It says that in the input (IXI015-HH-1258-DTI-00.nii.gz) has only one frame, which probably means that it is not the right input
On 08/06/2018 04:33 PM, Renew Andrade wrote: > > External Email - Use Caution > > Hello Community! > > I have an issue while running dt_recon because as can be seen in the > output terminal there is some error in matrix dimensions. > > > Renes-MacBook-Air-2:~ andraderenew$ dt_recon --b > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt > > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt > > --i > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz > > --s /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_recon > --o /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon > -rwxrwxrwx 1 andraderenew staff 660396 Feb 23 2015 > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz > INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir > dt_recon logfile > Mon Aug 6 15:24:20 -05 2018 > VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ > setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir > cd /Users/andraderenew > /Applications/freesurfer/bin/dt_recon --b > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt > > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt > > --i > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz > > --s /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_recon > --o /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon > Renes-MacBook-Air-2.local > andraderenew > /usr/local/fsl/bin/eddy_correct > ECRefTP 0 > #@#------------------------------- > Converting input > Mon Aug 6 15:24:20 -05 2018 > cd /Users/andraderenew > mri_convert > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz > > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii > mri_convert.bin > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz > > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998806, -0.048201, -0.00797414) > j_ras = (-0.0487688, 0.993409, 0.10373) > k_ras = (-0.00292168, -0.103995, 0.994574) > writing to > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii... > > > #@#------------------------------- > Eddy/Motion Correct > Mon Aug 6 15:24:20 -05 2018 > cd > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/ectmp > eddy_correct > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii > 0 > processing > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec_tmp0000 > > > #@#------------------------------- > Fitting Tensors > Mon Aug 6 15:24:39 -05 2018 > gzip > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii > > > gzip > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii > > > cd /Users/andraderenew > mri_glmfit --y > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz > > --glmdir > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon > --dti > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt > > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt > > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ > cwd /Users/andraderenew > cmdline mri_glmfit.bin --y > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz > > --glmdir > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon > --dti > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt > > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt > > > sysname Darwin > hostname Renes-MacBook-Air-2.local > machine x86_64 > user andraderenew > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz > logyflag 1 > usedti 1 > glmdir /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon > Loading y from > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz > ... done reading. > Using DTI > Loading BValues from > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt > Found 16 bvalues > Loading BVectors from > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt > Found 16 bvectorss > Detected BVec file as FSL formatted > Saving design matrix to > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/Xg.dat > Computing normalized matrix > Normalized matrix condition is 63.8107 > Matrix condition is 4.98981e+06 > Pruning voxels by thr: 1.175494e-38 > Found 253458 voxels in mask > Saving mask to > /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/mask.nii.gz > search space = 1552430.250000 > ERROR: dimension mismatch between y and X. > y has 1 inputs, X has 16 rows. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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