Hi David, I've tried to answer your questions below. doug
On 03/30/2018 01:48 PM, David Beeler wrote: > Hi all, > Sorry in advance, this is a bit of an annoying one! > > I am trying to use freesurfer's automatically generated MT label as a > parcel to constrain activity measured during a functional MT > localizer. I am currently doing my analysis in the volume and I'd like > to transform the MT surface label into the subject's volume functional > space (i.e. the same space as the sig.nii.gz for a particular > contrast), take the voxels in sig.nii.gz that are within the MT label, > and project them back onto the surface (preferably to be viewed as an > overlay with freeview). I will eventually run the analysis on the > surface as well (making this much less roundabout, but I also use > volume parcels so understanding how to correctly go between the volume > and surface is important to me). > > In my pipeline I start off by running preproc-sess, then I register > and transform my preprocessed functional data (fmcpr.nii.gz) to the > subject's anatomical (without upsampling). After doing mkanalysis and > mkcontrast, I run selxavg on this volume. So the functional data is > aligned with the anatomical, but still has low res dimensions. > > If it's not too much to ask, would it be possible to provide the > specific commands to do all these transformations properly? I'll > provide some of the commands I've tried below so you can see where I'm > going wrong: > > First I want to transform the MT label to the functional volume. I've > tried: > > mri_label2vol --subject $SUBJID --label > $SUBJECTS_DIR/$SUBJID/label/rh.MT.label --o > $OUTPUTDIR/rh.MT.volume.anat.nii.gz --temp > $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --identity --fill-ribbon --hemi rh > > ...which I would expect to put the label in high resolution anatomical > volume space (orig.mgz), but it doesn't fill the graymatter ribbon > nicely at all. I would have expected this to work. Can you send a pic? I just ran it myself, and it seemed to do ok. > > I then use mri_vol2vol to transform to functional/sig.nii.gz space (I > could also just downsample with mri_convert since I've already aligned > my sig.nii.gz to my anatomical, this gives me the same result). I am > using regheader here, is this okay? > > mri_vol2vol --regheader --mov $OUTPUTDIR.rh.MT.volume.anat.nii.gz > --targ meanfunc.nii.gz --o rh.MT.volume.func.nii.gz --nearest > > ...and this works pretty well, but it's a little sparse so I may need > to dilate it with mri_morphology. I think this step is fine. Why do this extra step? I think you could do it with a single call to mri_label2vol using --regheader and specifying the func template. Why are you using --regheader here instead of the register.dof6.lta? > > Next I use matlab to take the voxels in sig.nii.gz that are also in > rh.MT.volume.func.nii.gz and I save that as a new volume, say > constrainedsig.nii.gz. You can do this with mri_mask sig.nii.gz rh.MT.volume.func.nii.gz constrainedsig.nii.gz > Now I want to transform constrainedsig.nii.gz to the surface. I have > tried going directly using the register.dof6.lta generated from > preproc-sess: > > mri_vol2surf --mov constrainedsig.nii.gz --reg register.dof6.lta > --projfrac 0.5 --interp nearest --hemi rh --o > $OUTPUTDIR/constrainedsig_surface.nii.gz This should have worked. Try doing directly on the rh.MT.volume.func.nii.gz > > ... and this is in the right area, but its shape doesn't match the > shape of the original label. So I've also tried backtracking and doing > another vol2vol and then vol2surf with regheader: > > mri_vol2vol --regheader --mov constrainedsig.nii.gz --targ > $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --o > $OUTPUTDIR/constainedsig_anatvolume.nii.gz > > mri_vol2surf --mov constrainedsig_anatvolume.nii.gz --hemi rh > --regheader S02 --o $OUTPUTDIR/constrainedsig_anatsurface > > ...and while this ends up in the right place, it is really patchy > (looking kind of like twisty zebra stripes). Seems to me like it has > the wrong dimensions or something, but mri_info says it's the same > dimensions as the volume I originally created with mri_label2vol. > > Any help is much appreciated, thanks! > David > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
