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:
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 o
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 behalf
of Douglas N Greve" <freesurfer-
Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
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 Te
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 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
On 11/16/2017 11:32 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Experts,
>
> I’m recently getting an error in make_average_subject and can’t find
> the reason.
>
> Please see the following for the error log from recon-all.log:
>
>
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:
Loading aseg from
Dear FreeSurfer Experts,
I’m getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:
Loading aseg from
Dear FS Experts,
I recently got the attached error in mris_preproc and mri_surf2surf in FS 6.0.
These commands work in FS 5.3. But somehow FS 60 doesn’t run the files
correctly.
Any ideas?
Thanks,
Tugce Duran
lh.thickness.mris_preproc.log
Description: lh.thickness.mris_preproc.log
Dear Doug Greve,
Where can I find the rh/lh.pial_avg file in fsaverage/surf/ created in
freesurfer 6.0?
Is this file named differently in FS 6.0 or do I need to process this step
(where it makes rh or lh.pial_avg) separetely?
Thanks,
Tugce Duran
___
hat this is only a visualization issue if all your
underlying analysis is done on the surface.
On 01/08/2018 01:14 PM, Duran, Tugce wrote:
>
> Hi FS experts,
>
> I’m running SurfStat on my freesurfer skullstriped data (recon-all
> with –nosku
5;
0020 mask=~(abs(surf.coord(1,:)) wrote:
You can map it onto fsaverage, which is made only from 40 subjects, so
there is a little more folding
On 01/09/2018 06:27 PM, Duran, Tugce wrote:
> Total N is 159. I have min # of 52 subjects for certain analyses. I used
avgsubj
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