Hi,

I also had a question about mri_convert. We collected high resolution anatomicals on monkeys that are 384x384 (224 slices), but freesurfer requires them to be 256x256x256. To conform to 256x256x256 we called mri_convert as follows:

mri_convert -i ${targ_dir}/${conformed_vol} -o ${targ_dir}/${conformed_vol} --conform

We did not receive any error messages, but later in processing (skull stripping) we got a message indicating that we were still working at 384x384x384.

I have a few questions:

1. Are we calling mri_convert incorrectly? That is, is there a way to use mri_convert to conform 384x384x384 to 256x256x256?

2. We tried cropping the mgz files (after unpacking) to make them 256x256 using a simple loop in matlab, then ran mri_convert on the cropped images, as well as other processing scripts, and managed to make it to skull stripping without erroring. That is, we ended up with 256x256x256 Is this approach okay? Will we have problems later in processing? Did mri_convert conform the 224 slices to 256 by interpolating and re-sampling the data, or did it pad the data?

3. Is there a better way to do what we are trying to do?

thanks! Rosa

Bruce Fischl fischl@nmr.mgh.harvard.edu writes:

Hi BA,

you can specify -odt short and it will be 16 bits/voxel, but by definition it won't be conformed (which means 8 bits/voxel among other things)

cheers Bruce On Wed, 13 Jan 2010, Brain Apprentice wrote:

...

Hello,

I was just wondering if there was a way in mri_convert to conform a MRI scan so that the output file is 16-bit?

The reason I ask is that I am trying to create dual pipelines. One pipe for Freesurfer and the other pipe for SPM and it would be nice to use mri_convert to generate the data for both from DICOM files.

Thanks,

BA _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Rosa Lafer-Sousa Research Assistant, Bevil Conway Wellesley College - Neuroscience 106 Central Street Wellesley, MA

210-325-3185 rlaferso@wellesley.edu