Dear all,
I run recon-all with the -autorecon1 and -autorecon2 options. Now I want to
store the segmentation results in a spm like way. One nifti file for each
matter. Can I do this with freesurfer? And how can I do this with freesurfer?
Best regards,
Iven Fellhauer
-
Hi Ivan
you can convert any volume to any supported output type using
mri_convert. It will figure out the format from the extension, so:
mri_convert aseg.mgz aseg.nii.gz
or
mri_convert aseg.mgz aseg.nii
should do the trick
cheers
Bruce
On Mon,
30 Jan 2012, Fellhauer, Iven wrote:
De
Hi Alex,
we don't have an elegant solution to this, but you can do it in matlab
easily enough. If your data D are in a N-by-327684 matrix (I assume that
this is left and right hemis), then
a.vol = permute(D(:,1:163842),[2 3 4 1]);
MRIwrite(a,'lh.yourdata.mgh');
b.vol = permute(D(:,163843:end),[
You'll need to set the following env variables:
setenv FS_USE_OCTAVE 1
setenv FS_OCTAVE_LIB /place/octave/lib
setenv FS_OCTAVE_BIN /place/octave/binary
doug
Kiley wrote:
> Hi,
>
> I am currently using my macbook to carryout the analysis steps of my
> retinotopy data. Since I was having proble
Yes, that does look excessive. There should be a "masks" volume that
gets created. This will have the individual masks for each subject. You
can load this something like
tksurfer fsaverage lh inflated -overlay masks.mgh -fthresh 0.5 -t masks.mgh
ie, load it as an overlay and timecourse. When yo
Does /8000_series/8000_series/qdec/example_contrast/y.mgh exist?
doug
Cat Chong wrote:
> yes, it does exist..
>
>
> *From:* Douglas N Greve
> *To:* Cat Chong
> *Cc:* "freesurfer@nmr.mgh.harvard.edu"
> *Sent:* Thursday, Jan
Does FS have a generic binary for natively getting simple stats from mgz
files -- e.g., min, max, range, percentiles, etc? i.e., something
analogous to 'fslstats', but which works directly on mgz files?
thanks,
-MH
--
Michael Harms, Ph.D.
---
I don't think so, but if you write out a list we can put them into
mri_info (at least the easy ones for now).
On Mon, 30 Jan 2012, Michael
Harms wrote:
>
> Does FS have a generic binary for natively getting simple stats from mgz
> files -- e.g., min, max, range, percentiles, etc? i.e., somethi
p.s. or maybe Doug has something?
On Mon, 30 Jan 2012, Michael Harms wrote:
>
> Does FS have a generic binary for natively getting simple stats from mgz
> files -- e.g., min, max, range, percentiles, etc? i.e., something
> analogous to 'fslstats', but which works directly on mgz files?
>
> thanks
mris_calc has a stats option (Rudolph's, not mine:).
Michael Harms wrote:
> Does FS have a generic binary for natively getting simple stats from mgz
> files -- e.g., min, max, range, percentiles, etc? i.e., something
> analogous to 'fslstats', but which works directly on mgz files?
>
> thanks,
Hi Bruce,
Can you elaborate briefly on the 6-connected bit? e.g., if one places a
CP manually in a voxel, and that CP is not face-connected on all sides
to either other manually-placed CPs, or CPs determined automatically by
FS, then it doesn't get counted as a CP after all?
Is there any volume
Hi Mike
can you tar and gzip a subject dir with strange results? All manually
specified CPs are included. Then there is an initial intensity segmentation
for stuff that is very likely to be wm, after-which there are a set of
region-growing steps. That's actually the cortical one.The subcortical
I see now that you can get the basics (min, max, mean, and std) for .mgz
volumes using mris_calc.
The great thing about 'fslstats' is that you can easily specify
thresholds to exclude voxels from the calculation, apply masks, and
limit the various calculations to the non-zero voxels if you wish.
Dear Doug,
I don't have an orig.mgz file for the cvs_avg35 and I suppose I need when I
will replace the fsaverage.In the mri file I have olny the norm.mgz
Can you please help me to get the orig.mgz for the cvs_avg35?
Many thanks,
Antonella
From: Douglas N Gr
Jeff,
to check the tal reg, use:
tkregister2 --s subjid --fstal --surfs
i've corrected the eTIV page to reflect this. --fstal loads mni305 as
the target. the target used in the tal reg step (711-2C...) is
registered with the mni305. note that --surfs is optional, as the
surfaces may not exis
Hi,
I was trying to run for my FA group study the following:
mri_glmfit-sim \
--glmdir Group_Analysis.glmdir \
--sim neg perm 1 3 permcsd\
--cwpvalthresh .05
but I got an error: Flag permcsd unrecognized and then is asking me agout --sim
sign.
Can you please help?
THANK YOU!
Antonella
__
Cloud,
in this instance, the documentation is ahead of what is available in the
public release. talairach_with_skull_2.lta will be available in the
next release. in the current release (5.1, and prior),
talairach_with_skull.lta is created in two places: during skullstrip,
and during the skull-l
Wil,
this is correct, we do not officially support a centos5 build, because
the centos4 build works on centos5, and we want to make public
distributions and maintenance as simple as possible.
in future, we will start releasing a centos6 build, because we will
begin using openmp in our builds, but
Malcolm,
To verify your build, our 'gold standard' is to inspect the
segmentations and surfaces manually. Of course, this requires skill
both in neuroanatomy, and what to look for in a typical freesurfer
recon. We do this with our 'buckner40' (40 subject) and 'adni60' (60
subject) datasets prior
Hello,
I'm trying to extract beta values in cortical thickness analysis. For
example, if I use qdec to look at the association between cortical
thickness and variables A and B, can I extract the vertex-wise parameter
estimates corresponding to the association between A and cortical thickness
acros
Hello Doug!
Thank you so much!
Sorry, I've just noticed a mistake... My matrix is 327684x2: the 1st
column denotes vertex numbers and the 2nd one contains corresponding
regression coefficients... I will try to display this tomorrow...
Probably, I will have some troubles with this, considering th
Folks,
Even when I use gcc-3.4.6 the compilation error recurs.
This problem is referred from line 405 of templates.MatrixSpec.cc in the
/mni/EBTKS-1.4-src
directory.
Here is the error again
cd EBTKS-1.4-src; \
make; \
make install;
make[1]: Entering directory
`/home/hazards
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