Hi Doug,
Thanks for your speedy response.
The image comes up fine in SPM, but not in other programs like MRIcro or
FSLview, where the anterior of the image in the axial plane faces down instead
of up.
Is there any (relatively) straightforward I can adjust this through mri_convert?
Thanks again,
A
On Wed, 4 Oct 2006, Fornito, Alexander wrote:
Hi,
I'm new to fMR and am using mri_convert to convert from siemens dicom to
analyze/spm format.I ran the command below and had a couple of questions:
1 - Why does the first INFO: line say that 807 files were found when only 805
were input?
Tha
Hi,
I'm new to fMR and am using mri_convert to convert from siemens dicom to
analyze/spm format.I ran the command below and had a couple of questions:
1 - Why does the first INFO: line say that 807 files were found when only 805
were input?
2 - Why were only 800 of 805 files converted?
3 - As
Hello, Is there any online resource for manual segmentations of subcorical objects, e.g. hippocampus, amygdala, caudate etc? I appreciate it. Shahab
Stay in the know. Pulse on the new Yahoo.com. Check it out.
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From a FreeSurfer stand-point it is fine. Your data integrity is, of
course, your own business, but I would advise being very careful with it
and putting a comment if you can into the dicom file indicating what you
did. You might approach the manufacturer (or whoever is creating the
dicoms) a
Hi Doug,
Thanks for the response. The issue is that the fields are missing,
but we know that the scans are acquired in the axial plane. Would it
be a horrible idea to insert into 20,37 the following values since
they correspond to a 'true' axial plane: 1\0\0\0\1\0 ? You mentioned
before that Fr
Hi Niels,
I can't remember what the original problem was. Were the dicom fields
missing or were they just wrong? We can handle wrong ones, but missing
ones cause our 3rd party dicom reader to fail, which we can't really do
anything about.
doug
Niels Bergsland wrote:
Hi again,
From the las
Hi all,
I flattened the occipital cortex and viewed it with tksurfer, but there
are two flattened surfaces, top and bottom on the tksurfer window.
Usually from my experience, there is one flattened surface.
Could someone suggest what might have gone wrong?
Nam.
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Hi Nam,
the patch is a different format than the surface. You need to specify a
surface (e.g. inflated) to tksurfer, then load the path in the file menu
of tksurfer.
Bruce
On Tue, 3 Oct 2006, Joongnam Yang wrote:
Dear all,
I did occipital cortex flattening and when I tried to display it on
Dear all,
I did occipital cortex flattening and when I tried to display it on tksurfer
using "tksurfer average lh occip.patch.flat",
I got the following error message, which I have never seen.
(the error message on memory)
surfer: current subjects dir: /home/nam/AVERAGE
surfer: not in "scripts"
Hi again,
From the last time that I asked about this, the project was
temporarily put on hold, but now it has started up again...
When looking back at the responses from last time, I realized that I
am not sure if I made it clear what I was proposing as a solution to
the missing fields 0020,003
Hi Li,
open a surface in tksurfer (e.g. inflated), then do file->load
patch->rh.patch.flat (this is the flattened version of rh.patch, the .out
file is just a log file)
cheers,
Bruce
On Tue, 3 Oct 2006, xingfeng lee wrote:
Dear FreeSurfer Experts,
I tested flatten using mris_flatten, it to
Dear FreeSurfer Experts,
I tested flatten using mris_flatten, it took 8 hours.
I want to see the result of the faltten, but i do not
know how to open these patch files,
rh.patch
rh.patch.flat
rh.patch.flat.out
could you help to give some suggestions?
Thanks in advance.
Li
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