ERROR: dimension mismatch between y and X. - Freesurfer

6 Aug 2018


      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.