And after creating the mgh volume, how can I read it? Is it possible to open it in tksurfer? Should I load it as an overlay? I've used one of my already pre-processed subjects, created a 'vol' with the same number of vertices of one of the hemisferes, and saved the output of save_mgh file as an rh.thickness.mgh file. However, when I don't seem to be able to open it in tksurfer...
Thanks
Ines
2007/8/6, Bruce Fischl fischl@nmr.mgh.harvard.edu:
they don't matter. For a real volume they would be the ras2vox transform and the mr parameters. For your purposes they can be any 4x4 and you can leave the mri_parms one out (it will detect and fill it in with zeros).
Send these to the list so other people can answer!
Bruce On Mon, 6 Aug 2007, Inês Souta wrote:
Hi again,
I still don't understand what all the input objects of save_mgh function stand for. 'vol' is the vector of thickness values, 'fname' is the name
of
the output .mgh file, and what about M and <mr_parms>? What do they
stand
for and how should I define them?
Thanks again,
Ines
2007/7/31, Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Ines,
use the mgh route. The "vol" is actually the vector of thickness
values,
with one entry per vertex on the surface.
cheers, Bruce On Tue, 31 Jul 2007, Inês Souta wrote:
Hello,
I was trying to create a cortical thickness map with constant values
in
order to perform some tests. At first I tried using mris_convert. I converted my thickness file into ascii:
mris_convert lh.thickness lh.thickess.asc
then I used matlab to change all the values in the last column to 2,0.
I
tried to convert the ascii file back to surface file by doing
mris_convert lh.thicness.asc lh.thickness
but I got "Segmentation fault". How can I convert may ascii file into
a
surface one?
After failling to acomplish this, I tried using the save_mgh and
load_mgh
file, nevertheless I'm not quite sure which input values are needed.
Where
can I put my fake values in the save_mgh file? And what is "vol"?
Thanks,
Ines
yes, you should be able to open it in tksurfer. What version of freesurfer do you have? On Mon, 6 Aug 2007, Inês Souta wrote:
And after creating the mgh volume, how can I read it? Is it possible to open it in tksurfer? Should I load it as an overlay? I've used one of my already pre-processed subjects, created a 'vol' with the same number of vertices of one of the hemisferes, and saved the output of save_mgh file as an rh.thickness.mgh file. However, when I don't seem to be able to open it in tksurfer...
Thanks
Ines
2007/8/6, Bruce Fischl fischl@nmr.mgh.harvard.edu:
they don't matter. For a real volume they would be the ras2vox transform and the mr parameters. For your purposes they can be any 4x4 and you can leave the mri_parms one out (it will detect and fill it in with zeros).
Send these to the list so other people can answer!
Bruce On Mon, 6 Aug 2007, Inês Souta wrote:
Hi again,
I still don't understand what all the input objects of save_mgh function stand for. 'vol' is the vector of thickness values, 'fname' is the name
of
the output .mgh file, and what about M and <mr_parms>? What do they
stand
for and how should I define them?
Thanks again,
Ines
2007/7/31, Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Ines,
use the mgh route. The "vol" is actually the vector of thickness
values,
with one entry per vertex on the surface.
cheers, Bruce On Tue, 31 Jul 2007, Inês Souta wrote:
Hello,
I was trying to create a cortical thickness map with constant values
in
order to perform some tests. At first I tried using mris_convert. I converted my thickness file into ascii:
mris_convert lh.thickness lh.thickess.asc
then I used matlab to change all the values in the last column to 2,0.
I
tried to convert the ascii file back to surface file by doing
mris_convert lh.thicness.asc lh.thickness
but I got "Segmentation fault". How can I convert may ascii file into
a
surface one?
After failling to acomplish this, I tried using the save_mgh and
load_mgh
file, nevertheless I'm not quite sure which input values are needed.
Where
can I put my fake values in the save_mgh file? And what is "vol"?
Thanks,
Ines
freesurfer v.3.0.5 for Linux-Centos4
2007/8/6, Bruce Fischl fischl@nmr.mgh.harvard.edu:
yes, you should be able to open it in tksurfer. What version of freesurfer do you have? On Mon, 6 Aug 2007, Inês Souta wrote:
And after creating the mgh volume, how can I read it? Is it possible to
open
it in tksurfer? Should I load it as an overlay? I've used one of my already pre-processed subjects, created a 'vol' with
the
same number of vertices of one of the hemisferes, and saved the output
of
save_mgh file as an rh.thickness.mgh file. However, when I don't seem to
be
able to open it in tksurfer...
Thanks
Ines
2007/8/6, Bruce Fischl fischl@nmr.mgh.harvard.edu:
they don't matter. For a real volume they would be the ras2vox
transform
and the mr parameters. For your purposes they can be any 4x4 and you
can
leave the mri_parms one out (it will detect and fill it in with zeros).
Send these to the list so other people can answer!
Bruce On Mon, 6 Aug 2007, Inês Souta wrote:
Hi again,
I still don't understand what all the input objects of save_mgh
function
stand for. 'vol' is the vector of thickness values, 'fname' is the
name
of
the output .mgh file, and what about M and <mr_parms>? What do they
stand
for and how should I define them?
Thanks again,
Ines
2007/7/31, Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Ines,
use the mgh route. The "vol" is actually the vector of thickness
values,
with one entry per vertex on the surface.
cheers, Bruce On Tue, 31 Jul 2007, Inês Souta wrote:
Hello,
I was trying to create a cortical thickness map with constant values
in
order to perform some tests. At first I tried using mris_convert. I converted my thickness file into ascii:
mris_convert lh.thickness lh.thickess.asc
then I used matlab to change all the values in the last column to
2,0.
I
tried to convert the ascii file back to surface file by doing
mris_convert lh.thicness.asc lh.thickness
but I got "Segmentation fault". How can I convert may ascii file
into
a
surface one?
After failling to acomplish this, I tried using the save_mgh and
load_mgh
file, nevertheless I'm not quite sure which input values are needed.
Where
can I put my fake values in the save_mgh file? And what is "vol"?
Thanks,
Ines
Sorry, I was saving it with the wrong extension. I am already able to open it in tksurfer! Thanks a lot,
Ines
2007/8/6, Inês Souta ines.souta@gmail.com:
freesurfer v.3.0.5 for Linux-Centos4
2007/8/6, Bruce Fischl fischl@nmr.mgh.harvard.edu:
yes, you should be able to open it in tksurfer. What version of freesurfer do you have? On Mon, 6 Aug 2007, Inês Souta wrote:
And after creating the mgh volume, how can I read it? Is it possible
to open
it in tksurfer? Should I load it as an overlay? I've used one of my already pre-processed subjects, created a 'vol'
with the
same number of vertices of one of the hemisferes, and saved the output
of
save_mgh file as an rh.thickness.mgh file. However, when I don't seem
to be
able to open it in tksurfer...
Thanks
Ines
2007/8/6, Bruce Fischl < fischl@nmr.mgh.harvard.edu>:
they don't matter. For a real volume they would be the ras2vox
transform
and the mr parameters. For your purposes they can be any 4x4 and you
can
leave the mri_parms one out (it will detect and fill it in with
zeros).
Send these to the list so other people can answer!
Bruce On Mon, 6 Aug 2007, Inês Souta wrote:
Hi again,
I still don't understand what all the input objects of save_mgh
function
stand for. 'vol' is the vector of thickness values, 'fname' is the
name
of
the output .mgh file, and what about M and <mr_parms>? What do they
stand
for and how should I define them?
Thanks again,
Ines
2007/7/31, Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Ines,
use the mgh route. The "vol" is actually the vector of thickness
values,
with one entry per vertex on the surface.
cheers, Bruce On Tue, 31 Jul 2007, Inês Souta wrote:
> Hello, > > I was trying to create a cortical thickness map with constant
values
in
> order to perform some tests. At first I tried using mris_convert.
I
> converted my thickness file into ascii: > > mris_convert lh.thickness lh.thickess.asc > > then I used matlab to change all the values in the last column to
2,0.
I
> tried to convert the ascii file back to surface file by doing > > mris_convert lh.thicness.asc lh.thickness > > but I got "Segmentation fault". How can I convert may ascii file
into
a
> surface one? > > After failling to acomplish this, I tried using the save_mgh and load_mgh > file, nevertheless I'm not quite sure which input values are
needed.
Where > can I put my fake values in the save_mgh file? And what is "vol"? > > Thanks, > > Ines >
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Inês Souta