Dear freesurfers
I want to convert an .mgh image to NIfTY format, but even when the conversion using "mri_convert" seems to be ok, when I try to open the nii, an error message appears "image doesn't appear to be a valid 2D or 3D image", there is any other way to convert an mgh image to nii?
In other cases when I tryed to convert other mgh's cointaining clusters extracted with matlab but saved with the same matrix header as "sig.mgh", FS says that nrows in volume exceeds 32768, and does not make the conversion? Any ideas?
Thanks in advanced, Gabriel.
Nifti can only handle 32k elements in any dimension. This is a problem for surfaces when they have upwards of 100k vertices. For our average subject (fsaverage and derivatives), this problem is solved by reshaping the number of vertices to be 27307x6=163842. If you are working with fsaverage, this should happen automatically (but might not for older FS versions). You can try converting to nifti using mri_surf2surf which offers a "--reshape" option.
doug
Gabriel Go.Es. wrote:
Dear freesurfers
I want to convert an .mgh image to NIfTY format, but even when the conversion using "mri_convert" seems to be ok, when I try to open the nii, an error message appears "image doesn't appear to be a valid 2D or 3D image", there is any other way to convert an mgh image to nii?
In other cases when I tryed to convert other mgh's cointaining clusters extracted with matlab but saved with the same matrix header as "sig.mgh", FS says that nrows in volume exceeds 32768, and does not make the conversion? Any ideas?
Thanks in advanced, Gabriel.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug Im using :
mri_surf2surf --sval $PATH/image.mgh --tval $PATH/image.nii --reshape --s my_avg_subject --hemi lh
and the nii output image still seems to be a not valit image, am I missign something?
Gabriel
Date: Fri, 27 May 2011 12:53:53 -0400 From: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mgh conversion
Nifti can only handle 32k elements in any dimension. This is a problem for surfaces when they have upwards of 100k vertices. For our average subject (fsaverage and derivatives), this problem is solved by reshaping the number of vertices to be 27307x6=163842. If you are working with fsaverage, this should happen automatically (but might not for older FS versions). You can try converting to nifti using mri_surf2surf which offers a "--reshape" option.
doug
Gabriel Go.Es. wrote:
Dear freesurfers
I want to convert an .mgh image to NIfTY format, but even when the conversion using "mri_convert" seems to be ok, when I try to open the nii, an error message appears "image doesn't appear to be a valid 2D or 3D image", there is any other way to convert an mgh image to nii?
In other cases when I tryed to convert other mgh's cointaining clusters extracted with matlab but saved with the same matrix header as "sig.mgh", FS says that nrows in volume exceeds 32768, and does not make the conversion? Any ideas?
Thanks in advanced, Gabriel.
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
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.
Use mri_info to see what it reshapes it to. You can also try adding --reshape-factor 6. doug
Gabriel Go.Es. wrote:
Dear Doug Im using :
mri_surf2surf --sval $PATH/image.mgh --tval $PATH/image.nii --reshape --s my_avg_subject --hemi lh
and the nii output image still seems to be a not valit image, am I missign something?
Gabriel
Date: Fri, 27 May 2011 12:53:53 -0400 From: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mgh conversion
Nifti can only handle 32k elements in any dimension. This is a problem for surfaces when they have upwards of 100k vertices. For our average subject (fsaverage and derivatives), this problem is solved by
reshaping
the number of vertices to be 27307x6=163842. If you are working with fsaverage, this should happen automatically (but might not for older FS versions). You can try converting to nifti using mri_surf2surf which offers a "--reshape" option.
doug
Gabriel Go.Es. wrote:
Dear freesurfers
I want to convert an .mgh image to NIfTY format, but even when the conversion using "mri_convert" seems to be ok, when I try to open the nii, an error message appears "image doesn't appear to be a valid 2D or 3D image", there is any other way to convert an mgh image to nii?
In other cases when I tryed to convert other mgh's cointaining clusters extracted with matlab but saved with the same matrix header as "sig.mgh", FS says that nrows in volume exceeds 32768, and does
not
make the conversion? Any ideas?
