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.
________________________________
Notice: This UI Health Care e-mail (including attachments) is
covered by the Electronic Communications Privacy Act, 18 U.S.C.
2510-2521 and is intended only for the use of the individual or
entity to which it is addressed, and may contain information that
is privileged, confidential, and exempt from disclosure under
applicable law. If you are not the intended recipient, any
dissemination, distribution or copying of this communication is
strictly prohibited. If you have received this communication in
error, please notify the sender immediately and delete or destroy
all copies of the original message and attachments thereto. Email
sent to or from UI Health Care may be retained as required by law
or regulation. Thank you.
________________________________
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
Notice: This UI Health Care e-mail (including attachments) is
covered by the Electronic Communications Privacy Act, 18 U.S.C.
2510-2521 and is intended only for the use of the individual or
entity to which it is addressed, and may contain information that is
privileged, confidential, and exempt from disclosure under
applicable law. If you are not the intended recipient, any
dissemination, distribution or copying of this communication is
strictly prohibited. If you have received this communication in
error, please notify the sender immediately and delete or destroy
all copies of the original message and attachments thereto. Email
sent to or from UI Health Care may be retained as required by law or
regulation. Thank you.
________________________________
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
Notice: This UI Health Care e-mail (including attachments) is covered
by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and
is intended only for the use of the individual or entity to which it
is addressed, and may contain information that is privileged,
confidential, and exempt from disclosure under applicable law. If you
are not the intended recipient, any dissemination, distribution or
copying of this communication is strictly prohibited. If you have
received this communication in error, please notify the sender
immediately and delete or destroy all copies of the original message
and attachments thereto. Email sent to or from UI Health Care may be
retained as required by law or regulation. Thank you.
________________________________
_______________________________________________
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.
