Thanks. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text
> -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, August 13, 2014 10:51 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] quick pointer: tool to extract gray/white contrast > vectors from [lr]h.w-g.pct.mgh > > use mri_convert with the --ascii flag > > --ascii > save output as ascii. This will be a data file with a single column of data. > The > fastest dimension will be col, then row,then slice, then frame. > > > On 08/13/2014 10:11 AM, Krieger, Donald N. wrote: > > > > I just want print the list of vertices with their contrast percentages > > into an ascii file. > > > > Regards, > > > > Don > > > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of > *Douglas > > Greve > > *Sent:* Wednesday, August 13, 2014 10:09 AM > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] quick pointer: tool to extract gray/white > > contrast vectors from [lr]h.w-g.pct.mgh > > > > > > I guess I don't understand what it is you want exactly. the gray/white > > contrast file is in the surf folder. Do you want to compute a mean > > over a given set of vertices? > > > > On 8/13/14 10:06 AM, Krieger, Donald N. wrote: > > > > Here is a fragment of the help text for recon-all which pointed me > > towards this: > > > > WM/GM Contrast (-<no>pctsurfcon) > > > > Computes the vertex-by-vertex percent contrast between white and > > gray matter. > > > > The computation is: > > > > 100*(W-G) > > > > pct = --------- > > > > 0.5*(W+G) > > > > The white matter is sampled 1mm below the white surface. The gray > > matter is > > > > sampled 30% the thickness into the cortex. The volume that is > > sampled is > > > > rawavg.mgz. The output is stored in the surf dir of the given > > subject as > > > > ?h.w-g.pct.mgh. Non-cortical regions (medial wall) are zeroed. > > > > It is this "pct" value along with the coordinates of the vertex > > that I am interested in. > > > > Regards, > > > > Don > > > > Don Krieger, Ph.D. > > > > Department of Neurological Surgery > > > > University of Pittsburgh > > > > (412)648-9654 Office > > > > (412)521-4431 Cell/Text > > > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of > > *Douglas Greve > > *Sent:* Wednesday, August 13, 2014 10:01 AM > > *To:* freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > *Subject:* Re: [Freesurfer] quick pointer: tool to extract > > gray/white contrast vectors from [lr]h.w-g.pct.mgh > > > > > > What do you mean by contrast vectors? > > > > On 8/13/14 9:36 AM, Krieger, Donald N. wrote: > > > > What is the tool to extract the contrast vectors from surf/[ > > lr]h.w-g.pct.mgh ? > > > > Thanks, > > > > Don > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto: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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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
