So the result of step 4 looks ok on the volume but not on the surface? How are you putting the volume-based ROI back on the surface? This is tricky because now it will be a 1mm thin label. You should use mri_vol2surf for this, maybe selecting the --projfrac-max to make sure that it grabs the value.


On 10/5/16 5:47 PM, Joel Bruss wrote:
Doug-

I'm sooo close but something isn't right.  I've run:

1)mri_vol2sur to sampel the ROI in subA surface space

2) mri_cor2label to convert it to a label

3) mri_label2lable to push it to subB

4) mri_label2vol to get back to a a volume

Steps 1-3 look great.  The output of step 4, loaded on subB inflated
surface looks cut off.  I suspect this is because it's actually down in
volume space now?  If I load the ROI over the wmparc file for subB, it
fits, it's just that I only have a strip of voxels on the WM surface
only.  I chose  the wmparc.mgz file for subB for both "--temp" and
''--regheader."  The result is the same if specify "--surf pial" or
choose nothing, it's also the same if I chose orig.mgz or brainmask.mgz
for the temp/header options.  How do I get the ROI to "fill in" like it
is in subA, originally?

I've attached a composite of the steps I've run.  I really hate to keep
pestering the listserv with this.  My apologies.

-Joel

On 10/04/2016 03:03 PM, Douglas N Greve wrote:
mri_label2vol will transfer it into the volume, no need for surf2vol

On 10/04/2016 03:54 PM, Joel Bruss wrote:
Doug (Bruce and Trisanna)-

Thank you all for your help.  I do, indeed, have a volume, then label,
and see now how to load and view this properly. I've gotten through the
"label2label" step and now have a label (from subA)  in subB space.  If
I now want to back-project this label to subB's input MRI volume, would
I run the following?

(Assuming I invert the steps I did to get the original binary mask to
subA's surface, as a label)

mri_label2vol --label $SUBJECTS_DIR/subA/tmpdir/rh.roi_to_subB.label \
--subject subB \
--temp brainmask.mgz \
--regheader brainmask.mgz \
--o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \
--surf pial

mri_surf2vol --surfval $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \
--volregidentity subB --template $SUBJECTS_DIR/subB/mri/orig.mgz --hemi rh \
--o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB_orig.mgz


"label2vol" works but I'm now stuck on the "surf2vol" command. I end up
with the following error:

ERROR: dimension inconsistency in source data
          Number of surface vertices = 128997
         Number of value vertices = 16777216

-Joel





On 10/04/2016 02:45 PM, Douglas N Greve wrote:
The rh.roiS.mgh file is a surface overlay (ie, one value per vertex),
not a surface itself (which would have a list of vertices, the XYZ for
each, and neighborhood relations). When you loaded rh.roiS.mgh as a
surface overlay, did you change the threshold to be 0.5? The default is
2, and if your ROI is binary (0,1), then no voxels would ever appear
above threshold


On 10/03/2016 03:20 PM, Joel Bruss wrote:
Sorry, it sent before I finished. I'll try this again.

On 09/30/2016 02:00 PM, Douglas N Greve wrote:
First, bring up the ROI on the volume along with the surface in the
volume. You can do this with FreeView. Make sure that the ROI intersects
the surface.
Yes, this looks fine
Then run mri_vol2surf so sample the binary ROI volume onto
the surface.
This is what I ran:

mri_vol2surf  --src $SUBJECTS_DIR/subA/tmpdir/roi.mgz \
--out $SUBJECTS_DIR/subA/tmpdir/rh.roiS.mgh \

You can view the ROI on the surface by loading it as an
overlay.
This is a volume or a surface now? Is it just a volume resampled to the

surface space? I can't get it to load in freeview as a surface (it just
crashes), and it doesn't look like anything as an overlay.


Then run mri_cor2label using the surface-sampled ROI as input
and specifying --surf (see the --help) to make this a surface-based
label.
I next ran this:
mri_cor2label --id 1 --c $SUBJECTS_DIR \
--i $SUBJECTS_DIR/subA/tmpdir/rh.roiS.mgh \
--l $SUBJECTS_DIR/subA/tmpdir/rh.roi.label \
--surf subA rh
You can also view this label in the surface in freeview.
At this point, it just kept loading and loading and loading and I'd
finally have to kill the process. I never could visualize this output.
      Finally,
run mri_label2label using the --regmethod surface
At this point, I must just be feeding bad data into good commands:
mri_label2vol --label $SUBJECTS_DIR/subA/tmpdir/rh.roi_to_subB.label \
--subject subB \
--temp brainmask.mgz \
--regheader brainmask.mgz \
--o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \
--surf pial

I don't know where things went wrong or how to view the output to diagnose.



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