? If so, it is probably
trying to get the subject from there. You can try putting the --s after
the --lta
On 2/21/2022 3:43 PM, Tisdall, Dylan wrote:
> External Email - Use Caution
>
> Hi all,
>
> Quick question on a puzzling error with bbreg
You need to first map your pet to the anatomical space using mri_vol2vol
and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead of
using the output from the gtm? Note that you cannot use the white matter
values that come from mgx.
If this is not something you have to do a lot of, you can put a
repositioning point. See the release notes.
On 2/21/2022 1:10 PM, Fischl, Bruce wrote:
Hi Edan
Control points might be helpful in both cases, but you are right it is
more often the case when the wm is too dark. Another thing you
Did the perms to that file change during the run?
On 2/17/2022 10:36 AM, Jacoby, John wrote:
Hi all,
I have a recon that looks like it ran (almost) to completion, but then
threw a permissions error in the stdout and directed me to the log. I
can't determine what the issue might have been. I'v
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Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS
VOI. How can I register the svs file to the Freesurfer-processed brain and
extract these values?
Thanks,
Alex
Alex Brown
CNS Core Facility
Department of Psycholo
You can use something like
mris_apply_reg --lta lh.white reg.lta lh.white.reg
The direction of reg.lta does not matter -- it will figure out the right
direction based on the geometry info
On 2/16/2022 12:20 PM, Gomez, Daniel wrote:
> Dear FS users,
>
> I’m trying to get surface indices from surf
you are right! Just fixed it.
thanks
On 2/18/2022 2:15 PM, Gomez, Daniel wrote:
> There is a minor bug/typo in mri_surf2vol that was leading to registration
> issues if the "--fillribbon" flag is used, like in my case.
>
> https://github.com/freesurfer/freesurfer/blob/dev/mri_surf2vol/mri_surf2v
Yes, it is. It is confusing when you talk about area and volume since
these are not point measures like thickness (ie, what is the volume or
area of a vertex?). The area of a vertex is computed as the mean of the
adjacent triangles of the vertex. The volume is the mean of the
neighboring trunca
On 2/19/2022 6:10 PM, fernanda rohrsetzer wrote:
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Hi guys,
I'm a beginner in Freesurfer and I want to perform an analysis of the
difference between 3 groups in cortical thickness,volume and area
having age, mean thickness and etiv as covariate.
my design
I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
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Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF)
for an SVS VOI. How can I register the svs file to the
Freesurfer-processed brain and e
I just updated the code to accept PVRs. I'm not sure what I have to do
to test it; I guess I need to run the null test like I did for the
non-PVR version. This will take a while. In the mean time, can you
download the development version and just try it on your data to see if
it crashes or give
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Hi Doug,
It is something we do *a lot* of, thus we hoped we'd be able to find a way
to make the recon-wm implement our edits without additional manual edits,
like we used to do with v6.
Do you have any idea what could have caused this change in stubborn
I think your best bet is either samseg or try expert options to tune
mri_segment and/or mris_make_surfaces
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Edan Daniel
Sent: Monday, February 21, 2022 6:30 PM
To: Freesurfer support list ; Greve, Douglas
N.,Ph.D.
Subject:
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Thanks!
On Mon, Feb 21, 2022 at 6:42 PM Fischl, Bruce
wrote:
> I think your best bet is either samseg or try expert options to tune
> mri_segment and/or mris_make_surfaces
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.ed
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Do you have a Freesurfer page I can read up on those hybrid ways just to see
whether that could be an option?
Also, although its a binary, you would recommend against have sex be a
continuous measurement like age, due to the design of how the contras
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Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and
glmdir/aux/bbpet2anat.lta.
RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I
believe it is recommended to extract gray matter localized PET data.
The GTM gives you values for each ROI regardless of whether it is GM,
WM, or CSF. They will probably give you similar answers, but the GTM
will be more robust.
On 2/21/2022 8:48 PM, Jennifer Bramen wrote:
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Thanks! Yes, I already mapped my PET to anatomical
On 2/21/2022 6:50 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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Do you have a Freesurfer page I can read up on those hybrid ways just
to see whether that could be an option?
No, this is a general statistics question, not something FS-specific.
If you already have the VOI that is aligned to the mprage via the
geometry in the volume header, then you can use
mri_compute_volume_fractions to compute the composition; specify
--regheader subject. To be clear, this assumes that the VOI is a single
voxel in a "volume" (eg, nii or mgz) and whe
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Hi Dr. Greve,
Thank you for your suggestion. Unfortunately, the same problem occurred
when I ran the command with --no-pcc. Folders and files with the same names
were created. and the following error message (identical to the previous
one) appeared.
e
No, not really. If you get the data to me, I'll take a look if I can.
Make sure to send specific information about vertices that you are
having problems with so I don't have to go looking for it.
On 2/21/2022 6:29 PM, Edan Daniel wrote:
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Hi Doug,
It is som
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