Hi,
I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label?
Thanks for help, John
try mri_cor2label
John Gelburg wrote:
Hi,
I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label?
Thanks for help, John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thanks, but isn't COR volume and my ANALYZE image is not the same thing?
On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
try mri_cor2label
John Gelburg wrote:
Hi,
I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label?
Thanks for help, John
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
It will still work.
from mri_cor2label --help :
Note: the name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc).
John Gelburg wrote:
thanks, but isn't COR volume and my ANALYZE image is not the same thing?
On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
try mri_cor2label John Gelburg wrote: Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
I am sorry, but I still struggle to make it work :( Here is my syntax: mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label I am getting "ERROR: must supply a label id" error message. I do not have any label id, because it's my custom mask, which was created in the SPM.
On Fri, Apr 9, 2010 at 11:14 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
It will still work.
from mri_cor2label --help :
Note: the name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc).
John Gelburg wrote:
thanks, but isn't COR volume and my ANALYZE image is not the same thing?
On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
try mri_cor2label
John Gelburg wrote:
Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
what is the value of the binary volume? You have to tell mri_cor2label that with --id <binary value> I think.
cheers Bruce
On Sun, 11 Apr 2010, John Gelburg wrote:
I am sorry, but I still struggle to make it work :( Here is my syntax: mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label I am getting "ERROR: must supply a label id" error message. I do not have any label id, because it's my custom mask, which was created in the SPM.
On Fri, Apr 9, 2010 at 11:14 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
It will still work.
from mri_cor2label --help :
Note: the name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc).
John Gelburg wrote:
thanks, but isn't COR volume and my ANALYZE image is not the same thing?
On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
try mri_cor2label
John Gelburg wrote:
Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The id is the value in the mask. So if it's a binary mask, use --id 1
John Gelburg wrote:
I am sorry, but I still struggle to make it work :( Here is my syntax: mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label I am getting "ERROR: must supply a label id" error message. I do not have any label id, because it's my custom mask, which was created in the SPM.
On Fri, Apr 9, 2010 at 11:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It will still work. from mri_cor2label --help : Note: the name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc). John Gelburg wrote: thanks, but isn't COR volume and my ANALYZE image is not the same thing? On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: try mri_cor2label John Gelburg wrote: Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Thank you. I succeeded to convert it, but the label is completely incorrect. Actually, I can not understand how exactly it can work: when I make an opposite direction with mri_label2vol I pass the registrer.dat file; however, in mri_cor2label there is no such option. How then this transformation can be achieved?
On Mon, Apr 12, 2010 at 7:01 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The id is the value in the mask. So if it's a binary mask, use --id 1
John Gelburg wrote:
I am sorry, but I still struggle to make it work :( Here is my syntax: mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label I am getting "ERROR: must supply a label id" error message. I do not have any label id, because it's my custom mask, which was created in the SPM.
On Fri, Apr 9, 2010 at 11:14 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It will still work.
from mri_cor2label --help :
Note: the name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc).
John Gelburg wrote:
thanks, but isn't COR volume and my ANALYZE image is not the same thing? On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: try mri_cor2label John Gelburg wrote: Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
John Gelburg