[Freesurfer] Question about Talairach

[Lauren Gresham]

Hello,

I was following the instructions on the wiki
 to
check the registrations on some subjects.

I ran the following command from my subjects dir, to view subject 001:
freeview -v 001/mri/T1.mgz
001/mri/brainmask.mgz:reg=001/mri/transforms/talairach.xfm

I get the following errors:

regio_read_mincxfm: No such file or directory
ERROR: could not read
/path/to/subjects_dir/001/mri/001/mri/transforms/talairach.xfm
ERROR: could not read
/path/to/subjects_dir/001/mri/001/mri/transforms/talairach.xfm
Read registration failed

The T1 file is loaded, but not the brainmask.mgz file.
It looks like the command was expecting relative paths for the registration
from the file, so I reran using:
freeview -v 001/mri/T1.mgz
001/mri/brainmask.mgz:reg=transforms/talairach.xfm

When I do that, it brings up both the T1 and brainmask file, but outputs a
different error:

Not reading in xfm fileinfo
Not reading in xfm fileinfo

The brainmask file appears shifted up and backwards considerably, but still
centered widthwise. However, I am not sure if this has something to do with
it
not loading the file correctly, or if the transform was indeed erroneous.

Appreciate any insight!

Lauren Gresham
Research Specialist
Waisman Waisman Laboratory for Brain Imaging & Behavior
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[Freesurfer] Question about Talairach

[Koene Van Dijk]

HiLauren,

This should be the correct command:

freeview -v tal_before/mri/T1.mgz -v 
tal_before/mri/brainmask.mgz:reg=transforms/talairach.xfm

(so remove the part "001/mri/" before "transforms").

Best,
Koene


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[Freesurfer] question about talairach transform used in skullstrip

[Guang Zeng]

Hi, there,

In the skullstrip step, mri_em_register command is called and a 
talairach_with_skull.lta file is produced. 
This lta file will be used in the following mri_watershed command. 

My questions are:
(1) Once we got the brainmask.auto.mgz, which command we can use to inverse the 
talairach transform, 
convert the coordinate to the original system?  

(2) How different it will be if no altas is used in the mri_watershed step?


Thanks a lot!

Guang

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Re: [Freesurfer] question about talairach transform used in skullstrip

[Nick Schmansky]

Guang,

brainmask.auto.mgz (and all the volume files produced in the recon-all
stream) remain in native space.  you can add -nowsatlas after
-skullstrip to recon-all to see the results without the atlas (results
differ depending on the input).  the tal transforms are used only to
align the atlas, and for user display in tkmedit and tksurfer.

Nick

On Tue, 2009-08-11 at 08:56 -0500, Guang Zeng wrote:
> 
> 
> Hi, there,
> 
> In the skullstrip step, mri_em_register command is called and a
> talairach_with_skull.lta file is produced. 
> This lta file will be used in the following mri_watershed command. 
> 
> My questions are:
> (1) Once we got the brainmask.auto.mgz, which command we can use to
> inverse the talairach transform, 
> convert the coordinate to the original system?  
> 
> (2) How different it will be if no altas is used in the mri_watershed
> step?
> 
> 
> Thanks a lot!
> 
> Guang
> 
> 
> __
> Get back to school stuff for them and cashback for you. Try Bing now.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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