First, I am a newcomer to the FreeSurfer community so bear with me.
I have installed a snapshot of FreeSurfer for OSX: freesurfer-Darwin- tiger-full.dmg
I seem to have everything working fine in terms of environment settings etc.
I created a subject directory and populated it with some T1 data using mksubjdirs and mri_convert (from an AFNI BRIK).
Now, upon running recon-all -sid <whatever> -stage1 I receive this output: INFO: SUBJECTS_DIR is /blah/blah/blah ######################################## program versions used $Id: recon-all-nmr,v 1.68 2005/07/07 04:59:34 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/ minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ !p$Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ ####################################### ERROR: cannot determine format of input
So, I decided maybe I should just write my own script to run the commands visible through the csurf GUI logfile. I was able to script up everything except when I hit the mri_fill() point, I receive this error: .... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find pons No such file or directory
Does anyone have any suggestions?
-T