Hi Doug,
Indeed, you are right, I forgot to run recon-all -autorecon3.
It is not well documented that after running -autorecon2-wm
one should also run -autorecon3. I had the impression that
this portion was executed automatically by -autorecon2-wm.
Ed
On 2 Feb 2011, at 18:03, Douglas N Greve wr
Hi Aga, are you using nifti? If analyze, that could be the problem. Do
your functionals and anatomicals have a different sign to their
determinants (you can check with mri_info). In principle, reg-feat2anat
should handle this but in some cases it does not. The 5.1 version will
handle it properl
I get this behavior with --out_orientation, but not with
--in_orientation. Are you sure it happens with both? And are you sure
you want to be changing the orientation? If you have a volume from a
person in the scanner head-first supine, then the answer is almost
surely no.
doug
Reza Farivar w
Thanks for the suggestion Ed. I've just added the text below to
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Troubleshooting. If
you know of another place where it would be useful, please let us know.
doug
"Note that after you run recon-all with the -autorecon2-wm flag, you
will still n
Dear Doug,
Thank you a lot!
Our feat data is always nifti, but anatomical FSL data is sometimes in the
analyze format. Is this already a problem?
I will now check the rest.
Thank you, cheers,
Aga
On 2/7/11 4:35 PM, "Douglas N Greve" wrote:
> Hi Aga, are you using nifti? If analyze, that could
Hello,
We are trying to set up the analysis for a periodic design alternating
between 30s rest and 30s active condition. Because abblocked doesn't
require a paradigm file, how do we specify which condition comes first
(rest or active)? We understand that abblocked expects that the
conditions wil
The contrasts are going to be created automatically. These will be:
fund - stands for "fundamental" - this is the F-test of the sine and
cosine components, probably what you want
fund-sin -- t-test of the sine component (this may also be useful)
fund-cos -- t-test of the cosine component (think of
Hello,
We are trying to set up the analysis for a periodic design alternating
between 30s rest and 30s active condition. Because abblocked doesn't
require a paradigm file, how do we specify which condition comes first
(rest or active)? We understand that abblocked expects that the
conditions wi
That is not a problem. By "anatomical" I meant the FreeSurfer anatomical
(eg, orig.mgz)
doug
Agnieszka Burzynska wrote:
> Dear Doug,
> Thank you a lot!
> Our feat data is always nifti, but anatomical FSL data is sometimes in the
> analyze format. Is this already a problem?
>
> I will now check th
Hi Doug,
For some reason, our mkanalysis-sess command only created an
analysis.info file and not a .cfg file, so we can't run the abblocked
analysis using sfa-sess. Do you know what might cause this?
We are using:
freesurfer v5
our subjects directory: /cluster/manoach/milton/subjects
command
sfa-sess is depricated now (should not even be in there). Use selxavg3-sess.
doug
Chindhuri Selvadurai wrote:
> Hi Doug,
>
> For some reason, our mkanalysis-sess command only created an
> analysis.info file and not a .cfg file, so we can't run the abblocked
> analysis using sfa-sess. Do you know
Please see the attached file.
If interested, pelase submit your C.V. and relevant reprints, together
with a cover letter describing current research interests and future
research goals, and also arrange to have three letters of reference sent
independently to:
Dr. Sylvain Moreno
Rotman Rese
Hello FS Experts,
I am trying to generate the whole brain gray matter image, I use aparc_aseg.mgz
- wm.mgz for gray matter mask, then use this mask for gray matter. Is it
correct? What is the difference between aseg.mgz and ribbon.mgz? Hope your
help. Thanks.
Aize
Dear freesurfer experts:
I noticed that there are two 'vol' fields when I use MRIread.
1) mri.vol
2) mri.analyzehdr.vol
My question is:
I have two arrays, one with 3D coordinates and a second 1 dimensional array
with corresponding phase values.
Which 'vol' field do I put the 3D coordinates i
The Solodkin/Small Brain Circuits Laboratory at the University of California,
Irvine, will soon have an opening for a research technician in image
processing. This job would be ideal for someone interested in applying basic
skills in signal processing or applied mathematics to a variety of funct
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