Thanks in advanced, Gabriel.
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
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.
Thank you again Doug,
I've tryed all the possibilities you said, but still not have a nii image, It says that it's reshaping to 6, but also when I change to another factor number it always says reshaping to 6, and the resultant nii image has still 163842 vertex so no program is able to read it, I'm working with FS version 5.0.
Gabriel
Date: Fri, 27 May 2011 16:58:33 -0400 From: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mgh conversion
Use mri_info to see what it reshapes it to. You can also try adding --reshape-factor 6. doug
Gabriel Go.Es. wrote:
Dear Doug Im using :
mri_surf2surf --sval $PATH/image.mgh --tval $PATH/image.nii --reshape --s my_avg_subject --hemi lh
and the nii output image still seems to be a not valit image, am I missign something?
Gabriel
Date: Fri, 27 May 2011 12:53:53 -0400 From: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mgh conversion
Nifti can only handle 32k elements in any dimension. This is a problem for surfaces when they have upwards of 100k vertices. For our average subject (fsaverage and derivatives), this problem is solved by
reshaping
the number of vertices to be 27307x6=163842. If you are working with fsaverage, this should happen automatically (but might not for older FS versions). You can try converting to nifti using mri_surf2surf which offers a "--reshape" option.
doug
Gabriel Go.Es. wrote:
Dear freesurfers
I want to convert an .mgh image to NIfTY format, but even when the conversion using "mri_convert" seems to be ok, when I try to open the nii, an error message appears "image doesn't appear to be a valid 2D or 3D image", there is any other way to convert an mgh image to nii?
In other cases when I tryed to convert other mgh's cointaining clusters extracted with matlab but saved with the same matrix header as "sig.mgh", FS says that nrows in volume exceeds 32768, and does
not
make the conversion? Any ideas?
Thanks in advanced, Gabriel.
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
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.
-- 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
Can you drop the image to me (don't email it). The drop site is below at the end of this email. doug
Gabriel Go.Es. wrote:
Thank you again Doug,
I've tryed all the possibilities you said, but still not have a nii image, It says that it's reshaping to 6, but also when I change to another factor number it always says reshaping to 6, and the resultant nii image has still 163842 vertex so no program is able to read it, I'm working with FS version 5.0.
Gabriel
Date: Fri, 27 May 2011 16:58:33 -0400 From: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mgh conversion
Use mri_info to see what it reshapes it to. You can also try adding --reshape-factor 6. doug
Gabriel Go.Es. wrote:
Dear Doug Im using :
mri_surf2surf --sval $PATH/image.mgh --tval $PATH/image.nii --reshape --s my_avg_subject --hemi lh
and the nii output image still seems to be a not valit image, am I missign something?
Gabriel
Date: Fri, 27 May 2011 12:53:53 -0400 From: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mgh conversion
Nifti can only handle 32k elements in any dimension. This is a
problem
for surfaces when they have upwards of 100k vertices. For our
average
subject (fsaverage and derivatives), this problem is solved by
reshaping
the number of vertices to be 27307x6=163842. If you are working with fsaverage, this should happen automatically (but might not for
older FS
versions). You can try converting to nifti using mri_surf2surf which offers a "--reshape" option.
doug
Gabriel Go.Es. wrote:
Dear freesurfers
I want to convert an .mgh image to NIfTY format, but even when the conversion using "mri_convert" seems to be ok, when I try to
open the
nii, an error message appears "image doesn't appear to be a
valid 2D
or 3D image", there is any other way to convert an mgh image
to nii?
In other cases when I tryed to convert other mgh's cointaining clusters extracted with matlab but saved with the same matrix
header
as "sig.mgh", FS says that nrows in volume exceeds 32768, and
does
not
make the conversion? Any ideas?
Thanks in advanced, Gabriel.
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
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.
-- 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
-
Douglas N Greve -
Gabriel Go.Es.