External Email - Use Caution Hi Dr. Fischl,
It looks like *pctsurfcon* was the tool you were referring to. Is this the right one? Also, would brain.mgz be the appropriate volume to use to extract the G-W contrast ratios for the cortical parcels? Finally, for mri_cnr according to this post, the CNR values are computed using the voxels at the interface of the white and pial surface ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38829.html) Are these voxels offset from the white and pial surfaces by a specific default distance? Thanks, Prad On Thu, May 28, 2020 at 10:47 AM Pradyumna Bharadwaj <p...@email.arizona.edu> wrote: > Is it the pctsurfcon tool? ( > https://surfer.nmr.mgh.harvard.edu/fswiki/pctsurfcon) > > On Thu, May 28, 2020 at 10:12 AM Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > >> External Email >> >> David and Doug: can you point Prad in the right direction for looking at >> gray and white signal changes and ratios? >> On Thu, 28 May 2020, Pradyumna >> Bharadwaj wrote: >> >> > >> > External Email - Use Caution >> > >> > Hi Dr. Fischl, >> > Thank you for suggesting that. >> > Would it be possible to share a link to a page with information about >> this >> > stream or to a patch? >> > >> > Thanks, >> > Prad >> > >> > On Thu, May 28, 2020 at 9:46 AM Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> > wrote: >> > External Email >> > >> > I see. I think Doug has a more modern stream for this that David >> > Salat >> > has also used a lot >> > On Thu, 28 May 2020, Pradyumna Bharadwaj wrote: >> > >> > > >> > > External Email - Use Caution >> > > >> > > Hi Dr. Fischl, >> > > Thanks for confirming that! >> > > We were broadly interested in testing whether age-related >> > differences in >> > > cortical measures were impacted by the CNR in each ROI. >> > > >> > > Best, >> > > Prad >> > > >> > > On Thu, May 28, 2020 at 9:33 AM Bruce Fischl >> > <fis...@nmr.mgh.harvard.edu> >> > > wrote: >> > > External Email >> > > >> > > Hi Prad >> > > >> > > what is your goal? What you describe below should work >> > > >> > > cheers >> > > Bruce >> > > On Thu, 28 May 2020, >> > > Pradyumna Bharadwaj wrote: >> > > >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Hi Dr. Fischl, >> > > > Thank you for clarifying that! >> > > > >> > > > As a follow up question, I just wanted to double check >> > that >> > > the method >> > > > outlined in this post is still a valid approach to >> > obtaining >> > > the CNR values >> > > > for each of the ROIs in theDesikan-Killianyatlas( >> https://www.mail-archive.com/freesurfer@nmr.mgh.harva >> > rd.edu/msg62066. >> > > html) >> > > > . >> > > > >> > > > Briefly, you recommended converting the aparc >> > annotation to >> > > labels in the >> > > > atlas, and applying mri_cnr to each label. >> > > > >> > > > Best, >> > > > Prad >> > > > >> > > > On Thu, May 28, 2020 at 9:14 AM Bruce Fischl >> > > <fis...@nmr.mgh.harvard.edu> >> > > > wrote: >> > > > External Email >> > > > >> > > > Hi Prad >> > > > >> > > > if you use the cortex.label is will avoid using >> > the >> > > non-cortical >> > > > regions in >> > > > the surface, like the midline, so should be a >> > more >> > > accurate >> > > > measure >> > > > >> > > > cheers >> > > > Bruce >> > > > >> > > > >> > > > On Thu, 28 May 2020, Pradyumna Bharadwaj wrote: >> > > > >> > > > > >> > > > > External Email - Use Caution >> > > > > >> > > > > Hi, >> > > > > >> > > > > I had a question about the -label flag in >> > mri_cnr. >> > > > > >> > > > > 1) When you do not use the -label option and >> > just use >> > > the >> > > > following command: >> > > > > mri_cnr $FREESURFER_HOME/subjects/bert/surf >> > >> > > > $FREESURFER_HOME/subjects/be >> > > > > rt/mri/norm.mgz >> > > > > >> > > > > The output is as follows >> > > > > >> > > > > white = 96.6+-6.0, gray = 75.7+-13.5, csf = >> > > 55.3+-16.6 >> > > > gray/white CNR = 1. >> > > > > 983, gray/csf CNR = 0.907 >> > > > > >> > > > > lh CNR = 1.445 >> > > > > >> > > > > white = 96.4+-6.0, gray = 76.0+-13.3, csf = >> > 55.6+-16.2 >> > > > gray/white CNR = 1.95 >> > > > > 2, gray/csf CNR = 0.943 >> > > > > >> > > > > rh CNR = 1.448 >> > > > > >> > > > > total CNR = 1.446 >> > > > > >> > > > > >> > > > > 2) When you add -label >> > > > >> > $FREESURFER_HOME/subjects/bert/label/lh.cortex.label >> > > > > >> > $FREESURFER_HOME/subjects/bert/label/rh.cortex.label >> > > to the >> > > > first command, >> > > > > you get different (lower) cnr values. >> > > > > >> > > > > white = 96.6+-6.0, gray = 73.1+-18.9, csf = >> > 50.8+-20.5 >> > > > gray/white CNR = 1.38 >> > > > > 9, gray/csf CNR = 0.644 >> > > > > >> > > > > lh CNR = 1.016 >> > > > > >> > > > > white = 96.4+-6.0, gray = 73.4+-18.8, csf = >> > 51.0+-20.3 >> > > > gray/white CNR = 1.35 >> > > > > 3, gray/csf CNR = 0.652 >> > > > > >> > > > > rh CNR = 1.002 >> > > > > >> > > > > total CNR = 1.009 >> > > > > >> > > > > How is the lh.cortex and rh.cortex label >> > changing the >> > > CNR >> > > > computation? >> > > > > >> > > > > Any inputs or thoughts on this matter are >> > greatly >> > > appreciated! >> > > > > >> > > > > Thanks, >> > > > > Prad >> > > > > >> > > > >_______________________________________________ >> > > > 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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