Dear freesurfer experts,
I am trying to create a V1 mask in volume, based on the V1 label, in
fsaverage space.
I use the following command: mri_label2vol --label
/Applications/freesurfer/subjects/fsaverage/label/rh.V1.label --temp
/Applications/freesurfer/subjects/fsaverage/mri/orig.mgz --hemi
Hi,
The one I tested with in the last couple of messages is just the standard
bert subject after having done:
cd ${SUBJECTS_DIR}/bert
cd surf
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right
And then running:
cd ../label
mris_apply_reg --src-label
Is this fsaverage or one of your own subjects?
On 10/17/2017 02:18 PM, Neuro Lists wrote:
> Hi Doug,
> Thanks a lot for looking into it. Unfortunately it's still not working
> though.
>
> See here:
> https://imgur.com/a/lxXUH
>
> Thanks again!
>
> On Mon, Oct 16, 2017 at 12:31 PM, Douglas
Hello everyone. I am having trouble understanding the statistical effects of a
covariate versus a nuisance factor in freesurfer and I would appreciate some
advice.
I want to run a correlation between cortical volume and the measurement of an
enzyme while covarying for ETICV.
In qdec, I select
Hi experts,
I am using Yeo atlas (7 networks) in my analysis. Where can I find name of
all the regions involved in each of these 7 networks in Yeo atlas?
Thanks.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
I think that is the issue. Freesurfer thinks there is brainstem in the
skull-stripped image. That’s why it labels whatever gray matter it sees as
brain stem.
We’ll add the brain stem to the data and run it like that.
Thanks!
Tugce
On 10/17/17, 1:28 PM,
Hi Doug,
Thanks a lot for looking into it. Unfortunately it's still not working
though.
See here:
https://imgur.com/a/lxXUH
Thanks again!
On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve
wrote:
> Sorry, try this
>
> mris_apply_reg --src-label lh.BA45.label --trg
Copy it before you run recon-all and copy it to brainmask.mgz (not to
auto). If there is no brainstem, then I think it will fail
On 10/17/2017 12:55 PM, Duran, Tugce wrote:
> Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to
> brainmask.auto.mgz and a link from
Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to
brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? Because
I also did that and saw some cerebral cortex labeled as brain stem. There is no
brain-stem in my skull-stripped data.
Tugce
dur...@iupui.edu
On
No, but I think if you copy it to brainmask.mgz that it will then use that
On 10/17/2017 12:28 PM, Duran, Tugce wrote:
> Is there a flag like –noskullstrip where we can skip brain-stem
> parcellation/labeling?
>
> Tugce
>
> On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
Is there a flag like –noskullstrip where we can skip brain-stem
parcellation/labeling?
Tugce
On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" wrote:
if they look
Hi Martin,
I've uploaded a .tgz file with a T1w volume, BOLD volume, and a valid LTA file.
https://gate.nmr.mgh.harvard.edu/filedrop2/?g=7f71pykmv7p
Chris
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
if they look ok, then I think they are ok
On 10/17/2017 12:05 PM, Duran, Tugce wrote:
> That is exaclty right! But how did freesurfer respond to that, performing the
> skull stripping to skull-stripped data?
> Should I trust the results since they looked okay?
>
> Tugce
>
>
> dur...@iupui.edu
That is exaclty right! But how did freesurfer respond to that, performing the
skull stripping to skull-stripped data?
Should I trust the results since they looked okay?
Tugce
dur...@iupui.edu
On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve"
if you put -all AFTER the -noskullstrip, then it would have performed
the skull stripping
On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Team,
>
> I have recently submitted my skull-stripped data into FreeSurfer v6.
> Since this is a separate process than the default recon-all
-- Forwarded message --
From: miracle ozzoude
Date: Sat, Oct 14, 2017 at 3:32 PM
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
To: Freesurfer support list
Hello Bruce,
Thank you for the response. I
Hello FreeSurfer experts,
I am trying to do a cross-sectional baseline analysis from the outputs of
the longitudinal processing stream, following the advice on a previous
question's thread:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-
March/044681.html
>From my reading of the
Dear FreeSurfer Team,
I have recently submitted my skull-stripped data into FreeSurfer v6. Since this
is a separate process than the default recon-all –all, I followed the
recommended steps that are posted on the FSwiki website, here is the link for
it:
Hi Chris,
thanks, can you send the images and the exact commands. We have had success in
the past, could be that you have a special case (e.g. maybe we never tested
registration across different resolutions or whatever?).
Thanks, Martin
https://gate.nmr.mgh.harvard.edu/filedrop2/
Dear Experts,
I have purchased a new pc. I want to use for MRI and EEG analysis by using
MATLAB, FSL, SPM, Fresurfer etc,. Which OS is suitable to handle these
software?
I have NVIDIA graphics card 610 in my system.
I am using Ubuntu in another systm and little bit of experience in cent os.
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