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:
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


--
Max Swartz
Biochemistry and Biological Physics
Miami University | Oxford, OH
513.886.6574