Hi Krish,
Thanks once again for providing that library. I came back to analyze the
data and got some problems storing the results into MGH format. Before I
try to figure out a fix (and send it back to you) I thought that may be
you could share an uptodated snapshot of the library (may be the issue
Hi Yaroslav and Pádraig,
Please follow the link pasted below to get an alpha version of pymgh.
It requires the latest Python and Numpy.
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/10224/1/2a5da2a125134fbdfc9e6850be1fcc09
(expires in 30 days )
Make sure PYTHONPATH has the d
Thank everyone for very informative comments!
I am a newbie in freesurfer myself, I just got a dataset for the
analysis (data was preprocessed in freesurfer), and since I am moving
myself toward doing any analysis in python, and the tools I use now are
python libraries, I wanted to load the data i
Pádraig is correct in stating that thickness data can be stored in an
mgh file. But the default output of the freesurer recon-all stream does
not store them in that format: it will output ?h.thickness files, which
are the proprietary format.
However, those can be converted to .mgh like this:
mri
MGH is just a generic volume-based format so I think thickness data will
be stored in a 1xNumVerticesx1x1 volume. Here is a python function which
reads in the volume data. It's basically a translation of the readmgh
function from the Freesurfer matlab toolbox. You can modify it to return
more p
Yaroslav,
The mgh format is pseudo-documented here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
But the thickness data is not stored in mgh format, but rather in
another proprietary format, with documentation here:
http://wideman-one.com/gw/brain/fs/surfacefileformats.htm
Yo
Here you go Yaroslav...
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
Krish
On Apr 24, 2008, at 11:49 AM, Yaroslav Halchenko wrote:
actually I need thickness data out of it. Is .mgh format documented
somewhere?
On Thu, 24 Apr 2008, Pádraig Kitterick wrote:
How much detail d
actually I need thickness data out of it. Is .mgh format documented
somewhere?
On Thu, 24 Apr 2008, Pádraig Kitterick wrote:
> How much detail do you need frmo the mgh file? I wrote a quick Python
> script which reads in at least the volume data but I think I just passed
> over most of the ot
How much detail do you need frmo the mgh file? I wrote a quick Python
script which reads in at least the volume data but I think I just passed
over most of the other stuff in there...
Yaroslav Halchenko wrote:
Does anyone know any handy module to at least read in .mgh files from
Python? Or sho
Does anyone know any handy module to at least read in .mgh files from
Python? Or should I simply try mri_convert them into .minc and use
netcdf module within python?
Thanks in advance for the ideas!
--
Yaroslav Halchenko
Research Assistant, Psychology Department, Rutgers-Newark
Student Ph.D. @
10 matches
Mail list logo
