Hi Freesurfers.
As I'm currently performing the Funcional Conectivity workflow with FSFAST,
the 4th step requires me to choose the areas to use as seeds. I would like
to use the hippocampal subfields as seeds, but I can't select them because
the aparc+aseg.mgz doesn't contains those labels. The on
> From: freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julio Alberto
> González Torre [al099...@uji.es]
> Sent: Friday, April 15, 2016 11:42 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfe
r is or else
> it won't fully run preprocessing.
> Hope this helps!
> Best,
> Talia
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julio Alberto
> González Torre [al
Hi Freesurfer users.
I am currently performing the steps of Functional Connectivity Walkthrough.
And after resolving the problems in the first steps, specially in the
preprocessing command (missing AFNI files), I'm now stuck in the 5th step:
Creating the FC seeds for each subject.
In the 4th step
Hi Freesurfer users.
I performed the recomended reconstruction of 82 subjects with Freesurfer.
The images used for this reconstruction were previously reoriented to AC-PC
position, because they were previously used for SPM purposes.
Now I'm trying to perform the FSFAST workflow, and I had to unp
I have the same problem.
I observed that this error appears when you select a factor with 3 or more
levels. Factors of 2 levels works fine.
2016-01-18 9:32 GMT+01:00 BAUTISTA-PERPINYA Maximilià <
maximila.bautista-perpi...@etu.unistra.fr>:
> Thank you for the reply Douglas,
>
> Factor 1 (diagnos
Hi Freesurfer users,
I am recently testing the QA Tools in order to identify errors, especially
aseg outliers.
I don''t know if this is the right place to make this question, but I
followed the instructions for download, install and usage, explained on:
https://surfer.nmr.mgh.harvard.edu/fswiki/Q
Hi Freesurfer experts.
Is there any tool to perfom volume calculations? Such binarize a volume,
intersect two volumes, sum volumes etc?
Thanks.
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Where could I upload it?
2016-01-07 14:44 GMT+01:00 Bruce Fischl :
> Hi Julio
>
> it's hard to tell why this is happening, but if you upload the entire
> subject directory and give us the coordinates of the inaccuracy we will
> take a look
>
> cheers
> Bruce
> O
One question about "-openmp". If I run multiple "recon-all" in different
terminals without using this flag...
Is there any problem with the 'gcareg' stage? For example, is there any
interference between subjects reconstruction?
Thanks.
2015-10-16 15:07 GMT+02:00 Bruce Fischl :
> Hi Linda
>
> di
Hi everybody. I have the same problem.
When I run the "recon-all -all", the first steps warns me about a
"deprecated" command when running the "nu_correct" step:
nu_correct -clobber ./tmp.mri_nu_correct.mni.13923/nu0.mnc
./tmp.mri_nu_correct.mni.13923/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.1392
I had the same problem too, using VBox and running the .vdi version of
FreeSurfer with no modifications.
When the "recon-all" reach to the talairach phase, the program stops with
this error:
#
> #@# Talairach Thu Oct 8 20:16:43 EDT 2015
> /media/sf_NEU
I have some questions about how to manually correct the white matter regions
.
It's the same manually edit the volume "brainmask.mgz" and use control
points? Would I get the same result? My intention is not to use control
points, but directly replace the voxels that have not been classified as whi
t; Hi Julio
>
> if they are white matter lesions you should be able to set those voxels to
> 110 in the brain.mgz, brain.finalsurfs.mgz and wm.mgz and rerun
> autorecon2-wm and autorecon3.
>
> cheers
> Bruce
>
> On Mon, 22 Oct 2012, Julio Alberto González Torre wrote:
>
&g
Hi.
My question is about dealing with multiple sclerosis lesions in white
matter.
I have previously worked with this sample in SPM8, and I have a binary mask
for each subject with the white matter lesions marked.
Instead of painting manually each lesion with the freesurfer interface,
could I pro
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