Doug-

Any further thoughts on this?


On 10/05/2016 04:47 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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>
>
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