Hi Russ,

I haven't been able to replicate your problem. As Anderson writes it should find it even without the explicit path. The search rules for config files are 

When you specify --config=my_file, i.e. without explicit path or extension, fnirt will search for ./my_file, ./my_file.cnf, ${FSLDIR}/etc/flirtsch/my_file and ${FSLDIR}/etc/flirtsch/my_file.cnf in that order and use the first one that is found.

and if an explicit path is specified it should use that. For my version all that seems to work. It basically tests to append and prepend the relevant strings and then attempts to open the file until it succeeds. In your case it must therefore fail to open the file when it resides in /space/raid/fmri/fsl-4.1.0-centos5_64/etc/flirtsch/ . What happens if you specify the full path on the command line, i.e.

space/raid/fmri/fsl-4.1.0-centos5_64/bin/fnirt --in=highres_head --aff=highres2standard.mat --cout=highres2standard_warp --iout=highres2standard --jout=highres2standard_jac --config=/space/raid/fmri/fsl-4.1.0-centos5_64/etc/flirtsch/T1_2_MNI152_2mm 

--ref=standard_head --refmask=standard_mask --warpres=10,10,10

?

Jesper

On 26 Aug 2008, at 06:19, Russ Poldrack wrote:

Hi Anderson - thanks. unfortunately changing it to the absolute path does not seem to have worked when running it from the GUI or command line. Any other suggestions?

Cheers,

Russ

On Mon, Aug 25, 2008 at 3:37 PM, Anderson Winkler <[log in to unmask]> wrote:

Hi Russ,

People from the FMRIB may give a better answer, but I noticed that FNIRT can
find the default config files (like T1_2_MNI152_2mm) even without the
extension .cnf or the full path (as long as $FSLDIR is properly set).  In
any case, you may try editing the file ${FSLDIR}/etc/fslconf/feat.tcl,
changing the last line, where it reads:

set fmri(fnirt_config) "T1_2_MNI152_2mm"

for:

set fmri(fnirt_config)
"/space/raid/fmri/fsl-4.1.0-centos5_64/etc/flirtsch/T1_2_MNI152_2mm.cnf"

to see if this solves the problem when calling from the GUI.

Anderson

--
Russell A. Poldrack, Ph.d.
Professor
Wendell Jeffrey and Bernice Wenzel Term Chair in Behavioral Neuroscience
UCLA Department of Psychology
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