Hello All,
Can you please tell me, when we get the results from QDEC {$SUBJECTS_DIR/qdec/Untitled/lh-Avg-thickness-age-Cor/sig.mgh} how can we threshold the image and include it as a seed into FSL tractography ? What command line should I use ?
Thank you for your help, Best regards, Alexandru Hanganu. ___________________________________
Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
Alexandru,
I can't say i've seen this done before, but i think what you would do is use mri_surf2vol to map the sig.mgh file back into your subject volume space. you would need a register file to do this, but it is included with a standard freesurfer recon. that is, the surface data is on the 'fsaverage' surface, and each subject has a talairach.xfm registration file created for it (and fsaverage is in talairach space). then you would use mri_binarize to threshold that volume down to just the voxel values at threshold, then find the remaining voxels and use those as the seed. you can save files with a .nii extension, for import into fsl's tools. see mri_surf2vol --help and mri_binarize --help
Nick
On Wed, 2008-12-10 at 17:19 +0000, Alexandru Hanganu wrote:
Hello All,
Can you please tell me, when we get the results from QDEC {$SUBJECTS_DIR/qdec/Untitled/lh-Avg-thickness-age-Cor/sig.mgh} how can we threshold the image and include it as a seed into FSL tractography ? What command line should I use ?
Thank you for your help, Best regards, Alexandru Hanganu. ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Nick for your answer. We will try this method.
________________________________ Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Alexandru Hanganu hanganu.alexandru@yahoo.de CC: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, den 11. Dezember 2008, 23:16:15 Uhr Betreff: Re: [Freesurfer] QDEC data into FSL
Alexandru,
I can't say i've seen this done before, but i think what you would do is use mri_surf2vol to map the sig.mgh file back into your subject volume space. you would need a register file to do this, but it is included with a standard freesurfer recon. that is, the surface data is on the 'fsaverage' surface, and each subject has a talairach.xfm registration file created for it (and fsaverage is in talairach space). then you would use mri_binarize to threshold that volume down to just the voxel values at threshold, then find the remaining voxels and use those as the seed. you can save files with a .nii extension, for import into fsl's tools. see mri_surf2vol --help and mri_binarize --help
Nick
On Wed, 2008-12-10 at 17:19 +0000, Alexandru Hanganu wrote:
Hello All,
Can you please tell me, when we get the results from QDEC {$SUBJECTS_DIR/qdec/Untitled/lh-Avg-thickness-age-Cor/sig.mgh} how can we threshold the image and include it as a seed into FSL tractography ? What command line should I use ?
Thank you for your help, Best regards, Alexandru Hanganu. ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Alexandru Hanganu -
Nick Schmansky