Dear FS guys,
I have run the FS 5.3 and get thickness files e.g. lh.thickness and rh.thickness, could FSL read these? should we use files like nii instead of mgz, or is there some options for FSL to read mgz too?
Thanks, Kaiming
Hi Kaiming
you can use mris_thickness to create a nifti thickness file if you want. They might be able to read .mgz, I'm not sure.
cheers Bruce On Wed, 4 Dec 2013, Kaiming Yin wrote:
Dear FS guys, I have run the FS 5.3 and get thickness files e.g. lh.thickness and rh.thickness, could FSL read these? should we use files like nii instead of mgz, or is there some options for FSL to read mgz too?
Thanks, Kaiming
We can create nifti files easily enough, but due to a shortcoming in the nifti header, it cannot represent structures with number of items exceeding 32k. The number of vertices is usually over 100k. If you use mri_surf2surf to do the conversion, you can "reshape" the structure size so that it fits, eg,
mri_surf2surf --s subject --hemi lh --sval lh.thickness --tval lh.thickness.nii --reshape
Note that this only works if the number of vertices has prime factors less than 32k
doug
On 12/04/2013 09:47 AM, Bruce Fischl wrote:
Hi Kaiming
you can use mris_thickness to create a nifti thickness file if you want. They might be able to read .mgz, I'm not sure.
cheers Bruce On Wed, 4 Dec 2013, Kaiming Yin wrote:
Dear FS guys, I have run the FS 5.3 and get thickness files e.g. lh.thickness and rh.thickness, could FSL read these? should we use files like nii instead of mgz, or is there some options for FSL to read mgz too?
Thanks, Kaiming
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Hi Bruce,
Yes I get the file rh.thickness.nii.gz, however it seems fs or fsl or imagej can not open it directly, should I add something?
cheers, Kaiming
it's a surface overlay (so one value per vertex), not a volume. You will probably want to use mri_surf2vol to sample it into the volume if you want fsl to open it On Wed, 4 Dec 2013, Kaiming Yin wrote:
Hi Bruce, Yes I get the file rh.thickness.nii.gz, however it seems fs or fsl or imagej can not open it directly, should I add something?
cheers, Kaiming
Hi Bruce,
I think I make it. I use the command like: mri_surf2vol --surfval subj/surf/rh.thickness --hemi rh --fillribbon --template subj/mri/orig.mgz --volregidentity subj/ --outvol subj/rh.ribbon.nii, and it works.
Last question on this is, once the surface file is changed into a volume file, how the file can be explained? In this case, I mean whether the brightness represents the cortical thickness, or the cortical itself in the image is drawn according to the thickness, so we can judge it directly from the image?
cheers, Kaiming
On Wed, Dec 4, 2013 at 5:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
it's a surface overlay (so one value per vertex), not a volume. You will probably want to use mri_surf2vol to sample it into the volume if you want fsl to open it
On Wed, 4 Dec 2013, Kaiming Yin wrote:
Hi Bruce,
Yes I get the file rh.thickness.nii.gz, however it seems fs or fsl or imagej can not open it directly, should I add something?
cheers, Kaiming
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Kaiming Yin