On 12/01/2013 11:40 PM, Arash Nazeri wrote: > Hi all, > > I wanted to make sure how one could assign intensities from the > subjacent white matter voxels to the cortical surfaces using mri_vol2surf. > > Based on the documentation page --projfrac, if used with negative > values, would assign white matter values to the surface. I was > wondering if this holds true for other options such as projfrac-avg, > projfrac-max, projdist-max ... . Further, I wanted to make sure if the > third value, designated as del, means the minimum value that could be > projected to the surface. > For instance: --projdist-max 0 -4 0.1 means to assign the maximum > value in the distance 0-4 mm of the gray/white matter boundary to the > white matter, that is larger than 0.1 . You basically have the right idea (ie, negative values go into the white matter). I'm not sure exactly what you are asking in your example. If you want to go from the gray/white surface into the WM by 4 mm, I would use --projdist-max -4 0 0.1 or --projdist-max 0 4 -0.1 This will sample along the normal in 40 places spaced 0.1mm apart and return the maximum. Note that this does not assure that all points will be in WM because 4mm may put you into the GM on an adjacent bank (but for a T1 this will be dark so probably does not affect the max). > > In case of the local/global outliers, is there any good way of > finding, discarding, and replacement of these values, through > thresholding+resampling for instance? We don't have anything. > > Finally, I was wondering how it is possible to use these resulting mgh > files for group comparison in an uncached dataset, presumably using > mris_preproc. You can save them in the surf folder and then use "--meas yourfile.mgh" with mris_preproc.
I'm not sure what you are aiming for, but David Salat did a similar analysis http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073 This was done using the pctsurfcon program, so you might want to take a look at that doug > > Bests, > Arash > > > _______________________________________________ > 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.
