Hello,
how is it the best line command to visualize in Tkmedit the cerebellar
segmentation?
Thanks a lot for your help
Massimiliano
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the only cerebellar segmentation we have currently is just gray/white,
and you can visualize it with:
tkmedit $subject norm.mgz -seg aseg.mgz
cheers,
Bruce
On Mon, 15 Dec 2008, Massimiliano
Calabrese
wrote:
Hello,
how is it the best line command to visualize in Tkmedit the cerebellar
Maartje,
I think you can make use of aparcstats2table when you first run
mris_anatomical_stats -l ?h.cortex.label -b -f
path_to_homedirectory/subject/stats/?h.cortex.stats subject ?h
for every subject and every hemisphere (preferably using a batch file
where you can list up all the
Ongoing Problems:
Bit of a delay having been away. Here is what I'm doing step by step and
then the error message at the bottom. Again I am using CentOS5 Linux shell
on a windows machine using Freesurfer V4.1.0 with the monitor settings on
32bit, and license file has been set up. Decided to try
Hello Julia,
Besides the definitions above the tables, there are some articles mentioned on
the wiki site- main page, scroll down- giving information about the definitions
of the areas. F.e. Desikan, 2006, about cortical parcellation.
Kind regards,
Maartje Katzenbauer
- Original Message
Thanks Doug, Nick and Marie for your great support!
With regards to what you wrote to Maartje about the total gray matter
volume I understand that the best way to measure it is using
mris_anatomical_stats -l ?h.cortex.label subject ?h
for every subject and every hemisphere. Maybe we should
Hi all,
It would be *really* great if there was a page somewhere (or just a file)
giving some info on the various measures that are captured in the aseg and
aparc files. For each measure (in the table or the comments above the table):
-- Description of what it includes -- some are obvious from
I would have thought that that mri_convert cmd (with .img) would have
worked. what went wrong?
Susie Heo wrote:
Hello,
I am hoping that someone can help me to solve my orientation/angle acquisition
problem:
1) I have an EPI oblique slice in Analyze format with incorrect
orientation/angle
Hi Petr, when you list your subjects, just use the subject's name. It
looks like you put path specifiers in there, ie, ./1013 shoudl be
simply 1013
doug
p.s.bjer...@studmed.uio.no wrote:
Hi,
Trying to make an average of about 60 subjects. The problem is that the
proper files are not
Hi Julien,
if you put the nu.mgz on our filedrop we'll take a look.
cheers,
Bruce
On Mon, 15 Dec
2008, Julien Dubois wrote:
Hi all
I can't get freesurfer to strip the skull properly, even with a water
threshold of 1%. There is still so much skull (csf) remaining that a
manual edit is not
Hello,
The ReleaseNotes for v4.1.0 and v4.0.5 indicate refer to a bug in
'mris_wm_volume' related to the white matter parcellation.
Was there actually a bug in mris_wm_volume itself? Or, is the issue
that the aseg.mgz had some incorrect labeling of non-white structures
relevant to the
Hi Xin, the problem is that neither the sform nor the qform are valid.
Did the message below not appear when you ran tkmedit?
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
Fix that, and everything will work fine.
doug
Wang, Xin
Thank you very much for your quick reply, Dr. Greve. I asked our institutional
MRI center for correct information on qform and sform since the header of nifti
files are created by their scripts. But I do not know what they can do to fix
this problem. I will appreciate if you have any further
hi everyone,
is it possible to combine, using mri_convert, a set of
3D spm/analyze files into a 4D analyze file ? can anyone help
me out with the syntax, if possible?
thanks,
sid.
___
Freesurfer
There are two things you can do,
mri_concat spm_*.img --o 4d.img
you can also do it with mri_convert, but I don't think it buys you
anything over using mri_concat.
doug
Siddharth Srivastava wrote:
hi everyone,
is it possible to combine, using mri_convert, a set of
3D
Hello,
In the stable 3 environment, I ran the func2roi-sess command. This is what
was included:
func2roi-sess -roidef dACC99_rh -analysis EMerror -anatlabel dACC-rh
-maskcontrast ASevfix -maskframe 5 -maskthresh 0.0043648054 -masktail pos
-maskmap sig -sf Subject_files/MTHFRn18-list -d
Hi Doug,
Thanks for the reply. I tried mri_concat as you suggested, and
got the following:
WARNING: analyzeRead(): matfile usual path tospmfile1-0003.mat exists but
could not read ...
may not be matlab4 mat file ... proceeding without it.
mri_convert will fail in the same way. But it should have worked. Can
you point me to the dir and give me read perms?
Siddharth Srivastava wrote:
Hi Doug,
Thanks for the reply. I tried mri_concat as you
suggested, and got the following:
WARNING: analyzeRead(): matfile usual
it's only positive for the contrast that you have specified. the roi
summary reports the HRF amplitudes for each condition. When you compute
the contrast of those, you should get the right sign.
doug
Dave Brohawn wrote:
Hello,
In the stable 3 environment, I ran the func2roi-sess command.
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