[Freesurfer] Tracula, adapt Freesurfer structure into other stucture hieraachy

2017-01-06 Thread Hao wen
Hello, Tracula expert: I am here again, I want to know right now, the 5.3 version tracula seems to only support Freesurfer recon-alled structure, so in the config file, it works like this: set subjlist = ( sub-PREVDEMALS0010001BE_ses-M0 ) because i want to apply tracula also into my own recon-

Re: [Freesurfer] Tracula, adapt Freesurfer structure into other stucture hieraachy

2017-01-06 Thread Yendiki, Anastasia
Hi Hao - The simplest way to get around this is to create under $SUBJECTS_DIR/ symbolic links to the subjects' recon-all directories, wherever those may be in your own hierarchy. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh

[Freesurfer] recon-all in stages with T2pial

2017-01-06 Thread miracle ozzoude
Hello Freesurfer, I was trying to run recon-all in stages (autorecon1, autorecon-2 and autorecon3) with T2. First, I ran autorecon1 with T2 (recon-all -autorecon1 -i input_volume -T2 /T2_volume -T2pial -s ) and i got an error (MRISread (./surf/lh.white): could not open file Loading mov Pro

Re: [Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans

2017-01-06 Thread Bruce Fischl
it shouldn't be, but it seems like it was complaining that the input wasn't "conformed". Can you run mri_info on the volume after you edited it? On Fri, 6 Jan 2017, Lucette Cysique wrote: Dear Bruce Many thanks We are doing the aseg edits in Freeview. Is that an issue? I will use the command

Re: [Freesurfer] Tracula, adapt Freesurfer structure into other stucture hieraachy

2017-01-06 Thread Hao wen
Hello: Ok, I got your point, thanks very much!!! BTW, look forward to the new version of Freesurfer Hao De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Yendiki, Anastasia Envoyé : vendredi 6 janvier 2017 14:59 À : Freesurfer support list Objet :

[Freesurfer] freeview error (libpng12.so.0) on Ubuntu

2017-01-06 Thread Jeffrey Crawford
Hello all! I know there are issues with freeview use on Ubuntu, but I hit a wall in fixing them. I am currently getting this error when typing "freeview" into the command prompt: "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file o