Hi,
We are not using the make_average_subject 6.0.0-patch. Do you think it would be
a possible solution? Where can I find that patch?
On the other hand, we've noticed that recon-all, which is a final
make_average_subject step, fails. I send you the recon-all.log. However, maybe
it is not rel
Shame to admit - we didn't think about it. After the visual inspection -
something obviously went wrong. We'll try to correct manually.
Thanks for the tip!
Best regards,
Patrycja
2017-11-28 16:00 GMT+01:00 Bruce Fischl :
> Hi Patrycja
>
> did you check to see if the talairach transform was reaso
Dear Bruce,
Thank you very much for reply.
I have to link fsavarage also. Because recently I have formated my system,
the link between freesurfer and fsaverage is broken.
I hope following link will be the correct one. If not please correct me.
ln -s /usr/local/freesurfer/subjects/fsaverage
/mnt/b
Dear FreeSurfer experts,
We want to implement a deface method to ensure anonymity of participants before
making the data available to researchers. Because the raw data is stored on the
imaging platform XNAT, we preferred the mask_face method implemented on the
XNAT server rather than FreeSurfer
On Wed, Nov 29, 2017 at 5:27 AM, R Edgar wrote:
> On 28 November 2017 at 09:12, Dr. M. Shahid
> wrote:
>
> > Has all of the GPU code also been updated in the new FS6.0 version or the
> > code is still from the old 5.x but can be compiled with new cuda
> toolkits?
>
> I made a small tweak for GCA
Hi Elizabeth
I guess it could help by removing a feature that is variable across
subjects so things like the talairach transform are more stable
cheers
Bruce
On Thu, 30
Nov 2017, Buimer, E.E.L. wrote:
Dear FreeSurfer experts,
We want to implement a deface method to ensure anonymity o
The make_average_subject patch can be downloaded here:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The readme file contains some instructions. This patch will definitely fix your
recon-all error, but I don’t think it’s related to the labeling issue. Though,
it’s worth a t
Hi Ri,
It looks like there might be an issue with the license saved at
/Applications/freesurfer6/.license. Try overwriting this file with your
license.txt
best,
Andrew
On Nov 29, 2017, at 6:23 PM, Ritobrato Datta
mailto:ridatpennc...@gmail.com>> wrote:
Hi All,
I am using Mac OS X Sierra an
Hi,
I have installed the patch and it doesn't fix the label files problem. We have
tried make_average_subject with the other 56 subjects and Medial_wall.label
contains about 300 vertexs. It is very different from the other 60 subjects.
Nevertheless, we have also repeated the test with Freesurf
Hi Freesurfer experts,
I want to concatenate multiple preprocessed fMRI runs in the form of .mgh
freesurfer surface space files (2-D matrices vertexes * time_frames). Is
there a tool that can do this easily, or do you have other recommendations
how to do this?
Thank you!
_
Hi - I'm still wondering what would be the best method to perform the mentioned
steps. Additionally, would mri_compute_overlap provide output related to
spatial overlap and difference, that we're looking for? Is it possible to do
this with thickness, or maybe not - because it doesn't consider ar
Hi all,
I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is
exiting with the output below. Most notably, I think, is the section of the
output that says "R: Subscript out of range.” repeatedly and then the section
afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8 9
hmmm, it might be easiest to do at least some of this in matlab
cheers
Bruce
On Thu, 30
Nov 2017, Rizvi, Batool wrote:
Hi – I’m still wondering what would be the best method to perform the mentioned
steps. Additionally, would
mri_compute_overlap provide output related to spatial overlap and
Hi Sol, 6.0 is built with qt 4.7, and the freesurfer development branch
currently uses qt 4.8.5
best,
Andrew
> On Nov 27, 2017, at 5:32 PM, Sol Jerome wrote:
>
> Andrew,
>
> Thanks, this helped me get past the error I was receiving. I am now
> trying to determine exactly which QT libraries ar
Okay, can you upload the compressed average subject to our ftp server
(https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) and I will take a
look?
thanks,
Andrew
On Nov 30, 2017, at 12:30 PM, M del Mar Velasco
mailto:melly_2...@hotmail.com>> wrote:
Hi,
I have installed the patch and i
Hi John, I’ve tried to replicate this issue with no success. I’m still a bit
confused as to when this errors occurs - are some subjects able to run
successfully? Is it subject-dependent or is there no clear pattern? It’s
possible that the matlab libraries have been corrupted, so one option would
Dear Freesurfer experts,
I want to register FA map in subject space to MNI. How can I do it using
freesurfer tools?
Any advice is highly appreciated!
J___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/li
Hi John
if your FA map is registered to the structurals (e.g. using bbregister)
then you would just compose that transform with the talairach.xfm in the
subject's mri/transforms dir.
cheers
Bruce
On Thu, 30 Nov 2017, John Anderson wrote:
> Dear Freesurfer experts,
> I want to register FA map i
Dear Dr Bruce,
Thank you so much for the quick response. Yes I used bbregister, but I don't
know how to transform correctly.
I appreciate your guidance!
peace
J
> Original Message
> Subject: Re: [Freesurfer] FA to MNI
> Local Time: November 30, 2017 3:54 PM
> UTC Time: November
On 30 November 2017 at 09:42, Dr. M. Shahid wrote:
>> > Has all of the GPU code also been updated in the new FS6.0 version or
>> > the
>> > code is still from the old 5.x but can be compiled with new cuda
>> > toolkits?
>>
>> I made a small tweak for GCAMorph (primarily ca_register) which might
>
20 matches
Mail list logo
