[Freesurfer] Assertion failed at line 827

2012-06-02 Thread Kiley Seymour
FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Dr Kiley Seymour Alexander von Humboldt Postdoctoral Fellow Klinik für Psychiatrie und Psychotherapie Charité Campus Mitte Charitéplatz 1 D-10117 Berlin tel: 0049-(0)30-450

[Freesurfer] mkbrainmask-sess

2012-03-23 Thread Kiley Seymour
Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -n

Re: [Freesurfer] mkbrainmask-sess

2012-03-25 Thread Kiley Seymour
Hi again, Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed? Thanks K From: Kiley Seymour To: "freesurfer@nmr.mgh.h

[Freesurfer] TR mismatch between analysis and data analysis

2012-03-26 Thread Kiley Seymour
trices   FreeSurfer Virtual Machine sudo password:  OLS Beta Pass    run 1    t= 0.0 :  FreeSurfer Virtual Machine sudo password:  ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0 From: Kiley Seymour To: "freesurfer@nmr.mgh.ha

[Freesurfer] Custom Fill does not fill

2012-03-30 Thread Kiley Seymour
Dear experts I have just completed all of the steps leading up to overlaying retinotopy activation on an inflated brain. I have been able to Make a Closed Path, but unfortunately when I press the Custom Fill nothing happens. Any ideas why this is the case. I have been using tksurfer-sess -c pol

[Freesurfer] mapping bow-tie retinotopy

2012-04-01 Thread Kiley Seymour
Dear freesurfers, I am wondering whether there is a simple way of analysing retinotopy data that was collected using a rotating bow-tie stimulus? Or should I somehow artificially segment the cycle into different visual field poition conditions and run a glm analysis? I just realised I have made a