Sorry for the delay. Answers below On 12/21/2015 03:58 PM, Woo, Jonghye wrote: > Dear Doug, > > I have following questions: I posted the question but no one answered it. > > 1. What is the best way to convert annotation to the segmentation mask > (volume)? mri_label2vol. Specify the annotation with the --annot flag. Run with --help to get more help. > > 2. I also asked the questions below. > I tried to use PALS B12 mask in fsaverage, and try to create a volume > mask (from the annot file). I used the command below: > mri_aparc2aseg --s my_subject --annot PALS_B12_Brodmann --o > PALS_B12_Brodmann_Mask.nii --annot-table lh_PALS_B12_table.txt > I’ve got the table from this command: mis_info > lh.PALS_B12_Brodmann.annot & mis_info rh.PALS_B12_Brodmann.annot > (https://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12) > After creating the mask, I compared the table and the mask but they > are not corresponding. Rather the labels in the segmentation mask was > corresponding to FreeSurferColorLUT.txt. How are you viewing this? If in tkmedit or freeview, are you specifying a color table? > > Do you have any suggestions? Thank you in advance. > > Best, > Jonghye > >> On Dec 21, 2015, at 11:50 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> Hi Jonghye, is this something that can be handled over email? Is is >> something that cannot be posted to the list? >> doug >> >> >> On 12/16/2015 11:08 AM, Woo, Jonghye wrote: >>> >>> Dear Doug, >>> >>> My name is Jonghye and I have a quick question in freesurfer. Can I >>> drop by your office for get some information this afternoon? Looking >>> forward to hearing from you. >>> >>> Best, >>> Jonghye >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto: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/ >> >
-- 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.
