Re: [Freesurfer] non-primate brains : for high res processing

I can speak of higher resolution images for recon processing.

Currently, "recon-all" script can take the option of "-cm" (conform to min voxel size). This may end up creating more slices than 256, but freesurfer should be able to handle as long as there are enough memory left. Make sure that you have 2 Gbyte of memory and 2 GByte of swap space. Here, we are approaching the 32 bit memory address limit. If you run out of memory, try reducing the number of slices. Freesurfer "recon" routines should be able to handle slices different from 256. (Exception: tkregister2 cannot handle more than 256 slices. I "cannot" speak for fsfast.)

Make sure that the direction cosines for animal brains match those of the human, i.e. x_(r,a,s), y_(r,a,s), z_(r,a,s), c_(r,a,s) are correct in the human brain sense. You may have to hand edit these values.

Too many freesurfer routines "assume" the uniform voxel sizes and thus the volume must be conformed to uniform voxel sizes.

You may see freesurfer routines fail on the high resolution images because of the highly grainy nature of the high resolution images. Therefore, you may have to run each routine by hand with additional options.

You may try "cheating" freesurfer routines by changing the voxel size to be 1 mm, even though the actual size is less than 1mm (i.e. editing orig/COR-.info information).

Tosa

Yasunari Tosa, Ph.D. R&D Engineer email: tosa@nmr.mgh.harvard.edu Mass. General Hospital NMR Center phone: Building 149 13th Street fax : Charlestown, MA 02129

Geoffrey Aguirre wrote:

Free surfers --

I am collecting data from dogs. Any advice regarding passing this 

data through the system? I have a couple of specific questions:

1. Should I acquire data with voxel sizes smaller than 1mm, given that

the brain is much smaller? How would I tell free-surfer to operate with this higher resolution data?

2. So far, automated skull stripping has been a failure, even with

definition of a "seed point" in the white matter. The routine strips away the brain around the seed point, leaving a large chunk of scalp and muscle with a bit of cortex attached. Any thoughts on how to get this going?

Thanks in advance for any help,

Geoff

--

Geoffrey Karl Aguirre, M.D., Ph.D. University of Pennsylvania Center for Cognitive Neuroscience 3815 Walnut Street Fax: (215) 898-1982 Philadelphia, PA 19104-6196 mailto:aguirre@neuro.med.upenn.edu http://ccn.upenn.edu/~aguirre

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer