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For most scanners, gradient nonlinearity correction is a relatively small effect that is most prominent in the periphery of the FOV (it is a bit larger in the HCP custom scanner because of design constraints). For 3D structural images (e.g. T1w, T2w, FLAIR) there is a small amount of distortion in the readout direction as well. Both of these effects are much smaller than the distortion in the phase encoding direction of EPI images, which should always be corrected for.
Matt.
On 5/14/19, 4:59 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Reuter" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of mreuter@nmr.mgh.harvard.edu> wrote:
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 Caution > Thank 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 Caution > > There 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 Caution > > Hi 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. > > > > 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 > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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