Hi Martin,
probably the reviewer does not mean anything related to FS. Rather, there is distortion during image acquisition (e.g. gradient non- linearities). The reviewer probably wants to know if gradient unwarparing was done prior to running FS. That is why Matthew asked what MRI data was collected exactly (sequence, scanner etc).
Best, Martin
On Mon, 2019-05-13 at 21:06 -0700, Martin Juneja wrote:
External Email - Use CautionThank you Matthew for your reply.
I just ran recon-all to get cortical thickness, area and volume values for specific ROIs using the steps here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and correlated the morphometric values with behavioral data. I am not sure how can I address reviewer's comment.
Any help would be really appreciated.
On Mon, May 13, 2019 at 5:41 PM Glasser, Matthew glasserm@wustl.edu wrote:
External Email - Use CautionThere are different kinds of geometric distortion that affect your data to differing extents. What kind of MRI data was in your study?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Juneja mj70481@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, May 13, 2019 at 6:53 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Geometric distortion
External Email - Use CautionHi experts,
I have following question from one of the reviewers regarding recon-all pipeline: "Was geometric distortion corrected? If not, this should be discussed or mentioned in the study limitation." I was wondering if the reviewer is referring to following step in the recon-all pipeline. Could you please help me in addressing this concern by the reviewer?
Thanks. MJ Cortical Parcellation (-<no>cortparc, -<no>cortparc2) Assigns a neuroanatomical label to each location on the cortical surface. Incorporates both geometric information derived from the cortical model (sulcus and curvature), and neuroanatomical convention. Calls mris_ca_label. -cortparc creates label/?h.aparc.annot, and -cortparc2 creates /label/?h.aparc.a2005s.annot.
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