Hello Freesurfer Team,
I attended the conference last week in Boston and really enjoyed all I
learned! But while trying to run through the Tracula tutorial with my own
data, I am having an error with my configuration file:
ERROR: must specify as many DWI dicoms as subjects.
My files are in nifti format, could this possibly be the cause of this
error? I have attached my configuration file for reference.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.5.0 x86_64
Thanks so much!
Jasmin
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR $SUBJECTS_DIR
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = $SUBJECTS_DIR
# Subject IDs
#
set subjlist = (40 39 36)
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified
#
set dcmroot = Users/jasminalves/Desktop/data/DTI
set dcmlist = (40/DTI.nii.gz DTI.bvec DTI.bval 39/DTI.nii.gz DTI.bvec DTI.bval
36/DTI.nii.gz DTI.bvec DTI.bval)
set bveclist = (Users/jasminalves/Desktop/data/DTI/40/DTI.bvec
Users/jasminalves/Desktop/data/DTI/39/DTI.bvec
Users/jasminalves/Desktop/data/DTI/36/DTI.bvec)
set bvecfile = (Users/jasminalves/Desktop/data/DTI/40/DTI.bvec
Users/jasminalves/Desktop/data/DTI/39/DTI.bvec
Users/jasminalves/Desktop/data/DTI/36/DTI.bvec)
set bvalfile = (Users/jasminalves/Desktop/data/DTI/40/DTI.bval
Users/jasminalves/Desktop/data/DTI/39/DTI.bval
Users/jasminalves/Desktop/data/DTI/36/DTI.bval)
set dob0 = 0
set doeddy = 1
set dorotbvecs = 1
set thrbet = 0.5
set doregflt = 0
set doregbbr = 1
set doregmni = 1
set mnitemp =
/Applications/Utilities/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz
set doregcvs = 0
set usemaskanat = 1
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.unc_AS rh.unc_AS \
lh.ilf_AS rh.ilf_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.ccg_PP rh.ccg_PP \
lh.cab_PP rh.cab_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0_______________________________________________
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