Dear all, I am an undergraduate student working in Dr. David Ress' lab at Brown University making a comparison of different brain segmentation applications among them freesurfer. However, I ran into much difficulty conducting a proper quantitative comparison of outputs. Indeed, I noticed that the data was shifted and possibly rotated in freesurfer. In order to superimpose the output by the different applications I must put all data back in its original coordinate system. I was wondering if there is a way of obtaining the transformation matrix used by freesufer. Thank you very much for your help. My very best regards, Akram.
Hi Akram,
you can either use matlab functions (e.g. MRIread, load_cor and load_mgh) or mri_info to get the ras2vox matrix.
cheers, Bruce
On Tue, 13 Sep 2005, Bakkour, Akram wrote:
Dear all, I am an undergraduate student working in Dr. David Ress' lab at Brown University making a comparison of different brain segmentation applications among them freesurfer. However, I ran into much difficulty conducting a proper quantitative comparison of outputs. Indeed, I noticed that the data was shifted and possibly rotated in freesurfer. In order to superimpose the output by the different applications I must put all data back in its original coordinate system. I was wondering if there is a way of obtaining the transformation matrix used by freesufer. Thank you very much for your help. My very best regards, Akram.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Your best bet is to use tkregister2 and mri_vol2vol, something like:
tkregister2 --targ orig --mov dicom --regheader --reg register.dat
where orig is the freesurfer orig volume and dicom is your original dicom (or some other format that has the orginal geometry). tkregister2 will bring up a window in which you can edit the registration (hopefully this won't be necessary). Save the registration matrix, then run mri_vol2vol, something like:
mri_vol2vol --in orig --out orig.dicomspace.img --temp dicom --xfm register.dat
run either of these commands with --help to get help
doug
On Tue, 13 Sep 2005, Bakkour, Akram wrote:
Dear all, I am an undergraduate student working in Dr. David Ress' lab at Brown University making a comparison of different brain segmentation applications among them freesurfer. However, I ran into much difficulty conducting a proper quantitative comparison of outputs. Indeed, I noticed that the data was shifted and possibly rotated in freesurfer. In order to superimpose the output by the different applications I must put all data back in its original coordinate system. I was wondering if there is a way of obtaining the transformation matrix used by freesufer. Thank you very much for your help. My very best regards, Akram.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bakkour, Akram -
Bruce Fischl -
Doug Greve