External Email - Use Caution        

Dear Freesurfers experts,

I'm a beginner in the diffusion imaging preprocessing. I was following the
freesurfer/dti tutorial with my own data when i get stuck in the trac-all
step. I have created the configuration files trying to follow the tutorial
instructions and when I tried to run the trac-all command I get the
following error:


pcpb3846:4220 lab1-rmn$ trac-all -prep -c
$TUTORIAL_DATA/outputs/dmrirc.tutorial

set: Variable name must contain alphanumeric characters.

ERROR: must specify either one number of control points

ERROR: or as many numbers as pathways




You can find my configuration file in attached. Any help would be very
appreciated.

Thank in advance.


Best regards,
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
set SUBJECTS_DIR=$TUTORIAL_DATA/4220


# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = $TUTORIAL_DATA/outputs

# Subject IDs
#
set subjlist = 4220

# Input diffusion DICOMs
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
set dcmroot = $TUTORIAL_DATA/4220/4220dti/memoria/DTI

set dcmlist = $TUTORIAL_DATA/4220/4220dti/memoria/DTI/IM-0001-0033.dcm

set doeddy = 0

set dorotbvecs = 0

set usemaskanat = 1

set thrbet = 0.3

set doregflt = 1

set doregbbr = 0

set doregmni = 1

set doregcvs = 0

set pathlist = lh.cst_AS rh.cst_AS \
                 lh.ilf_AS rh.ilf_AS \
                 lh.unc_AS rh.unc_AS \
                 fmajor_PP fminor_PP \
                 lh.atr_PP rh.atr_PP \
                 lh.cab_PP rh.cab_PP \
                 lh.ccg_PP rh.ccg_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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Reply via email to