[Freesurfer] Parenchyma over CSF rartio

Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ? Tha

Re: [Freesurfer] mri_glmfit-sim error

Can you run mri_glmfit-sim with --debug as the first option, then capture the output by putting "|& tee new.log" (no quotes) and post new.log doug On 10/24/14 9:33 PM, wrz891...@163.com wrote: Thanks a lot ! It just stopped woking at the last line and it didn't generate the results ,so I

Re: [Freesurfer] permission denied

Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote: Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest

Re: [Freesurfer] (no subject)

Sorry, nothing has been decided yet. doug On 10/26/14 4:00 AM, Nagy Szilvia wrote: Dear Freesurfers, I would interest about when will the freesurfer course takes place in 2015? I realy need this info due to a travel grant deadline. Thanks, Szilvia Nagy

Re: [Freesurfer] Changing subject names after processing

Great, I'll do that. Thank you very much! Am 26.10.2014 um 17:12 schrieb Martin Reuter : > One possible solution: > Rename the time point in cross, in the base txt file (directly under the base > directory, something with tps in it), in the base/mri/transforms/* files and > in the long director

Re: [Freesurfer] Changing subject names after processing

One possible solution: Rename the time point in cross, in the base txt file (directly under the base directory, something with tps in it), in the base/mri/transforms/* files and in the long directory names and long/mri/transform files. I think these are all the places where subject names are sto

Re: [Freesurfer] Changing subject names after processing

Hi Janosch, You could do that, but no further processing will be possible. The long runs take the asegs from the cross sectional runs and many other results from the base. Without base and long they can probably be used for statistical analysis (the roi stuff should work ,  for surfaces the bas

Re: [Freesurfer] Changing subject names after processing

Hi Martin and Doug, thanks for your answers! >>> theoretically it would be sufficient to rename the longitudinal directories accordingly as the base should not change at all, only some of the filenames -- not tested! Did I understand it correctly that if one has gone through the whole longitu

Re: [Freesurfer] Freesurfer course 2015 Brazil

Thank you very much for your reply! Cheers, Andrea From: Pedro Paulo de Magalhães Oliveira Junior Sent: ‎Sunday‎, ‎October‎ ‎26‎, ‎2014 ‎7‎:‎19‎ ‎PM To: freesurfer@nmr.mgh.harvard.edu Cc: Andrea Horváth We don't have a date yet. An estimate would be March/April

Re: [Freesurfer] Freesurfer course 2015 Brazil

We don't have a date yet. An estimate would be March/April - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 O

[Freesurfer] permission denied

Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I tr

[Freesurfer] (no subject)

Dear Freesurfers, I would interest about when will the freesurfer course takes place in 2015? I realy need this info due to a travel grant deadline. Thanks, Szilvia Nagy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.h