Hi Jonathan,

On Feb 20, 2010, at 10:15 AM, freesurfer-request@nmr.mgh.harvard.edu wrote:

Message: 2 Date: Fri, 19 Feb 2010 17:08:06 -0500 From: Jonathan Winkle jwink@mit.edu Subject: [Freesurfer] Distorted images To: freesurfer@nmr.mgh.harvard.edu Message-ID: 4B7F0BC6.3020207@mit.edu Content-Type: text/plain; charset="iso-8859-1"

Hi!

I'm new to freesurfer and I am trying to reconstruct some recent scans of a rhesus macaque. The dicoms appear to be fine, but after converting to cor files the images appear distorted. I have attached a screenshot as an example of what the images look like. For converting the dicoms to cor I used:

"mri_convert $path/1500-4-1.dcm $path/001 -ot COR -nc -sc 0.5"

I am using freesurfer 3 on ubuntu.

Any help you can give is much appreciated!

Have a look at the attached tar.gz, it contains the scripts I use to process rhesus data. Especially myscripts_anat might be helpful (and unpack_CIT.csh for how to import DICOM data). For me it works to go from macaque anatomical scans to reconstructed surfaces (but I never actually used the recons for morphometry so the thickness values might be completely off). I am sure there are other people on this list who can give more experienced advise regarding monkey processing, but until they comment have a look at my scripts :). What I do not know is, is whether the scripts in the attachement will reach the list... Oh, there is also a somewhat old copy of my "myscripts_anat" folder on the freesurfer wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData) but I would rather try the attached ones... (Oh well, these scripts were never meant to be distributed so they are full of typos and comments are often actually about older versions of the scripts, but hey better than nothing...)

Best Sebastian