Hello,
I think that the problem may lie with MRIread.
I have 1 x 82 Array of phase volumes.
I also then have a separate 3 x 82 array of coordinates (that correspond to
each of the normalized 0 to 1 phase values above.
My question is: if I input the phases in vol, what field do I place the
coo
Final question:
My values are normalized: from 0 to 1 ... How do I change the overlay colours
so that this is scaled correctly?
I am assuming I have to make a file of some sort ...
Thanks, I think I am almost there ... -jason.
On 05/02/2011 01:03, "Bruce Fischl" wrote:
try one '-' in '-over
try one '-' in '-overlay', not two
On Sat, 5 Feb 2011, Jason Connolly wrote:
> Hi Bruce,
>
> I used mri_vol2surf, but there appears to be no overlay colours ... Here is
> the output ...
>
> Any ideas would be great ...
>
> tksurfer bert rh inflated --overlay
> /Applications/fesurfer/subjects/ber
Hi Bruce,
I used mri_vol2surf, but there appears to be no overlay colours ... Here is the
output ...
Any ideas would be great ...
tksurfer bert rh inflated --overlay
/Applications/fesurfer/subjects/bert/surf/test_LH.mgh
WARNING: flag --overlay unrecognized
WARNING: flag /Applications/freesurfe
no, you can use it to sample volume data onto the surface using
mri_vol2surf
On Sat, 5 Feb 2011, Jason
Connolly wrote:
> Can I display register.dat in tksurfer?
>
> Thanks, -j.
>
>
> On 05/02/2011 00:21, "Bruce Fischl" wrote:
>
> that writes the file named register.dat that has the affine regi
Can I display register.dat in tksurfer?
Thanks, -j.
On 05/02/2011 00:21, "Bruce Fischl" wrote:
that writes the file named register.dat that has the affine registration
matrix (and some other things)
On
Sat, 5 Feb 2011, Jason Connolly wrote:
> Hi Bruce,
>
> Here it is:
>
> bbregister --s bert
that writes the file named register.dat that has the affine registration
matrix (and some other things)
On
Sat, 5 Feb 2011, Jason Connolly wrote:
> Hi Bruce,
>
> Here it is:
>
> bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz
> --reg register.dat --bold --init-hea
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz
--reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" wrote:
can you send us your command line?
On Sat, 5 Feb 2011, Jason Connolly wrote:
> Hi Doug,
>
> I am now
can you send us your command line?
On Sat, 5 Feb 2011, Jason Connolly wrote:
> Hi Doug,
>
> I am now at the bbregister stage ... I ran this but it is not clear to me
> where the output is? I don't see an output flag ...
>
> Can you tell me where to look for my output?
>
> Almost there!
>
> Many
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where
the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" wrote:
Thank you. -jason.
On 04/02
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" wrote:
You can load in the functional with MRIread since you are going to be
replacing all the pixel data anyway with your single time point. Just
use the single argument. The second is if you dont want to read in the
pixel data.
Jason
You can load in the functional with MRIread since you are going to be
replacing all the pixel data anyway with your single time point. Just
use the single argument. The second is if you dont want to read in the
pixel data.
Jason Connolly wrote:
> Thanks.
>
> So, to clarify, I am trying to just
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with
a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" wrote:
It's the vol field.
doug
Jason Conn
It's the vol field.
doug
Jason Connolly wrote:
> Hi Doug,
>
> You state:
>
> "then replace the pixel data with your
> analyzed data"
>
> I cannot seem to find the field for the pixel data. Can you tell me where to
> position these values?
>
> Thanks! -jason.
>
>
> On 04/02/2011 18:15, "Douglas
Hi Doug,
You state:
"then replace the pixel data with your
analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to
position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" wrote:
You should save it out as nifti (see MRIwrite.m and
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would
suggest using MRIread.m to read in your file in order to create the
proper header information, then replace the pixel data with your
analyzed data, then use MRIwrite.m to save it out. Then use bbregister
to register this vo
you should be able to use mri_surf2surf to map them all to fsaverage
On Fri,
4 Feb 2011, Jason Connolly wrote:
> Hi Bruce,
>
> I guess the problem I have at hand is how to map them to fsaverage. Do I
> have to convert the arrays somehow to nifti format first? I tried looking
> this up on the
Hi Bruce,
I guess the problem I have at hand is how to map them to fsaverage. Do I have
to convert the arrays somehow to nifti format first? I tried looking this up
on the web but couldn't find a solution ...
Many thanks,
Jason.
On 04/02/2011 13:48, "Bruce Fischl" wrote:
Hi Jason
why no
Hi Jason
why not map them all to fsaverage and display them on a common surface?
cheers
Bruce
On Fri, 4 Feb 2011, Jason Connolly wrote:
> Dear freesurfer experts:
>
> I have been using matlab to analyze a retinotopic dataset.
>
> However, the 3D volumes are not in standardized space (and I wis
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display
multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is
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