External Email - Use Caution Thanks a lot Bruce.
On Tue, May 14, 2019 at 10:21 AM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > it's not the morphometric measures that are smooth, it is the gradient > nonlinearities. So they warp the gray and white surface by pretty much the > same amount and preserve the thickness (unless you are using a head-only > system, which you are not) > > On Tue, 14 May 2019, Martin Juneja wrote: > > > > > External Email - Use Caution > > > > Thank you so much Martin, Matthew and Bruce for all the detailed > information. > > Just to answer your question regarding MRI data: T1-weighted data were > collected using a 3.0 Tesla > > Siemens Tim Trio scanner (Siemens, Erlangen, Germany). T1-weighted > magnetization-prepared rapid > > gradient-echo (MPRAGE) images were collected over 176 sagittal slices > (TR/TE/flip angle = 2.1 > > s/2.25 ms/12°, 256 × 256 matrix) with voxel size = 1 × 1 × 1 mm. > > > > Also, I did not perform any gradient unwarping manually, so I am not > sure if this is done > > automatically. > > > > So as far as I understand from the discussion, to reply reviewer's > question, can I handle that > > something like this: > > > > "Geometric distortion of T1-weighted data was not manually corrected for > our current morphometric > > analysis. This is because T1-weighted data for this study were collected > using a 3.0 Tesla Siemens > > Tim Trio scanner. Gradient nonlinearity correction in most of the > scanners, including Siemens, has > > a relatively small/no effect on morphometric measures such thickness, > area and volume, because > > morphometric measures are spatially smooth and they warp both the white > and pial surfaces > > similarly. Therefore, the distance between these surface doesn't change > much. However, such effects > > can be very prominent in the periphery of the FOV. For instance, B0 > effects can be large > > and localized to regions near air/tissue interfaces (mostly inferior > frontal and inferior > > temporal). Since our results showed the association between morphometric > measures of MPFC and > > behavior (XYZ), therefore, our findings are not due to geometric > distortion." > > > > I am not expert in this field, so I would really appreciate any further > help. > > Thanks. > > > > > > > > On Tue, May 14, 2019 at 7:13 AM Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > > the gradient nonlinearities have almost no effect on thickness. > Since they > > are spatially smooth they warp both the white and pial surfaces > similarly, > > so the distance between them doesn't change much. > > > > B0 effects can be large locally depending on your field strength > and > > bandwidth. These are pretty localized to regions near air/tissue > interfaces > > (mostly inferior frontal and inferior temporal). If those are not > the > > regiosn you are finding thickness effects, then I think you are > safe > > concluding it is not geometric distortion. In any case unless the > > condition you are looking at modifies the air/tissue interface > it's hard to > > see why it would create an effect (although it can substantially > distort > > thickness values for low-ish bandwidth sequences). > > > > cheers > > Bruce > > > > On Tue, 14 May 2019, Martin Reuter 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 < > glass...@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-boun...@nmr.mgh.harvard.edu> on behalf of > Martin > > >>> Juneja <mj70...@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 > > > > > > _______________________________________________ > > > 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 > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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