Hi Doug,
I see what you mean now. mri_cor2label should do it. Thanks again.
Cheers,
-Morgan
Doug Greve wrote:
No, use mri_cor2label to create the label file. I think the 2nd
example matches what you want to do.
doug
Morgan Hough wrote:
Hi Doug,
Thanks for the ftp fix. I have downloaded these fine now.
I don't see a use case for making a label in mri_binarize's help.
When I project the volumes to surfaces I actually save them as nifti
files so I can keep using avwmaths++ when I want to. What I think I
am missing now is the way to make that into a label file that I can
then use to constrain mris_anatomical_stats to a particular patch of
the cortical ribbon. Can mri_binarize produce such a file? Is there
something I can feed its output into that would accomplish that?
Cheers,
-Morgan
Doug Greve wrote:
Sorry, should be accessible now. To do what you need, you can just
run mri_binarize on the output (or input) of vol2surf. I've put an
uptodate copy of mri_binarize there too.
doug
Morgan Hough wrote:
Thanks Doug,
I am having some trouble downloading this but the tksurfer
interface suffices for now.
I would still be interested in making a label from a volumetric
projection as this is something I can foresee being useful for
other things as well. Is there anyway to do this after a
mri_vol2surf projection? I would want to set a threshold and have
anything above that threshold be made into a label for that surface.
Cheers,
-Morgan
Doug Greve wrote:
I have a relatively new program that does this. Actually, it is
an old program with a cryptic name (mri_cor2label). I've put a new
(linux) version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label
See the help.
I don't know why mri_mergelabels does not work. Is it possible
that the tail command is platform dependent?
doug
Morgan Hough wrote:
Hi Bruce,
I have been using mri_vol2surf to project nifti volumes onto
subject surfaces but I am not sure I understand how to then
convert the ouput .mgh file into a label that can then be used to
sample the surface measures of that subject. I have attached an
image of one subject (con_2304_roi_lh_lat.tif) with one
volumetric ROI projected to the surface. As you can see it
contains perhaps three patches that I would like to treat as one
label with which I could then use to sample the surface measures
of the subject. Is this something I can do with mri_vol2surf?
If I draw three labels on that subjects' surface, how do you then
merge those labels together to be able to sample from the
combined area? I have tried mri_mergelabel but I get a tail error
when I try this:
mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o
lh.combo-it.label
tail: cannot open `+3' for reading: No such file or directory
tail: cannot open `+3' for reading: No such file or directory
Done
Cheers,
-Morgan
Bruce Fischl wrote:
Hi Morgan,
what format is your volume ROI in? I think Doug's mri_vol2surf
will do this. If you have it in our label format file, then just
loading it into tksurfer will work if all the vertex #s are -1
(it will sample it onto the surface)
Bruce
On Thu, 24 May 2007, Morgan Hough wrote:
I was wondering if I can make a cortical label from a volume
ROI from the commandline. I would like to extract thickness
values from a region defined in each subject's volume space.
Thanks in advance.
Cheers,
-Morgan
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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