External Email - Use Caution Dear All,
I am encountering an issue while running Tracula from the dmrirc file. An additional line was required to run smoothly, without errors. I added " set usethalnuc = 0 " and it proceeded without errors, yet when " set usethalnuc = 1 " was added I encountered an error message. I might have missed some relevant information on the page, but could you please clarify what this setting does? Additionally, which preprocessing step might I have missed if Tracula only works with set usethalnuc = 0? Thank you for your help in advance! Kind regards, Diana PS: I am also enclosing the test dmrirc file that I was using.
# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /Volumes/Diana/Preprocessed/DTI/Test_script/ADDI_013 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Volumes/Diana/Preprocessed/DTI/Test_script/ADDI_013 # Subject IDs # set subjlist = (ADDI_013_recon_all) set dcmlist = (data.nii.gz) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # 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 = /Volumes/Diana/Preprocessed/DTI/Test_script/ADDI_013 # Diffusion gradient tables (file names can be relative to dcmroot) # Must be specified only if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bvecfile = (bvecs) # Diffusion b-value tables (file names can be relative to dcmroot) # Must be specified only if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvalfile = (bvals) # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # set dob0 = 0 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm \ # dewey/fphas/XXX-1.dcm \ # louie/fphas/XXX-1.dcm) # # Field mapping TE difference (this is found in the scanner protocol printout) # Only used if dob0 = 1 # Default: Read from field mapping phase DICOM # # set dTE = 0.0025 # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # # set thrbet = 0.5 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 1 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # # 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 ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # # set reinit = 0 # set the direction of the scanning set pedir = "y" # or "-y", "x", "-x", "z", or "-z" depending on your data # it was advised to use thalamic segmentation, but I have no clue how to do it set usethalnuc = 0
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