Hi Christopher – If you have not resolved this, please send along the bvals and gradient table files. It seems to expect a 35th volume in your nifti file, which has 34 volumes.

Best,

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Ferrier, Christopher Q." <cferri@lsuhsc.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, September 5, 2017 at 5:50 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error with TRACULA using dcm and nii

Hi Freesurfer Team!. We are trying to use TRACULA to analyze the structural connectivity of PD patients scanned on a 3 tesla Philips Ingenia. We have run the tutorial data without any problems but encounter errors when using our own data. We ran recon-all on all of our subjects without any problem and follow the exact steps that worked for the tutorial data but encounter different errors when using the dcm or nii version of the DTI scans. Our nii files go from scanner to CD to Osirix to DICOM to dcm2nii which gives us the nii files and the bvals and bvecs.  Here is the error for the nii DTI scans (included bvals and gradients in the config file for the nii files). 
[Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial 
ERROR: flag -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial unrecognized
-prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial
[Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c /Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial 
INFO: SUBJECTS_DIR is /Volumes/CFERRIER/Freesurfer_temp/PD800/diffusion_recons
INFO: Diffusion root is /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT
Actual FREESURFER_HOME /Applications/Freesurfer
trac-preproc -c /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/dmrirc.local -log /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.log -cmd /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.cmd
#-------------------------------------
/Applications/Freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Thu Aug 31 14:45:46 CDT 2017
mri_convert --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999339, -0.0363145, -0.00163044)
j_ras = (-0.0363101, 0.99508, 0.0921851)
k_ras = (0.00172524, -0.0921834, 0.995741)
writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz...
cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvecs/PD800_bvecs.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs
cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvals/PD800_bvals.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals
orientLAS /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -9.1875
mri_convert -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 -ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 7.38609 19.7949 1.17333 -rt nearest /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 -ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 7.38609 19.7949 1.17333 -rt nearest /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz 
normalizing out_i_direction: (-0.999339, -0.0363145, -0.00163044) -> (-0.999339, -0.0363145, -0.00163044)
normalizing out_j_direction: (-0.0363101, 0.99508, 0.0921851) -> (-0.0363101, 0.99508, 0.0921851)
normalizing out_k_direction: (0.00172524, -0.0921834, 0.995741) -> (0.00172524, -0.0921834, 0.995741)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999339, -0.0363145, -0.00163044)
j_ras = (-0.0363101, 0.99508, 0.0921851)
k_ras = (0.00172524, -0.0921834, 0.995741)
Reslicing using nearest 
writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz...
INFO: found /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals, copying
INFO: found /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs, converting to LAS
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.bvecs /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.bvals /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals
eddy_correct /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz 0
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0000
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0001
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0002
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0003
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0004
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0005
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0006
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0007
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0008
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0009
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0010
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0011
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0012
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0013
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0014
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0015
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0016
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0017
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0018
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0019
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0020
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0021
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0022
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0023
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0024
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0025
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0026
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0027
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0028
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0029
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0030
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0031
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0032
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0033
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.norot
xfmrot /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.ecclog /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.norot /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
ln -sf /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/data.nii.gz
mri_convert --frame 34 /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/lowb.nii.gz
mri_convert.bin --frame 34 /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/lowb.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999339, -0.0363145, -0.00163044)
j_ras = (-0.0363101, 0.99508, 0.0921851)
k_ras = (0.00172524, -0.0921834, 0.995741)
keeping frame 34
   ERROR: valid frame numbers are between 0 and 33
Darwin Christinas-iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64

 
trac-preproc exited with ERRORS at Thu Aug 31 14:54:59 CDT 2017

Here is the error I encounter when running the original dicom files through tracula 

[Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c /Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial
INFO: SUBJECTS_DIR is /Volumes/CFERRIER/Freesurfer_temp/PD800/diffusion_recons
INFO: Diffusion root is /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT
Actual FREESURFER_HOME /Applications/Freesurfer
trac-preproc -c /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/dmrirc.local -log /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.log -cmd /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.cmd
#-------------------------------------
/Applications/Freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Thu Aug 31 15:31:12 CDT 2017
mri_convert --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm...
Starting DICOMRead2()
dcmfile = /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm
dcmdir = /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii
WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm
ERROR: don't know how to get DWI parameters from --Philips --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm
break DICOMRead.c:5228
Ref Series No = 601
Found 5 files, checking for dicoms
WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm
ERROR: don't know how to get DWI parameters from --Philips --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm
break DICOMRead.c:5228
WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm
ERROR: don't know how to get DWI parameters from --Philips Healthcare--
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm
break DICOMRead.c:5228
WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm
ERROR: don't know how to get DWI parameters from --Philips Healthcare--
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm
break DICOMRead.c:5228
Found 1 dicom files in series.
WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm
ERROR: don't know how to get DWI parameters from --Philips --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm
break DICOMRead.c:5228
WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm
ERROR: don't know how to get DWI parameters from --Philips Healthcare--
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm
break DICOMRead.c:5228
WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm
ERROR: don't know how to get DWI parameters from --Philips Healthcare--
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm
break DICOMRead.c:5228
First Sorting
Computing Slice Direction


 WARNING: it appears that the image position for all slices is the same. 
 This is a problem with the DICOM file. Using direction cosines from col and row
 to compute slice direction, but the output may be misoriented. 

Vs: 0 0 0
Vs: nan nan nan
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 1
ndcmfiles = 1
PE Dir = UNKNOWN (dicom read)
Loading pixel data
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -0, 0)
j_ras = (-0, -0, 0)
k_ras = (nan, nan, nan)
writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm > /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dcminfo.dat
cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvecs/PD800_bvecs.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs
cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvals/PD800_bvals.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals
orientLAS /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz
mat = NULL!
MatrixFree: NULL mat POINTER!

mat = NULL!
MatrixFree: NULL mat POINTER!

mat = NULL!
MatrixFree: NULL mat POINTER!

INFO: input image orientation is III
INFO: input image determinant is nan
order: Subscript out of range.
Darwin Christinas-iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Thu Aug 31 15:32:20 CDT 2017
 


Thanks for your help. We tried to go through everything but nothing seems to be working.