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/bert/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 = 1.952, 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 = 1.389, 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 = 1.353, 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
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.
- 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
- 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
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-Killiany atlas ( 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 CautionHi,
I had a question about the -label flag in mri_cnr.
- 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
- 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
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-Killiany atlas(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
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 CautionHi 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-Killiany atlas(
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
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 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
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 CautionHi 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 > <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
External Email - Use Caution
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 CautionHi 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 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 > <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
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 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 CautionHi 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 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 > <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
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 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 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
External Email - Use Caution
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:
External Email
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Prad
that is a hard question to answer. brain.mgz has been more aggressively bias corrected than norm and will have removed most of the variability in the wm. If gm is all you care about you could use it, but if you also care about wm you might use the norm (or even the nu)
cheers Bruce On Fri, 29 May 2020, Pradyumna Bharadwaj wrote:
External Email - Use Caution
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: External Email
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 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 pialsurface(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg3882 9.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 ROIsintheDesikan-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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I see. Thanks for answering all my questions!
Best, Prad
On Fri, May 29, 2020 at 9:45 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
External Email
Hi Prad
that is a hard question to answer. brain.mgz has been more aggressively bias corrected than norm and will have removed most of the variability in the wm. If gm is all you care about you could use it, but if you also care about wm you might use the norm (or even the nu)
cheers Bruce On Fri, 29 May 2020, Pradyumna Bharadwaj wrote:
External Email - Use CautionThanks 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: External Email
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 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 pialsurface(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg3882
9.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 theROIsintheDesikan-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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Pradyumna Bharadwaj