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
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