Thank you

And how could I get the ratio of gm/wm at each vertex, rather than the pct?

Nenad

On 2014-04-01 17:32, Douglas N Greve wrote:

The easiest way would be to edit pctsurfcon in the following way

Change set wm = $tmpdir/$hemi.wm.$ext To set wm = $outdir/$hemi.wm.$ext

and

set gm = $tmpdir/$hemi.gm.$ext To set gm = $outdir/$hemi.gm.$ext

This will create ?h.wm.mgh and ?h.gm.mgh in subject/surf

doug

On 04/01/2014 12:26 PM, N. Medic wrote:

...

Dear FreeSurfers,

The pctsurfcon calculates the contrast between the white and gray matter using the formula below and saves the output in the ?h.w-g.pct.mgh file, which can be used for analysis.

        100*(W-G)
 pct = ---------
       0.5*(W+G)

However, I would like to get separate measures of white and gray matter intensity, as well as a ratio of gray to white matter (as in the Salat 2009 and 2011 Neuroimage papers). How can this be done?

Your help will be greatly appreciated

Nenad

---

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Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Thanks again, it worked

Nenad

On 2014-04-01 17:58, Douglas N Greve wrote:

try fscalc lh.gm.mgh div lh.wm.mgh -o lh.ratio.mgh

doug

On 04/01/2014 12:42 PM, N. Medic wrote:

...

Thank you

And how could I get the ratio of gm/wm at each vertex, rather than the pct?

Nenad

On 2014-04-01 17:32, Douglas N Greve wrote:

...

The easiest way would be to edit pctsurfcon in the following way

Change set wm = $tmpdir/$hemi.wm.$ext To set wm = $outdir/$hemi.wm.$ext

and

set gm = $tmpdir/$hemi.gm.$ext

To set gm = $outdir/$hemi.gm.$ext

This will create ?h.wm.mgh and ?h.gm.mgh in subject/surf

doug

On 04/01/2014 12:26 PM, N. Medic wrote:

...

Dear FreeSurfers,

The pctsurfcon calculates the contrast between the white and gray matter using the formula below and saves the output in the ?h.w-g.pct.mgh file, which can be used for analysis.

         100*(W-G)
  pct = ---------
        0.5*(W+G)

However, I would like to get separate measures of white and gray matter intensity, as well as a ratio of gray to white matter (as in the Salat 2009 and 2011 Neuroimage papers). How can this be done?

Your help will be greatly appreciated

Nenad

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer