Hello All,
I have a simple question. I have functional data (3 mm cubic voxels) from 20
subjects that I am using mri_vol2surf to resample on the fsaverage surface. I
want to run qdec or mri_glmfit on these data. In order to do grp stats with
functional data, what surface do I need to specify in
Hello FreeSurfers,
recon-all -make is working now, but it's taking as long as it did the first
time I ran it. I originally ran "recon-all -s cb -i CB_anat+org.BRIK -i
CB_anat2+orig.BRIK -all" (for example) back in May and haven't messed with
the results except for generating some label files with
You can edit just the base if you will only be working with the
longitudinal stream. Currently, running the cross-sectional stream is
necessary only to get the 'norm.mgz' file, for input to the base
subject.
n.
On Sun, 2010-02-14 at 14:06 -0800, Mehul Sampat wrote:
> Hi Nick (and Martin)
>
> C
To get the Destrieux atlas parcellations in the wmparc, first have a
look at the -wmparc section of the recon-all table:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
those last two commands would be modified like this:
mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown
--ribbo
the default surf is the 'white' surf, but this only means the
coordinates in the output surface file will have the white surface
coordinates. the vertices still remain one-to-one matched between the
white-pial-and-inflated-(and-sphere), so the -surf arg is irrelevant for
your group analysis.
n.
recon-all -make all uses the unix 'make' utility, and the file
$FREESURFER_HOME/bin/recon-all.makefile, to examine the 'build'
dependencies between files. that is, looking at this table:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
it can be seen that files are dependent on files
ok thats what i thought but just wanted to double check...
Thx
- Original Message -
From: "Nick Schmansky"
To: "Ritobrato Datta"
Cc: "freesurfer"
Sent: Tuesday, February 16, 2010 12:58:07 PM GMT -05:00 US/Canada Eastern
Subject: Re: [Freesurfer] question abt mri_vol2surf
the defau
Dear experts,
i try to run the command mris_anatomical_stats to get GrayVol, ThickAvg,
etc from the left cortex as following:
mris_anatomical_stats -l lh.cortex.label -f nmr033_2/stats/lh.cortex.stats
nmr033_2 lh
so the output is like following and did not generate any stats
file(lh.cortex.stats
hmmm, sounds like a bug. If you tar and gzip the subject and drop it on
our site we'll take a look.
On Tue, 16 Feb 2010 yzha...@artsci.wustl.edu
wrote:
> Dear experts,
>
> i try to run the command mris_anatomical_stats to get GrayVol, ThickAvg,
> etc from the left cortex as following:
>
> mris_a
I managed to obtain outputs from recon-all lGI now I would like to obtain
a mean gyrification index (not sure if the mean is meaningful?!) for all
vertices within 3 ROIs as defined by Destrieux atlas -
How should I do this? Can I treat lGI surfaces just as thockness maps in
which case can I us
I have a colleague who is interested in the DTI toolkit to coregister
DTI results with FreeSurfer's segmentation. Is that available in any form yet?
Thanks,
Dana
Dana W. Moore, Ph.D.
Neuropsychology Fellow
Cornell Neuropsychology Service
Weill Medical College of Cornell University
New York Pre
Hi Dana,
sure, that stuff is available. You should be able to use bbregister to
register the dti to the anatomicals
cheers
Bruce
On Tue, 16 Feb 2010, Dana W. Moore
wrote:
> I have a colleague who is interested in the DTI toolkit to coregister
> DTI results with FreeSurfer's segmentation. Is th
Hello,
Thanks Bruce,
Super, it works well!
I tried to make my rois in a script (to do it in many subjects), by using the
commands:
select_talairach_point x1 y1 z1
select_orig_vertex_coordinates
mark_vertex
path_new_path_from_marked_vertices
but I did not manage to get the vertex number (index
Hi Leila,
it will set the global variable named "select" after the call to
select_talairach_point x1 y1 z1. You can then use it (with $select)
afterwards.
cheers,
Bruce
On Wed, 17 Feb 2010, Ben Hamida Cammoun
Leila Faiza wrote:
Hello,
Thanks Bruce,
Super, it works well!
I tried to make
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