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
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