[Freesurfer] dt_recon b-values and b-vectors

Howdy,

I'm trying to run *dt_recon* on some DTI data but seem to be having some trouble with the number of b-values and b-vectors not matching the number of data frames we have (see dt_recon logfile below).

Some basic parameters of our sequence are as follows:

- TR = 10 s - TE = 96.2 ms - slice thickness = 4 mm - FOV = 25.6 cm 9 25.6 cm - flip angle = 90 - slice orientation= axial - matrix size = 64 x 64 - maximum b value = 1,000.65

The scan was developed from the protocol described in the following paper: http://link.springer.com/content/pdf/10.1007%2Fs00429-013-0506-x.pdf

The scan is supposed to be in 30 directions, but we have 36 b-values and b-vectors. Our DTI EPI BRIK file contains 28 data frames. It is my understanding that these three values should match, but I am lost when it comes to execution of this task.

Our b-values, b-vectors, and dt_recon.log file are shown below:

*bval:* 0 999.4792194 999.2313486 1000.074909 998.9414996 999.2023637 1000.18885 0 999.3712757 998.6526501 999.0604376 998.6166688 1000.30379 998.9614892 0 998.9295058 998.802572 999.6841127 999.3692767 1000.26581 998.9774808 0 999.8200418 1000.64961 1000.268808 999.6821137 999.595159 999.5162001 0 999.8890059 999.7680689 999.378272 999.6581262 999.645133 998.8895267 0

*bvec:* 0 0 0 1 0 0 0.166 0.986 0 -0.11 0.664 0.74 0.901 -0.419 -0.11 -0.169 -0.601 0.781 -0.815 -0.386 0.433 0 0 0 0.656 0.366 0.66 0.582 0.8 0.143 0.9 0.259 0.35 0.693 -0.698 0.178 0.357 -0.924 -0.14 0.543 -0.488 -0.683 0 0 0 -0.525 -0.396 0.753 -0.639 0.689 0.341 -0.33 -0.013 -0.944 -0.524 -0.783 0.335 0.609 -0.065 -0.791 0.22 -0.233 -0.947 0 0 0 -0.004 -0.91 -0.415 -0.511 0.627 -0.589 0.414 0.737 0.535 -0.679 0.139 -0.721 0.884 -0.296 0.362 0.262 0.432 0.863 0 0 0 0.088 0.185 -0.979 0.294 -0.907 0.302 0.887 -0.089 -0.453 0.257 -0.443 0.859 0.086 0.867 -0.491 0.863 0.504 -0.025 0 0 0

dt_recon logfile Tue Jan 14 11:03:29 EST 2014 VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files /usr/local/freesurfer/bin/dt_recon --i /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK --s 802_ucni_FS --o /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --b /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec xoth2 swartzms /usr/share/fsl/5.0/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Tue Jan 14 11:03:29 EST 2014 cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files mri_convert /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii mri_convert /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii warning: string DATASET_NAME does not end with "~" $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK... AFNI Header Information ============================================ DATASET_RANK : spatial dims 3, sub-bricks 28 DATASET_DIMENSIONS: (64, 64, 35) TYPESTRING : 3DIM_HEAD_ANAT SCENE_DATA : view type 0, func type 2, verify 0 ORIGIN : (126.000000, -126.000000, -68.000000) DELTA : (-4.000000, 4.000000, 4.000000) IDCODE_STRING : CIR_2tEY1lHce4a BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.000000 max 128.024994 BRICK_STATS : min 0.000000 max 21.291500 BRICK_STATS : min 0.000000 max 29.162399 BRICK_STATS : min 0.000000 max 20.906200 BRICK_STATS : min 0.000000 max 20.719999 BRICK_STATS : min 0.000000 max 22.354900 BRICK_STATS : min 0.000000 max 21.723499 BRICK_STATS : min 0.000000 max 126.376999 BRICK_STATS : min 0.000000 max 21.332399 BRICK_STATS : min 0.000000 max 23.682100 BRICK_STATS : min 0.000000 max 20.807301 BRICK_STATS : min 0.000000 max 23.097000 BRICK_STATS : min 0.000000 max 23.482201 BRICK_STATS : min 0.000000 max 23.115200 BRICK_STATS : min 0.000000 max 119.787003 BRICK_STATS : min 0.000000 max 23.863899 BRICK_STATS : min 0.000000 max 22.267799 BRICK_STATS : min 0.000000 max 21.466900 BRICK_STATS : min 0.000000 max 22.947701 BRICK_STATS : min 0.000000 max 20.433399 BRICK_STATS : min 0.000000 max 20.641600 BRICK_STATS : min 0.000000 max 127.492996 BRICK_STATS : min 0.000000 max 22.346399 BRICK_STATS : min 0.000000 max 20.726400 BRICK_STATS : min 0.000000 max 21.634701 BRICK_STATS : min 0.000000 max 19.920799 BRICK_STATS : min 0.000000 max 20.998699 BRICK_STATS : min 0.000000 max 21.381701 BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 ==================================================================== INFO: number of frames dataset_rank[1] = 28 : numtypes = 28 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 128.024994 <--> actual max = 128.024704 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.291500 <--> actual max = 21.291540 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 29.162399 <--> actual max = 29.162401 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.906200 <--> actual max = 20.906200 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.719999 <--> actual max = 20.720045 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.354900 <--> actual max = 22.354910 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.723499 <--> actual max = 21.723537 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 126.376999 <--> actual max = 126.377357 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.332399 <--> actual max = 21.332430 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.682100 <--> actual max = 23.682091 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.807301 <--> actual max = 20.807331 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.097000 <--> actual max = 23.096958 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.482201 <--> actual max = 23.482182 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.115200 <--> actual max = 23.115194 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 119.787003 <--> actual max = 119.786865 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.863899 <--> actual max = 23.863934 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.267799 <--> actual max = 22.267784 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.466900 <--> actual max = 21.466867 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.947701 <--> actual max = 22.947695 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.433399 <--> actual max = 20.433388 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.641600 <--> actual max = 20.641575 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 127.492996 <--> actual max = 127.493370 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.346399 <--> actual max = 22.346439 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.726400 <--> actual max = 20.726437 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.634701 <--> actual max = 21.634733 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 19.920799 <--> actual max = 19.920761 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.998699 <--> actual max = 20.998676 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.381701 <--> actual max = 21.381670 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii...

#@#------------------------------- Eddy/Motion Correct Tue Jan 14 11:03:30 EST 2014 cd /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/ectmp eddy_correct /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii 0 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0000 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0001 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0002 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0003 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0004 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0005 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0006 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0007 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0008 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0009 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0010 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0011 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0012 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0013 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0014 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0015 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0016 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0017 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0018 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0019 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0020 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0021 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0022 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0023 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0024 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0025 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0026 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0027

#@#------------------------------- Fitting Tensors Tue Jan 14 11:10:32 EST 2014 cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files mri_glmfit --y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii --glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --dti /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files cmdline mri_glmfit --y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii --glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --dti /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec sysname Linux hostname xoth2 machine x86_64 user swartzms FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii logyflag 1 usedti 1 glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files Loading y from /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii Using DTI Loading BValues from /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval Found 36 bvalues Loading BVectors from /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec Found 36 bvectorss Detected BVec file as MGH formatted Saving design matrix to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/Xg.dat Normalized matrix condition is 23.5551 Matrix condition is 1.66263e+06 Pruning voxels by thr: 50.000000 Found 255 voxels in mask Saving mask to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/mask.nii search space = 16320.000000 ERROR: dimension mismatch between y and X. y has 28 inputs, X has 36 rows.

Any suggestions or insight you can provide is much appreciated.

Thanks in advance,

- Max