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Thanks for clarifying that! Just one more question: For either pctsurfcon or mri_cnr, is brain.mgz the more appropriate volume to extract the g-w contrasts or g-w or g-csf CNR values from cortical parcels? (compared to norm.mgz)
Thanks, Prad
On Fri, May 29, 2020 at 9:32 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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Hi Prad
for mri_cnr, yes, it samples inwards and outwards 1mm along the surface normal. And I think pctsurfcon is the tool I meant, but hopefully David and/or Doug can confirm cheers Bruce On Fri, 29 May 2020, Pradyumna Bharadwaj wrote:
External Email - Use CautionHi 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 prad@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 fischl@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 <fischl@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 > <fischl@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 intheDesikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.ha
rva > 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 > > <fischl@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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