Hi,
I am a freesurfer starter. I am trying to overlay statistical maps ,which I've created with FSL, on the brain surface. I've some questions regarding to that:
1) can the newest version of freesurfer deal with NIFTI files? (Because everytime when I try to use NIFTI files I get an error message.)
2) how can use mat files which I create with FSL-Flirt to overlay functional maps to the brain surface?
3) I do not want to use talaraich registration. Is there a possibility to omit talaraich registration.
Thanks a lot
Marek
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1) can you send us the exact error message and what version you are using?
2) which mat files do you mean? If you mean the ones that come with analyze format then we will read them automatically.
3) You can run recon-all with -notalairach at the end of the cmd line.
cheers, Bruce
On Mon, 26 Feb 2007, Marek Kosinski wrote:
Hi,
I am a freesurfer starter. I am trying to overlay statistical maps ,which I've created with FSL, on the brain surface. I've some questions regarding to that:
- can the newest version of freesurfer deal with
NIFTI files? (Because everytime when I try to use NIFTI files I get an error message.)
- how can use mat files which I create with FSL-Flirt
to overlay functional maps to the brain surface?
- I do not want to use talaraich registration. Is
there a possibility to omit talaraich registration.
Thanks a lot
Marek
Der frühe Vogel fängt den Wurm. Hier gelangen Sie zum neuen Yahoo! Mail: http://mail.yahoo.de _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Marek Kosinski wrote:
Hi,
I am a freesurfer starter. I am trying to overlay statistical maps ,which I've created with FSL, on the brain surface. I've some questions regarding to that:
- can the newest version of freesurfer deal with
NIFTI files? (Because everytime when I try to use NIFTI files I get an error message.)
Yes, the newest version can read and write nifti (including gzipped).
- how can use mat files which I create with FSL-Flirt
to overlay functional maps to the brain surface?
You have to convert to a freesurfer register.dat. The easiest thing to do is to run reg-feat2anat. This will use flirt to compute the freesurfer registration matrix. See the docs in surfer.nmr.mgh.harvard.edu/fswiki/FslWorkFlows
- I do not want to use talaraich registration. Is
there a possibility to omit talaraich registration.
Why not? It does not take very long. It does not actually apply the registration, it just computes it. Finally, if you have it, then you can get talairach coords from tkmedit and tksurfer.
doug
Thanks a lot
Marek
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Marek Kosinski