Just an aside: if you acquire oblique (e.g. AC/PC aligned), and don’t want FS to rotate the volume back into the native scanner space as part of its “conformation” step, you can edit the s/qform of the NIFTI header to appear as a non-oblique acquisition. As Bruce noted, this isn’t a big deal, although avoiding the rotation in the conformation step does eliminate a resampling during the conformation step which will blur/smooth the data to a small degree.

cheers, -MH

-- Michael Harms, Ph.D.

----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu

On 4/13/16, 12:34 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

Hi Kate

I don't think that will matter. Try running it through from the original dicoms and see if things seem accurate. That isn't actually an artifact, it just looks strange because of the slight angle of the view. My guess is we will handle this fine

cheers Bruce

On Wed, 13 Apr 2016, Katherine Reiter wrote:

Hello freesurfer experts, I am working with a dataset that was acquired with oblique slices aligned to each participant's ac-pc line.

1. I've run a handful of subjects through mri_convert and the recon

stream and each subject has a slight abnormality in the ventral temporal regions. It's subtle but apparent in each acquisition (image attached and the abnormality is apparent at the red cross). We believed it to be an alignment issue due to the oblique slices. Is there any way to fix this abnormality?

2. Are there any different preprocessing steps that should be added to

mri_convert or the recon stream?

Thanks much in advance! Kate

Katherine Reiter, M.S.

Clinical Psychology Doctoral Student

Marquette University

Phone: (414) 288-3807Email: katherine.reiter@marquette.edu

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