28 May
2020
28 May
'20
12:46 p.m.
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:
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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 in the Desikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.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