There are two ways you can do this. 1. Make an expert options file with the contents mri_aparc2aseg --wmparc-dmax 100 Run run recon-all like recon-all -s subject -wmparc -expert YourXOptsFile
2. Look in recon-all.log for the mri_aparc2aseg command, cut and paste it into the terminal, add --wmparc-dmax 100, and run On 11/19/2014 11:34 AM, Michele Cavallari wrote: > Hi Douglas, thanks for your reply. Is there a way to rerun only WM > segmentation with the threshold option, without going through the > whole time-consuming FS pipeline? > Thank you! > > On Tue, Nov 18, 2014 at 10:37 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > The unsegmented is all the WM that is further than 5mm from > cortex. You can change the threshold so that it labels all of WM > regardless of the distance. Other than that, I don't have much to > suggest. > doug > > > On 11/18/14 6:13 PM, Michele Cavallari wrote: >> Hi, I am planning to perform some regional analysis of the >> frontal white matter as a whole, and asking here for >> suggestions/help. >> From the FS output wmparc.mgz I could select and merge the >> following labels to define my ROI >> >> parsorbitalis [4019, 3019] >> parstriangularis [4020, 3020] >> lateralorbitofrontal [4012, 3012] >> medialorbitofrontal [4014, 3014] >> rostralmiddlefrontal [4027, 3027] >> frontalpole [4032, 3032] >> superiofrontal [4028, 3028] >> caudalmiddlefrontal [4003, 3003] >> paracentral [4017, 3017] >> parsopercularis [4018, 3018] >> postcentral [4022, 3022] >> precentral [4024, 3024] >> rostralantcingulate [4026, 3026] >> >> However, a non-negligible portion of the subcortical frontal WM >> is classified as unsegmented WM [5001, 5002] by FS. Would you >> recommend any other FS output or template/atlas that I could use >> for the purpose of measuring MRI signal in the frontal WM? >> >> Thanks >> >> >> >> _______________________________________________ >> 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 > > > 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 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
