[Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

2017-04-08 Thread Antonin Skoch
Dear experts, I noticed inconsistency between recon-all -help and actual code of recon-all in -autorecon2-wm option. According to the recon-all --help the -autorecon2-wm processes stages 15-23 (fill through make white surfaces) and -autorecon2-cp processes stages 12-23 (normalization2 throuhgh

[Freesurfer] segmentation help

2017-04-08 Thread Dilip Puri
Hi all, I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment HippoCampus. My input file xyz.img and output file will be like xyz_seg.img which contains only hippocampus image it like Grond Truth image for my original input image. Here is sample files including original and segm

Re: [Freesurfer] Freeview

2017-04-08 Thread Ruopeng Wang
Existing labels are the labels that the current loaded volume contains. For example, 1109 exists in the look up table. But the volume you loaded does not contain that label. So it is not possible to show that label for the volume. Ruopeng > On Apr 8, 2017, at 6:53 AM, N Saf wrote: > > Dear Fr

[Freesurfer] Freeview

2017-04-08 Thread N Saf
Dear FreeSurfer experts, I have two questions please. 1- I cannot understand the concept of "existing labels". Why few labels (such as #19) do exist in the LUT, but they cannot be overlaid on the brain? What should I do if I need to map one of those labels on the brain that disappear when I press

Re: [Freesurfer] withdrawing from the mailing list.

2017-04-08 Thread Paolo
You porbably already received a reply to your question, in any case, to unsubscribe completely or receive a daily digest only, you can use this link https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer and go to the bottom of the page, to this section: *"To unsubscribe from Freesurfer, g