Dear FS experts
Here I found a warning that seem to be related to the error message I posted
before.
mri_convert /usr/local/freesurfer/subjects/s237/mri/rawavg.mgz
/usr/local/freesurfer/subjects/s237/mri/orig.mgz --conform
WARNING
=====
Dear FS experts
We analysed data with FS 4.0.1. In the past, when analyzed this data with FS
3.0.5 everthing worked fine. Now with FS 4.0.1 an error occurred maybe due
to a dimension mismatch.
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.mgz wm.mgz fil
Mishkin,
try this:
mri_vol2vol --mov aseg.mgz \
--targ original.mnc \
--o aseg-in-native.mnc \
--regheader \
--interp nearest
Nick
On Thu, 2007-12-13 at 22:05 -0500, Mishkin Derakhshan wrote:
> Hi,
> I am having troubles getting the right options with mri_conver
Hi,
I am having troubles getting the right options with mri_convert.
I ran:
recon-all -autorecon1 -i original.mnc -s subj1
recon-all -subcortseg -s subj1
I now want to convert aseg.mgz into aseg.mnc but in the same space and
with the same orientation as my original.mnc file.
My original.mnc file
Hi Binyam,
for cortical analysis it shouldn't be an issue. Subcortically the atlas
does consist of adults, but in our experience it only makes a difference
at younger ages than the ones you are imaging. We to provide tools for
building your own atlas if you are interested.
cheers,
Bruce
On T
Freesurfers,
I had a couple of questions regarding your atlas.
I'm working with a children and young adult subject population (ages 7-18). I'm
interested in anatomical measures such as cortical thickness, and volumes of
different structures. What are your thoughts on what atlas to use for thes
Hi Simon,
yes, you would need to skip the watershed step (it is our skull
stripping), or better yet, replace it with bet, since at some points we
need the skull on e.g. to do TIV estimation. Do you find our skullstripping
is failing? In our hands the current version is extremely robust - worki
I've been having problems with a few brains (errors during
processing). I found advice on the web about running BET (the FSL
brain extraction tool) prior to running recon-all
http://lcni.uoregon.edu/mediawiki/index.php/SOFT:FSL_FreeSurfer
I've tried this and that has helped. (Searching the
mri_probedicom will dump a lot of stuff, but not everything. If you know
what you want, you can have it dump particular tags.
Michael Harms wrote:
Hello,
Will any of the FS utilities read a Siemens DICOM file and dump the
(complete) DICOM header information to the terminal or text file? I've
You can get the DCMTK to install and use its dcmdump utility.
http://dicom.offis.de/dcmtk.php.en
On Thu, 13 Dec 2007, Michael Harms wrote:
Hello,
Will any of the FS utilities read a Siemens DICOM file and dump the
(complete) DICOM header information to the terminal or text file? I've
looked
Hello,
Will any of the FS utilities read a Siemens DICOM file and dump the
(complete) DICOM header information to the terminal or text file? I've
looked at the options for mri_info and unpacksdcmdir, but as far as I
can tell neither have this capability. We have a handy Sun executable
that can d
Hello,
I've been looking through the archives and still have some questions
about getting the best data for GM volume, WM volume, and the volumes of
each sub-cortical structure. This is lengthy, but I'm trying to save a
lot of future man-hours that I wasted on the first dataset I was doing.
*
Hi Abel,
no, there's no automated tool for this without special purpose
acquistions. You'll need to edit the brainmask.mgz to remove the dura
that the pial surface is grabbing.
sorry :<
Bruce
On Thu, 13 Dec 2007, abel cruz vadell
wrote:
Hi everyone
Checking the automatic pial segmentati
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