Thanks Doug, I think it doesn't look good... but I am not an expert, could you give me an opinion based in the attached images please?
Left: tkmedit -f $SPM8_DIR/canonical/avg152T1.nii -overlay ROI45.nii -fthresh 0.5 Right: tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg $FREESURFER_HOME/average/mni152.register.dat
(in this case the ROI45_2mm.nii is the MNI_Frontal_Inf_Tri_L_roi.mat from MarsBar AAL-s, I have them in 1mm version as well).
When I created my own registration.dat file the visualization was similar.
Do you think that this could work better if I just used a subject by subject approach instead of using fsaverage? I just need to report the average thickness of some ROI-s back to SPM.
Thank you very much, Gari
On 2012-07-18, at 17:57, Douglas N Greve wrote:
On 07/17/2012 05:17 PM, Garikoitz Lerma Usabiaga wrote:
Thanks Doug,
I've done it with the one in SPM: tkmedit -f $SPM8_DIR/canonical/avg152T1.nii -overlay ROI45.nii -fthresh 0.5 is this ok or should I test it with the one from FSL as well? My partner is working with SPM and MarsBar.
That is ok. How does it look? Until it looks ok in the volume, it is not worth trying to map it onto the surface. doug
Both in FS and in SPM the ROI is the same, troubles start when I register it (spmregister) and try to visualize in the MNI305 fsaverage with tkmedit. After the mri_vol2surf the ROI is completely displaced (compared with the lh.aparc.annot or lh.aparc.2009a.annot, it is always bigger and displaced).
Do you think the problem is the registration between 152 and 305?
thanks! Gari
On 2012-07-17, at 19:43, Douglas N Greve wrote:
Hi Gari, Does it appear in the right place if you run tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -overlay ROI45.nii
doug
On 07/17/2012 01:20 PM, Garikoitz Lerma Usabiaga wrote:
Hi freesurfer experts, I want to use a volume based MNI152 ROI in Freesurfer, when I check it over fsaverage with the following command the ROI is not in the correct position...:
/ /tkmedit fsaverage T1.mgz -overlay ROI45.nii//-overlay-reg $FREESURFER_HOME/average/mni152.register.dat / / And I have the same problem when I convert it to surface: cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov ../../ROI2/ROI45.nii \ --reg $FREESURFER_HOME/average/mni152.register.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI45.mgh \ --reshape
- Is this a correct way of using it? Should I get proper results or I
am missing anything? and,
- Does it make sense creating a new fsaverage using the
/spm8/canonical/avg152T1.nii, then applying the ROI which is already in 152 space, and referring the cortical thickness of all the subjects to this "new fsaverage"? (the functional analysis is being carried in SPM as well).
Many thanks for your answers, Gari
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
