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
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
