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: [email protected] On 4/13/16, 12:34 PM, "[email protected] on behalf of Bruce Fischl" <[email protected] on behalf of [email protected]> 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: [email protected] > > > ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
