Hi,
I can not find my way to map the results of the FSL fMRI group analysis (FLAME1+2) from different subjects on their average surface. Here is in more details what I have done:
1. fMRI analysis of each subject in FSL 2. group analysis (FLAME1+2) in FSL 3. cortical reconstruction of each subject in FS 4. average subject, surface, volume in FS
and I would like to
a) project results of 2 on results of 4 b) project an ROI from histological atlas on a)
Is this doable? Thanks a lot in advance.
Martin
Hi Martin, I'll leave a) for Doug (and yes it is doable). For b) we'll need more info. What kind of atlas? Is it in some common space?
cheers, Bruce On Tue, 13 Nov 2007, Martin Kavec wrote:
Hi,
I can not find my way to map the results of the FSL fMRI group analysis (FLAME1+2) from different subjects on their average surface. Here is in more details what I have done:
- fMRI analysis of each subject in FSL
- group analysis (FLAME1+2) in FSL
- cortical reconstruction of each subject in FS
- average subject, surface, volume in FS
and I would like to
a) project results of 2 on results of 4 b) project an ROI from histological atlas on a)
Is this doable? Thanks a lot in advance.
Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for reply, Bruce
On Tuesday 13 November 2007 13:43:03 you wrote:
Hi Martin, I'll leave a) for Doug (and yes it is doable). For b) we'll need more info. What kind of atlas? Is it in some common space?
It is a Julich probabilistic histological atlas, which is a part of the latest FSL. I' am not 100% sure it is in common space, but I would guess it is.
Thanks,
Martin
Martin Kavec wrote:
Hi,
I can not find my way to map the results of the FSL fMRI group analysis (FLAME1+2) from different subjects on their average surface. Here is in more details what I have done:
- fMRI analysis of each subject in FSL
- group analysis (FLAME1+2) in FSL
- cortical reconstruction of each subject in FS
- average subject, surface, volume in FS
and I would like to
a) project results of 2 on results of 4 b) project an ROI from histological atlas on a)
Is this doable? Thanks a lot in advance.
Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what areas specifically? We have analyzed their data and have a paper accepted at Cerebral Cortex on the surface-based equivalent atlas, which is quite a bit more accurate than the linear or nonlinear volumetric ones, and are getting ready to release it for general use.
cheers, Bruce On Tue, 13 Nov 2007, Martin Kavec wrote:
Thanks for reply, Bruce
On Tuesday 13 November 2007 13:43:03 you wrote:
Hi Martin, I'll leave a) for Doug (and yes it is doable). For b) we'll need more info. What kind of atlas? Is it in some common space?
It is a Julich probabilistic histological atlas, which is a part of the latest FSL. I' am not 100% sure it is in common space, but I would guess it is.
Thanks,
Martin
Martin Kavec wrote:
Hi,
I can not find my way to map the results of the FSL fMRI group analysis (FLAME1+2) from different subjects on their average surface. Here is in more details what I have done:
- fMRI analysis of each subject in FSL
- group analysis (FLAME1+2) in FSL
- cortical reconstruction of each subject in FS
- average subject, surface, volume in FS
and I would like to
a) project results of 2 on results of 4 b) project an ROI from histological atlas on a)
Is this doable? Thanks a lot in advance.
Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bruce,
it's auditory cortex I am interested in. If there is a tutorial or explanation somewhere, could you please point me to it. Is this already available in FS?
Thanks Martin
On Tuesday 13 November 2007 14:38:52 you wrote:
what areas specifically? We have analyzed their data and have a paper accepted at Cerebral Cortex on the surface-based equivalent atlas, which is quite a bit more accurate than the linear or nonlinear volumetric ones, and are getting ready to release it for general use.
cheers, Bruce
we haven't distributed it yet, but it would just take the form of label maps with associated probabilities in fsaverage space. You would need to do our surface-based averaging for it to apply. We haven't gotten the auditory cortex data yet, but probably could if you were interested.
On Tue, 13 Nov 2007, Martin Kavec wrote:
Bruce,
it's auditory cortex I am interested in. If there is a tutorial or explanation somewhere, could you please point me to it. Is this already available in FS?
Thanks Martin
On Tuesday 13 November 2007 14:38:52 you wrote:
what areas specifically? We have analyzed their data and have a paper accepted at Cerebral Cortex on the surface-based equivalent atlas, which is quite a bit more accurate than the linear or nonlinear volumetric ones, and are getting ready to release it for general use.
cheers, Bruce
You mean you want to display your group volume-based results on the average surface? That's unusual, but it can be done. You need to create a registration file between your group average and the standard space templage, eg, something like:
fslregister --mov $FSLDIR/etc/standard/avg152T1.nii.gz --s youraveragesubject --reg register.dat
Check it visually:
tkregister2 --mov $FSLDIR/etc/standard/avg152T1.nii.gz --s youraveragesubject --reg register.dat --surf
Then render your FLAME results on the surface
tksurfer youraveragesubject lh inflated -overlay flamestat.nii.gz --overlay-reg register.dat
You can map the surface-based ROIs into the standard space with something like:
mri_label2vol --annot $SUBJECTS_DIR/youraveragesubject/label/lh.aparc.annot --temp FSLDIR/etc/standard/avg152T1.nii.gz --reg register.dat --subject ouraveragesubject --hemi lh --o lh.aparc.mni152.nii.gz
This will create a segmentation volume. The mapping between segmentation index and brain area can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt
doug
Martin Kavec wrote:
Hi,
I can not find my way to map the results of the FSL fMRI group analysis (FLAME1+2) from different subjects on their average surface. Here is in more details what I have done:
- fMRI analysis of each subject in FSL
- group analysis (FLAME1+2) in FSL
- cortical reconstruction of each subject in FS
- average subject, surface, volume in FS
and I would like to
a) project results of 2 on results of 4 b) project an ROI from histological atlas on a)
Is this doable? Thanks a lot in advance.
Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Martin Kavec