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
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
mri_vol2surf should work to resample the mask to the surface. Make sure to use nearest neighbor. Making it an actual label is a little bit trickier, however, you can create an annotation with mris_seg2annot
doug
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 _______________________________________________ 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
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Morgan,
I think you can do it in the tksurfer drawing interface (click the "add to existing label" button)
cheers, Bruce On Tue, 26 Jun 2007, 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ 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
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 _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 > _______________________________________________ > 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 >> _______________________________________________ >> 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Morgan Hough