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
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 standardize
i_vol2surf to
sample it to the surface (either native anatomical or to some other
subject).
doug
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 wi
ta, then use MRIwrite.m to save it out. Then use bbregister
> to register this volume to the anatomical, then use mri_vol2surf to
> sample it to the surface (either native anatomical or to some other
> subject).
>
> doug
>
> Jason Connolly wrote:
>
>> Dear fre
pixel data.
Jason Connolly wrote:
> 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 ...
>
>
>
>
&
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.
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 D
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:
dfPlot.tcl
Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
On 05/02/2011 00:32, "Bruce Fischl" wrote:
no, you can use it to sample volume data onto the surface using
mri_vol2surf
On Sat, 5 Feb 2011, Jason
Conn
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
&
coordinates for the phase values in?
Many thanks,
Jason.
On 05/02/2011 01:03, "Bruce Fischl" wrote:
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 colour
Dear freesurfer experts:
I noticed that there are two 'vol' fields when I use MRIread.
1) mri.vol
2) mri.analyzehdr.vol
My question is:
I have two arrays, one with 3D coordinates and a second 1 dimensional array
with corresponding phase values.
Which 'vol' field do I put the 3D coordinates i
Dear freesurfer experts,
I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates
and phase values using MRIread and MRIwrite (f_LH12.mgz).
I then brought these data into freesurfer using the following:
bbregister --s fsaverage --mov
/Applications/freesurfer/subjects/fsav
Thank you for your advice Doug.
Best wishes,
-jason.
>-Original Message-
>From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
>Sent: 09 February 2011 16:42
>To: Jason Connolly
>Cc: 'freesurfer@nmr.mgh.harvard.edu'
>Subject: Re: [Freesurfer] phase
that all the voxels are
'forced' to display on the surface?
Many thanks,
Jason.
>-Original Message-
>From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
>Sent: 09 February 2011 16:42
>To: Jason Connolly
>Cc: 'freesurfer@nmr.mgh.harvard.edu'
&g
Dear freesurfer experts:
I am new to fs-fast and I am currently running sfa-sess on some retinotopy data
and I think the main error is "cannot determine format of 005/f"
I read in a previous post related to retinotopy that you need to add the full
path to the .nii files and then it will work.
Dear freesurfer experts:
Recon-all is running in a few seconds (obvious error).
I am getting the following screen output on Linux, when I run recon-all:
recon-all -i /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img -s
arlene -force
INFO: /usr/local/freesurfer/subjects/arlene exists
Thanks. It's working now. J
>-Original Message-
>From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
>Sent: 13 May 2010 15:12
>To: Jason Connolly
>Cc: 'freesurfer@nmr.mgh.harvard.edu'
>Subject: Re: [Freesurfer] freesurfer recon-all running in a
Dear Freesurfer experts,
We are attempting to segment a template monkey brain.
The following is the command line input:
recon-all -i
/usr/local/freesurfer/subjects/template_2/mri/orig/MonkTempl_w81096_T1.nii.gz
-s template -all -notal-check -force -noaseg
It runs for a few hours and then we
Dear Free Surfers,
I'm having a problem I've seen posts about in the archive, but have not been
able to see the solution to it.
If I start tksurfer bert rh pial (as the example says), the display only shows
a small fraction of the brain and nothing more. I've tried some of the
suggestions such
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