Hi -- A quick (hopefully) question about img2stdcoord. My aim is to take thresholded group ("2nd level") stats performed on low-res functional data and get the maxima-coordinates in publishable MNI-coordinates. Have been attempting to so by with: /apps/linux/fsl-3.3/bin/img2stdcoord -verbose -img SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked -std avg152T1_brain -xfm MyFunctionalMask-to-MNI152_dof8.mat xyx.mat img2stdcoord can read/see all of the files (and reports correct values for vox dimensions and the like) EXCEPT the file with the coordinates (xyz.mat). The error message reads "Could not open matrix file xyx.mat" xyz.mat is just a plain vanilla .ascii format file: 1 2 3 4 5 6 (have also tried real coordinates, double spaces, and the like) If anyone has some advice, I would be grateful, Alex Shackman ---------------------------------------------------------- {full output from program} /apps/linux/fsl-3.2/bin/img2talcoord -verbose -img SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked -tal avg152T1_brain -vox -xfm MyFunctionalMask-to-MNI152_dof8.mat xyx.mat Talairach Volume:: SIZE = 91 x 109 x 91 Talairach Volume:: DIMS = 2 x 2 x 2 mm IMG Volume:: SIZE = 49 x 49 x 49 IMG Volume:: DIMS = 5 x 5 x 5 mm affmat = -0.000377 -0.984038 0.000460 205.183000 1.018640 -0.000362 0.005542 -6.167220 -0.005541 0.000446 1.018640 -84.861400 0.000000 0.000000 0.000000 1.000000 talvox2world = -2.000000 0.000000 0.000000 90.000000 0.000000 2.000000 0.000000 -126.000000 0.000000 0.000000 2.000000 -72.000000 0.000000 0.000000 0.000000 1.000000 Coordinates in Talairach volume (in mm): Could not open matrix file xyx.mat ------------------------------------ {directory contents} avg152T1_brain.hdr avg152T1_brain.img MyFunctionalMask-to-MNI152_dof8.mat SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked.hdr SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked.img xyz.mat all permissions = -rwxrwxrwx ---------------------------------- avwhd SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked filename SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked sizeof_hdr 348 data_type db_name extents 0 session_error 0 regular r hkey_un0 dim0 3 dim1 49 dim2 49 dim3 49 dim4 1 dim5 1 dim6 1 dim7 1 vox_units cal_units unused1 0 datatype 16 bitpix 32 pixdim0 0.0000000000 pixdim1 -5.0000000000 pixdim2 5.0000000000 pixdim3 5.0000000000 pixdim4 2.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 0.0000 funused1 0.0000 funused2 0.0000 funused3 0.0000 cal_max 4.7638 cal_min 0.0000 compressed 0 verified 0 glmax 0 glmin 0 descrip FSL3.2beta aux_file none orient 0 originator origin1 0 origin2 0 origin3 0 generated scannum patient_id exp_date exp_time hist_un0 views 0 vols_added 0 start_field 0 field_skip 0 omax 0 omin 0 smin 0 smin 0 file_type ANALYZE-7.5 file_code 0 ---------------------------------------------------------- avwhd avg152T1_brain Byte swapping filename avg152T1_brain sizeof_hdr 348 data_type dsr db_name T1.hdr extents 0 session_error 0 regular r hkey_un0 0 dim0 4 dim1 91 dim2 109 dim3 91 dim4 1 dim5 0 dim6 0 dim7 0 vox_units mm cal_units unused1 0 datatype 2 bitpix 8 pixdim0 0.0000000000 pixdim1 -2.0000000000 pixdim2 2.0000000000 pixdim3 2.0000000000 pixdim4 0.0000000000 pixdim5 0.0000000000 pixdim6 0.0000000000 pixdim7 0.0000000000 vox_offset 0.0000 funused1 1715.0446 funused2 0.0000 funused3 0.0000 cal_max 0.0000 cal_min 0.0000 compressed 0 verified 0 glmax 255 glmin 0 descrip ICBM AVG 152 T1 TAL LIN aux_file none orient 0 originator . origin1 46 origin2 64 origin3 37 generated scannum patient_id exp_date exp_time hist_un0 views 0 vols_added 0 start_field 0 field_skip 0 omax 0 omin 0 smin 0 smin 0 file_type ANALYZE-7.5 file_code 0 ---------------------------------------------------------- {contents of .xfm} -0.000377214 -0.984038 0.000459994 205.183 1.01864 -0.000361974 0.00554151 -6.16722 -0.00554134 0.000446339 1.01864 -84.8614 0 0 0 1 ---------------------------------------------------------- Alexander J. Shackman Laboratory for Affective Neuroscience Waisman Laboratory for Brain Imaging & Behavior University of Wisconsin-Madison 1202 West Johnson Street Madison, Wisconsin 53706 Telephone: +1 (608) 358-5025 FAX: +1 (608) 265-2875 EMAIL: [log in to unmask] http://psyphz.psych.wisc.edu/~shackman