Hi,
I'm now getting an error that it cannot read a necessary matfile. The log file is pasted below:
Thanks in advance, Cate
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mri_motion_correct.fsl log file $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ /Applications/freesurfer/bin//mri_motion_correct.fsl
/Volumes/phelpslab/Cate/extinction/AS083182 Darwin saks.psych.nyu.edu 8.9.1 Darwin Kernel Version 8.9.1: Thu Feb 22 20:55:00 PST 2007; root:xnu-792.18.15~1/RELEASE_I386 i386 i386 Tue Jun 12 13:59:15 EDT 2007 /Applications/freesurfer/bin//mri_convert /Applications/freesurfer/fsl/bin/flirt ----------------------------------------- Converting /Volumes/phelpslab/Cate/extinction/AS083182/mri/orig/002.mgz Tue Jun 12 13:59:17 EDT 2007 /Volumes/phelpslab/Cate/extinction/AS083182 mri_convert /Volumes/phelpslab/Cate/extinction/AS083182/mri/orig/002.mgz /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.img -odt float mri_convert /Volumes/phelpslab/Cate/extinction/AS083182/mri/orig/002.mgz /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.img -odt float reading from /Volumes/phelpslab/Cate/extinction/AS083182/mri/orig/002.mgz... TR=2500.00, TE=4.38, TI=900.00, flip angle=8.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) changing data type from 4 to 3 (noscale = 0)... writing to /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.img... Analyze Output Matrix -0.000 -0.000 -1.000 80.325; -1.000 -0.000 0.000 129.500; 0.000 -1.000 0.000 128.777; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /Volumes/phelpslab/Cate/extinction/AS083182/mri/orig/003.mgz Tue Jun 12 13:59:20 EDT 2007 /Volumes/phelpslab/Cate/extinction/AS083182 mri_convert /Volumes/phelpslab/Cate/extinction/AS083182/mri/orig/003.mgz /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img -odt float mri_convert /Volumes/phelpslab/Cate/extinction/AS083182/mri/orig/003.mgz /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img -odt float reading from /Volumes/phelpslab/Cate/extinction/AS083182/mri/orig/003.mgz... TR=2500.00, TE=4.38, TI=900.00, flip angle=8.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) changing data type from 4 to 3 (noscale = 0)... writing to /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img... Analyze Output Matrix -0.000 -0.000 -1.000 89.000; -1.000 -0.000 0.000 126.608; 0.000 -1.000 0.000 129.500; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img Tue Jun 12 13:59:22 EDT 2007 /Volumes/phelpslab/Cate/extinction/AS083182 fsl_rigid_register -maxangle 90 -r /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.img -i /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img -o /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/resampled.img -tmpdir /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476 -cleanup \n\n $Id: fsl_rigid_register,v 1.26 2007/06/12 15:11:07 greve Exp $ Tue Jun 12 13:59:23 EDT 2007 /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/resampled.img -------------------------------------- /Volumes/phelpslab/Cate/extinction/AS083182 mri_convert /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.img /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/refvol.fsl_rigid_register.nii mri_convert /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.img /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/refvol.fsl_rigid_register.nii matfile: only read 130 bytes of name (33554432 specified)
MatlabRead: readHeader returned NULL
reading from /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.img... WARNING: analyzeRead(): matfile /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. WARNING: could not find /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.mat file for direction cosine info. WARNING: Analyze 7.5 hdr->hist.orient value = -1, not valid. WARNING: assuming transverse flipped TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/refvol.fsl_rigid_register.nii... -------------------------------------- /Volumes/phelpslab/Cate/extinction/AS083182 mri_convert /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/invol.fsl_rigid_register.nii mri_convert /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/invol.fsl_rigid_register.nii matfile: only read 130 bytes of name (33554432 specified)
MatlabRead: readHeader returned NULL
reading from /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img... WARNING: analyzeRead(): matfile /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. WARNING: could not find /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.mat file for direction cosine info. WARNING: Analyze 7.5 hdr->hist.orient value = -1, not valid. WARNING: assuming transverse flipped TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/invol.fsl_rigid_register.nii... -------------------------------------- /Volumes/phelpslab/Cate/extinction/AS083182 tkregister2_cmdl --targ /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-1.img --mov /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/cor-2.img --reg /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/tkregister.dat --fslregout /Volumes/phelpslab/Cate/extinction/AS083182/mri/tmp-mri_motion_correct.fsl-12476/initxfm.fslmat --regheader --noedit --s doesnotmatter tcsh: tkregister2_cmdl: Command not found.