Use mri_surf2vol on thicknessess that have been mapped to fsaverage.
This will put everything in fsaverage space. I don't know if that is
what you mean by the standard template
doug
On 1/16/14 9:19 PM, Muhammad Naveed Iqbal Qureshi wrote:
Dear Experts,
I need to know how can I convert the
Dear Experts,
I need to know how can I convert the .thickness files into volume file that can
be opened in SPM and show the thickness of each voxel in the standard templete
of the brain.
Thank you
Best Regards,
Muhammad
Naveed Iqbal Qureshi
_
Bump, I'm having this problem as well and would really like to use the cuda
version of mri_ca_register.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Tran, Kevin
(NIH/NIMH) [C]
Sent: Saturday, 7 December 2013
Hi!
I'm wondering if the latest version of Freeview is available in standalone
version. I'm currently using FreeSurfer v5.1's tktools for correcting the
recon-all outputs, but would like to switch to Freeview. However the version
that I have doesn't seem to have the Recon tools, and if I instal
Hi Mark
does the input to mri_ca_normalize look ok (the nu.mgz)? Is the
talairach.xfm ok?
Bruce
On Thu, 16 Jan 2014, Mark Plantz wrote:
Hello freesurfers,
I am running into a problem during the "CA Normalize" sequence of
autorecon-2. It looks like freesurfer is having a hard time creat
Hello freesurfers,
I am running into a problem during the "CA Normalize" sequence of
autorecon-2. It looks like freesurfer is having a hard time creating
control points based off the atlas I am using. The output is as follows:
"finding control points in ...found 0 control
points"
Thi
Hi Krista,
I believe the v?.thresh labels are thresholded at p=0.8. This threshold
is based on comparisons of actual and predicted V1 boundary with an
independent dataset.
Relevant pub:
https://surfer.nmr.mgh.harvard.edu/ftp/articles/hinds2008accurate.pdf
-Louis
On Thu, 16 Jan 2014, krista
Hi all,
Can anyone provide information regarding how v1.thresh.label and
v2.thresh.label that are automatically implemented in FreeSurfer are
thresholded?
Thanks!
Krista
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you have to use your own regressor. This is not usually done with
thickness because thickness does not scale with head size
On 01/16/2014 04:32 PM, Danielle Miller wrote:
> Hi Doug,
>
> Thank-you for the responses!
>
> An additional question: does mri_glmfit or preproc take into account
> head
Dear freesurfer community,
My question is directed to those who have experience with editing
brain.finalsurfs.mgz.
According to the tutorials, after making edits on brainmask.finalsurfs.mgz
(which is normally done when the pial surface is not accurate), we can run,
recon-all -autorecon-pial -
I am using version 5- Stable 5 Nightly.
On Jan 16, 2014, at 1:00 PM, Douglas N Greve wrote:
> What version of FreeSurfer are you using?
>
> On 01/16/2014 12:39 PM, Tessa Vuper wrote:
>> Hi all,
>>
>> I receive the following error when I run the selxavg3 -sess command:
>>
>> ERROR: cannot
>> find
what file do you source to set up the env?
On 01/16/2014 01:12 PM, Tessa Vuper wrote:
> I am using version 5- Stable 5 Nightly.
>
> On Jan 16, 2014, at 1:00 PM, Douglas N Greve wrote:
>
>> What version of FreeSurfer are you using?
>>
>> On 01/16/2014 12:39 PM, Tessa Vuper wrote:
>>> Hi all,
>>>
What version of FreeSurfer are you using?
On 01/16/2014 12:39 PM, Tessa Vuper wrote:
> Hi all,
>
> I receive the following error when I run the selxavg3 -sess command:
>
> ERROR: cannot
> find /usr/local/freesurfer/stable5/bin/fsl.5.0.2.xyztrans.sch
>
> Any thoughts on how to fix this?
>
> Thank
On 01/16/2014 11:57 AM, Danielle Miller wrote:
> Hi Freesurfer Experts,
>
> I have some questions regarding mri_glmfit - some basic and some not
> so basic - that I hope you can help me with.
>
> 1.) I want to do a thickness analysis looking at the effect of a
> continuous variable on thickness
Hi all,
I receive the following error when I run the selxavg3 -sess command:
ERROR: cannot find /usr/local/freesurfer/stable5/bin/fsl.
5.0.2.xyztrans.sch
Any thoughts on how to fix this?
Thank you so much for your help,
tessa
Tessa Vuper
Clinical Research Coordinator, Manoach Lab
Psychiatri
Hi Freesurfer Experts,
I have some questions regarding mri_glmfit - some basic and some not so
basic - that I hope you can help me with.
1.) I want to do a thickness analysis looking at the effect of a continuous
variable on thickness while regressing out effects of both continuous and
categorica
As far as I know it does the same thing, but I would run both on one
data set to make sure.
On 01/16/2014 02:51 AM, Alexander Lebedev wrote:
> *_Dear Freesurfers,_*
>
> I have quite a large dataset processed with FS 5.1. However, half of
> the output was qcached in FS 5.3. I just wanted to cl
Hi Arash
have you registered them? You can reslice the wm.mgz to have the same
voxel geometry as the flair using
mri_convert -rl flair.mgz wm.mgz wm.resliced.mgz
but only if they are in register. Otherwise you need to apply the
registration transform as well, which you can also do in mri_con
Dear Martin and Bruce,
thank you very much for your detailed answers! This helps a lot!
Best,
Janosch
Am 15.01.2014 um 21:53 schrieb Martin Reuter :
> Hi Janosch,
>
> there is no fixed naming convention for subjectids from our side, only
> recommendations. If you like you can call the first
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