Newer version of linux changed the way cshell behaves which causes bbregister to crash in some instances.

Get a new version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister

doug

On 5/6/13 8:10 PM, Todd Thompson wrote:

Hi, all. I'm trying to refine my pial surfaces with a T2 (or, in this case, t2*) image and I'm running into an error inside bbregister/fslregister.

I'm running the command: recon-all -s gf04 -3T -autorecon3 -T2pial -T2 /mindhive/gablab/fluid/Analysis/Nipype/flash/gf04/tissue_parameters/T2star.mgz

and the recon process makes it to the point of #@# Refine Pial Surfs w/ T2/FLAIR

when it runs: bbregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/orig/T2raw.mgz --lta /mindhive/gablab/fluid/Data/gf04/mri/transforms/T2raw.lta --init-fsl --T2

bbregister does some initial processing, then calls fslregister, like so: fslregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/template.nii --reg /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister --dof 6 --fsvol brainmask

which immediately crashes with: /mindhive/gablab/fluid/Data/gf04 mri_convert ERROR: could not determine file for /mindhive/gablab/fluid/Data/gf04/mri/ERROR: /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister/refvol.fslregister.nii

And so on.

running the fslregister command manually and changing "brainmask" to "brainmask.mgz" seems to fix the problem (after manually creating/filling the appropriate tmp directory, of course).

Any thoughts?

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