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 <greve@nmr.mgh.harvard.edu mailto:greve@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