Dear Freesufer experts,
I am wondering if it is possible to tell mri_vol2surf to ignore certain
voxels in the src volume, for instance, by setting their intensity to -999.
I'm trying to project only gray matter voxels from a PET scan onto the
fsaverage surface, but when I use an only-GM PET image
Sorry, I guess it got out of date. We don't it much
Bruce
On May 29, 2012, at 9:12 PM, Shay Ohayon wrote:
> Hi again,
>
> OK. I managed to reverse engineer things back from mri_tessalate.c
> Here is the code snippet that should be added to read_surf to parse these new
> files:
> NEW_QUAD_FIL
Hi again,
OK. I managed to reverse engineer things back from mri_tessalate.c
Here is the code snippet that should be added to read_surf to parse these
new files:
NEW_QUAD_FILE_MAGIC_NUMBER =16777213;
elseif (magic == NEW_QUAD_FILE_MAGIC_NUMBER)
vnum = fread3(fid);
fnum = fread3(fid);
vertex
Hi,
I am trying to read a surface generated by mri_tessellate using matlab's
API (read_surf.m)
However, it seems like the function is not up-to-date, because the magic
number in the surface file is 16777213, and the two magic-numbers
recognized by read_surf are
16777214 and 16777215.
Is there a n
It's no longer in the volume, it is on the surface. It should have as
many voxels as there are vertices in the surface
On 5/29/12 5:55 PM, Kushal Kapse wrote:
> hi doug/freesurfer users
>
>
> after doing mri_vol2surf.i went and imported the files in matlab by using
> f=MRIread ('filename.mgh
hi doug/freesurfer users
after doing mri_vol2surf.i went and imported the files in matlab by using
f=MRIread ('filename.mgh') for the original functional (func.nii) file and
spm001lh.mgh file...it seems the original func files has nvoxels=204800 and
spm001lh file has nvolxels=118234.fo
Hi Suzanne, it does not mean that there is anything wrong with your
data. I've seen this before on some data sets. I have a work-around that
might work. How many data sets do you have to run?
doug
On 05/29/2012 02:35 PM, suzanne oosterwijk wrote:
>
> Hi,
>
> Recently I ran recon1 for several par
How much is the dilation (perpendicular to the cortical surface) for
the creation of the white matter ROIs? Is there a citation for this?
Chris Bell
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hi doug,
now it works finei can check the activations of a particular condition on
surfacethanks for all you help
kk
- Original Message -
From: "Douglas Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, May 29, 2012 9:29:50 AM
Subject: Re: [Freesurfer
tksurfer subjectname lh inflated -overlay spm001.mgh
You can then scroll through the different time points with the overlay
configuration
On 5/29/12 9:35 AM, Kushal Kapse wrote:
> so if i have output as .mgh filehow can i check the output on surface...i
> try tksurfer and it just shows in
so if i have output as .mgh filehow can i check the output on surface...i
try tksurfer and it just shows inflated surfacethe qsurfer doesnt load coz
it keeps looking for .w file format...is there any change in commands to
make so that i can visualize the output of functionaltosurface
it does not produce a .w file the output is spm001.mgh
On 5/29/12 9:00 AM, Kushal Kapse wrote:
> hi doug/bruce:
>
> it still says it cannot find .w fileplease check at the bottom
>
> [kkapse@dendrite 15546_03908]$ /home/kkapse/mri_vol2surf.linux --src
> func.nii.gz --reg register.dat --h
hi doug/bruce:
it still says it cannot find .w fileplease check at the bottom
[kkapse@dendrite 15546_03908]$ /home/kkapse/mri_vol2surf.linux --src
func.nii.gz --reg register.dat --hemi rh --out spm001.mgh
srcvol = func.nii.gz
srcreg = register.dat
srcregold = 0
srcwarp unspecified
surf
Hi Kushal, you cannot use .w file for 4D outputs. Use this cmd:
mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out
spm001.mgh
doug
On 5/29/12 8:46 AM, Kushal Kapse wrote:
> hi doug,
>
> as per our last conversation of 4d time series on surface, i did mri_vol2surf
> as p
can you tell us what you mean when you say "the output doesn't work", and
how you checked the output on the surface? If you specify mgz as the
output format make sure the --out file name ends in .mgz
cheers
Bruce
On Tue, 29 May
2012, Kushal Kapse wrote:
> hi doug,
>
> as per our last conversat
hi doug,
as per our last conversation of 4d time series on surface, i did mri_vol2surf
as per tutorial on wiki..i used the new mri_vol2surf which u send methis
was my command:
mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out
spm001-lh.w --out_type paint
but i cant
MNI305 space
doug
On 5/29/12 2:29 AM, ZhiLiangLong wrote:
Hi all:
In FS, does the fsaverage template belong to MNI space or
Talairach space?
Thanks!
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