Hi Doug,
Would your mri_segstats command work if instead of aseg.mgz, Sabin
passed in the cerbellum parcellation in the same anatomical space as
aseg?
--Thomas
On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
wrote:
> After you run preproc-sess, there will be a file called register.dof6.dat.
> M
yes
On 6/24/16 9:19 AM, Thomas Yeo wrote:
> Hi Doug,
>
> Would your mri_segstats command work if instead of aseg.mgz, Sabin
> passed in the cerbellum parcellation in the same anatomical space as
> aseg?
>
> --Thomas
>
> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
> wrote:
>> After you run pr
On 23 June 2016 at 22:44, Derek Pisner wrote:
> Fixed the gcc problems as well (this required a tweak to host_config.h in
> /usr/local/cuda/include). Now, I've hit another roadblock:
>
> Makefile:4542: recipe for target 'libutils_cuda_a-mrisurf.o' failed
> make[3]: *** [libutils_cuda_a-mrisurf.o
Hi Doug, thanks.
Hi Sabin, you can use the following steps to transform the Buckner
cerebellum atlas to your subject's native anatomical space and then
follow Doug's instructions (taken and adapted from another user
Bronwyn's email):
1. Run MNI152 1mm template through recon-all
recon-all -i FSL_M
Hi,
Is it possible to overlay .mgh files with statistics (e.g. p-maps) directly
in FreeView, for purposes of visualizing the results, the same way you can
in tksurfer? When I try load an overlay in FreeView, it seems to be
expecting a volume file.
Thank you!
sincerely yours,
Lars M. Rimol,
Hi,
This question might have already been answered before but is there a way to
take a coordinate in MNI space and create, say, a 5mm sphere in the volume? My
goal is to take the sphere in the volume and convert it to a label using
something like mri_vol2surf.
Thanks for your help,
Afsana
_
you can load the overlay on the surface either by highlighting the
surface and doing it from the interface or on the command line via:
freeview -f surface:overlay=file_name
cheers
Bruce
On Fri,
24 Jun 2016, Lars M. Rimol wrote:
Hi,
Is it possible to overlay .mgh files with statistics (e
I tried updating my Nvidia drivers. but now whenever I try to open freeview it
says " aborted ( core dumped).
please help.
Thanks
Regards
Tilak
From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 5:27:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: fre
Is that all? Are there any other error messages?
On 06/24/2016 10:25 AM, Ramtilak Gattu wrote:
I tried updating my Nvidia drivers. but now whenever I try to open
freeview it says " aborted ( core dumped).
please help.
Thanks
Regards
Tilak
--
That is all . No error messages at all.
From: Ramtilak Gattu
Sent: Friday, June 24, 2016 10:25:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem
I tried updating my Nvidia drivers. but now whenever I try to open freeview it
says " ab
.mgz file! can you tell me why?
crash-20160624-204118-guest-_recon_all0.pklz
File: crash-20160624-204118-guest-_recon_all0.pklz
Node: _recon_all0
Working directory:
/tmp/tmpzZyfB0/reconall_workflow/recon_all/mapflow/_recon_all0
Node inputs:
T1_files =
['/home/guest/HAO/Clinica/cl
.mgz file! can you tell me why?
crash-20160624-204118-guest-_recon_all0.pklz
File: crash-20160624-204118-guest-_recon_all0.pklz
Node: _recon_all0
Working directory:
/tmp/tmpzZyfB0/reconall_workflow/recon_all/mapflow/_recon_all0
Node inputs:
T1_files =
['/home/guest/HAO/Clinica/cl
Hi,
Over at our nibabel Python package, we've got stuck trying to work out
what license we should give to a file we got from Freesurfer version
3.0.3:
https://github.com/nipy/nibabel/pull/461
The file is `subjects/bert/surf/lh.inflated.nofix` from Freesurfer 3.0.3.
It looks like this is a modif
Hi Matthew
we typically ask people to get licenses from us so we can keep track of
them.
cheers
Bruce
On Fri, 24 Jun 2016, Matthew Brett wrote:
> Hi,
>
> Over at our nibabel Python package, we've got stuck trying to work out
> what license we should give to a file we got from Freesurfer version
Hi,
On Fri, Jun 24, 2016 at 2:44 PM, Bruce Fischl
wrote:
> Hi Matthew
>
> we typically ask people to get licenses from us so we can keep track of
> them.
So, what we want to do, is to put this single data file into a
bitbucket repository, that we then pull down when we want to run the
tests.
yes, it's fine
Bruce
On Fri, 24 Jun 2016, Matthew Brett wrote:
> Hi,
>
> On Fri, Jun 24, 2016 at 2:44 PM, Bruce Fischl
> wrote:
>> Hi Matthew
>>
>> we typically ask people to get licenses from us so we can keep track of
>> them.
>
> So, what we want to do, is to put this single data file into a
Great - thanks,
Matthew
On Fri, Jun 24, 2016 at 3:26 PM, Bruce Fischl
wrote:
> yes, it's fine
>
> Bruce
> On Fri, 24 Jun 2016, Matthew Brett wrote:
>
>> Hi,
>>
>> On Fri, Jun 24, 2016 at 2:44 PM, Bruce Fischl
>> wrote:
>>> Hi Matthew
>>>
>>> we typically ask people to get licenses from us so we
Hello again,
Sorry for posting twice, but does someone know what might be the problem?
Thank you in advance.
I’m trying to run recon-all -lgi - s Subjectname on my data but i am
getting this error!
***
Error in dsearchn (line 79)
[d(
Hi freeserver folks,
First time poster here. First off, thanks so much to the folks who
work on and make this software available to the public. It seems like
pretty incredible tech, from what little I understand of it. :)
My problem is that the freesurfer process appears to be stuck on the
recon-
Hi Dan
that defect is too big, there must be something wrong. Check to see if the
surface is connected to dura or across the hemis or something. You can look
at the lh.inflated.nofix and/or the lh.orig.nofix to see where the defects
are. Then you'll need to correct something once you've figure
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