If you only want to use the image then your simple conversion will do. Of course it will be in a space different from native/user and MNI. But why would it be a problem?
If you want to e.g. overlay the image (or some derivative) to another in native/user or MNI space then you need registration after conversion. If you have FSL FEAT analysis, you can let reg-feat2anat to calculate the required registration for you. Alternatively, you can just register T1 of Freesurfer to T1 of FSL, and register T1 of FSL to whatever image you need. In the end you will have the transformation matrix (.mat file) which you can then apply on the converted image.
Cheers,
Auer, Tibor M.D. Ph.D.
MRC Cognition and Brain Sciences Unit
15 Chaucer Road
Cambridge
CB2 7EF
United Kingdom
Phone/Work: +44-(0)1223-355294 (ext. 869)
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-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Erica Tatham
Sent: Wednesday, February 13, 2013 6:22 PM
To: [log in to unmask]
Subject: [FSL] Converting images from Freesurfer from FSL
Hello Colleagues,
I am currently analyzing my DTI data in FSL and Freesurfer. I constructed a cortical map in Freesurfer and want to convert it back to images that can be used by FSL.
I read that Freesurfer functions in Talairach space while FSL functions in MNI. I worry that the simple conversion I am doing below (from mgz to nifti zip) will not account for these differences in space. If anyone has any knowledge on whether FSL grabs MNI co-ordinates from Freesurfer or whether I need to do additional steps, that would be greatly appreciated.
mri_convert brainmask.mgz brainmask.nii.gz
Thank you for any information you can provide me,
Erica Tatham
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