Hi Kaveh,
yes, you can create a 2d patch using tksurfer to cut it out, then
mris_flatten to flatten it.
cheers
Bruce
On Thu, 5 Apr 2012, Kaveh Kohan wrote:
Thank you for all replies. One more question to bother you. in :
http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsrecon.ppt
In
Any thought on this? I am wondering there might be something wrong with
FSL registration. I don't know what bbregister uses for registration but as
far as I know flirt is unable to register 4d-image (such as fmri ) to 3D;
it only accepts 3d as input and output. Is it possible to register
read_surf.m will do the trick, but be sure to use 1-based indices! And note
that the timeCourse.mgz you read is almost certainly a surface overlay with
137654 vertices and 236 time points, so if you read the surface
f.vol(1,j,1,:) would be the timecourse for the jth index returned by
read_surf
You should not use --regheader with --reg, but that should not have
caused a seg fault. I'm not sure what went wrong, but try removing
--regheader and see if it works.
doug
On 4/2/12 2:38 AM, Kaveh Kohan wrote:
Thank you very much for the replies.
I checked the wiki and tutorial and I
I have tried and it did not work (the same seg fault, see below). It seems
that it successfully performs the mapping but it fails in final step
probably saving the results. Is the data format that I used OK?
I am using Ubuntu 10.10, the version of mri_vol2surf is stable5. Please
let me knoe if
Hmmm, I don't know why it is doing that. Does it really print using
old after the seg fault was that accidentally pasted in? It should not
be printing that twice, maybe it's a clue.
doug
On 04/02/2012 10:26 AM, Kaveh Kohan wrote:
I have tried and it did not work (the same seg fault, see
It looks like your registration failed (though it completed without
error). Did you check it with tkregister? I don't think that would
explain the segfault, but it is worth tracking it down.
doug
On 4/2/12 2:54 PM, Kaveh Kohan wrote:
I have also attached the fmri-TO-orig.dat.log maybe that
No it did not work, mri_vol2surf still produces the same error (see below).
In the link below, I have shared the freesurfer results (in the FREESURFER
folder) plus fmri image (in the NITFI folder). I am wondering if there is
anything wrong with my installation of the mri_vol2surf (stable 5). The
Hi FreeSurfer Users,
I am new to the Freesurfer, I have a question regarding mapping of the
resting state fMRI time courses on the cortex area. I apologise in case my
question is naive. please bear with me:
Is it possible to have time-courses sampled from cortex? I mean how can I
get
You should register the fMRI to the anatomical with bbregister. Run it
with --help for more info, also see the wiki tutorial on fMRI integration.
You can then sample the time series to the surface with mri_vol2surf
doug
On 4/1/12 1:52 PM, Kaveh Kohan wrote:
Hi FreeSurfer Users,
I am new to
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