[Freesurfer] How does freesurfer take the individual landmarks of different regions take into acccount

Dear Bruce et al., Submitting a paper in which I use freesurfer for the analysis of the auditory cortex, I was asked how freesurfer actually takes individual boundaries (e.g. of Heschl's gyrus) into account? Both atlases (Desikan and Destrieux) are based on about 10-20 subjects. How are these

Re: [Freesurfer] Discrepancy between surface data of Heschl's gyrus and its image

in the individual subject coordinates or take the jacobians into account. cheers Bruce On Tue, 2 Apr 2013, Klein, Holger wrote: Dear Freesurfers, I averaged 42 subjects with make_average_subject focusing on Heschl's Gyrus and finally got the image attached (for both atlases (Desikan = Atlas I

[Freesurfer] make_average_subject failure

Dear Freesurfers, Command line: make_average_subject --out average --subjects ... (n=60) . . . . . Applying LTAtransformInterp (resample_type 1) writing to /Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/orig-A2/WE.mgh... ERROR: failure writing

[Freesurfer] mri_vol2surf visualization problem

Dear FreeSurfers, To get a better view on the pial surface of the Heschl' Gyri I used the command mri_vol2surf after having created the suitable volume with label2vol. My goal is to get the pial surface of this single label. My Command is: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --surf pial

Re: [Freesurfer] mri_vol2surf visualization problem

output format should I use for the surface I create with this command? Thanks, Holger 2012/2/16 Bruce Fischl fis...@nmr.mgh.harvard.edu p.s. could you cc the list on your replies so others can learn (I did on mine) On Thu, 16 Feb 2012, Klein, Holger wrote: Dear Bruce, Thanks for your help

Re: [Freesurfer] mri_vol2surf visualization problem

Bruce Fischl fis...@nmr.mgh.harvard.edu what is your command line? That isn't an error - it just detects that the patch isn't flattened and so will show it in the original space. Does it show up? On Thu, 16 Feb 2012, Klein, Holger wrote: Dear Bruce, The patch (only 16 kb

Re: [Freesurfer] mri_vol2surf visualization problem

Dear Bruce, I tried it again, and it worked out well. Mea culpa - I'm deeply sorry. Is there a chance to load the patch in freeview? Thanks a lot, Holger 2012/2/16 Klein, Holger klein.hol...@googlemail.com Dear Bruce, Command for the patch: label2patch wh lh lh.G_temp_sup-G_T_trans.label

[Freesurfer] mri_vol2surf

Dear FreeSurfers, To get a better view on the pial surface of the Heschl' Gyri I used the command mri_vol2surf after having created the suitable label with (label2vol). My goal is to get My Command was: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --srcreg register.dat --out_type paint --o

[Freesurfer] Running mri_anatomical_stats on many subjects

Dear Freesurfers, Is there a possibility to run mri_anatomical_stats on many subjects? Otherwise it would be quite time_consuming. Many thanks, Holger ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Destrieux atlas 2002

Dear freesurfers, dear Mr. Destrieux, I have a question concerning the destrieux atlas 2002: I need a distinct label G_temp_sup-G_temp_transv_and_interm_S , which is only available in this atlas version. I tried using ?.atlas2002_simple.gcs, but this atlas does not output the requested label -

[Freesurfer] mri_annotation2label

Dear freesurfers, I have created labels by using the command: mri_annotation2label command (aparc.a2009s): Are these new labels only for the subject I mentioned in the last command or can I use them for other subjects aswell (e.g. in order to measure Volumetry of the auditory Cortex)? THX,

[Freesurfer] Auditory Cortex Labels missing

Dear Freesurfers, I'm looking for a suitable solution for Volumetry of the auditory Cortex. As a proxy for Heschl Gyrus I tried the Gyrus temporalis transversus label - as it is posted in the Color LUT. After typing: asegstats2table --subjects WD \ --segno 1034 \ --tablefile aseg.vol.table I