Hi, I am having some difficulties performing motion correction on multiple structural runs in Freesurfer. In order to ensure that it is not my data which is problematic, I have tried to use register.csh on bert tutorial data. Following the instructions in the tutorial, I used the command:
register.csh 001 002 003 1reg in order to make a motion corrected data set from the three sturctural runs. However, I get the following error message from the afni binaries: **************** Cannot access /tmp/base+orig.HEAD: No such file or directory Cannot access /tmp/base+orig.BRIK: No such file or directory to3d: 2D slices into 3D datasets for AFNI, by RW Cox Reading images: 12 3D dataset written to disk testing Cannot access /tmp/new+orig.HEAD: No such file or directory Cannot access /tmp/new+orig.BRIK: No such file or directory to3d: 2D slices into 3D datasets for AFNI, by RW Cox Reading images: 12 3D dataset written to disk /tmp /home/jnsb/surfer_7.02/bert Cannot access base.res+orig.HEAD: No such file or directory Cannot access base.res+orig.BRIK: No such file or directory Program: adwarp.c Author: R. W. Cox and B. D. Ward Initial Release: 02 April 1999 Latest Revision: 15 August 2001 ** Error: -apar & -dpar are in same +view! annot access new.res+orig.HEAD: No such file or directory Cannot access new.res+orig.BRIK: No such file or directory Program: adwarp.c Author: R. W. Cox and B. D. Ward Initial Release: 02 April 1999 Latest Revision: 15 August 2001 ** Error: -apar & -dpar are in same +view! If this is OK, use -force and -prefix options. done resizing Cannot access dset+orig.HEAD: No such file or directory Cannot access dset+orig.BRIK: No such file or directory ** Couldn't open -base dataset base.res+orig[0] done registering Cannot open regist.afni: No such file or directory Cannot access reg.res+orig.HEAD: No such file or directory Cannot access reg.res+orig.BRIK: No such file or directory Subscript out of range ********************** So it seems that the AFNI binaries cannot find the afni datasets which have been placed in the /tmp directory (although I can see that they are there). I am not sure why that is...is there an environmental variable for freesurfer that controls this operation? OR alternatively, perhaps you could tell me the AFNI command lines, and flags, that are used by register.csh so that I may work-around this step via shell scripting. thanks in advance, Tim Souza ---------------------- Timothy Souza Brown University Department of Neuroscience [EMAIL PROTECTED] ph: 401-863-1258 fax: 401-863-1074 ------------------------