External Email - Use Caution Dear TRACULA experts
I use the newest version of TRACULA (FS 7.2, official release) and face the same problem as already reported by another user https://secure-web.cisco.com/1X5AHUcHXClyJtmxIDuq0cEQ7oR9Y81XGrojDN0ZsSnvYnGDGkc3PkrsOOuuSVcwMfyYRGrw-7aqgWwyPzXJYunzUQPhoSR3UURfJ5klz37OeD7-aMDu5aa3sGVJ7A9yQK4NlRW8DDvWeWLUDMY5zi7nReTCRkssePLKyMERx_qP3vQXvGBbul7ET6IUZDTEh8keWBMhMl-chnuQjckEXM9hQ-9tP3Azc8Sd9adRihxBYI_5u_b3Jpii2e2MtdNWhPBSGCk7Uclu432P9W5nGrw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70584.html As suggested by the answer to the above link, this other user did not use an official release of FS, and no explicit solution was mentioned in this link. I used an official version, but got the same error. BTW, if using TRACULA in FS 7.1.1, this error did not occur. The error that occurs is the following (log and config file attached): error: niiRead(): error opening file /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/01_TRACULA_Results_NIFTI_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz As described by the other user, the file is initially created, but then renamed to dwi.nii.gz and therefore not present in the dmri directory. BTW, my data is already in LAS orientation. The error only occurs if using NIFTI files but not if using the DICOM files. Actually, I could use DICOMs, but I faced the problem that dTE could not be found in the DICOM header and/or b0info.dat file, respectively, (see error below) because only one TE is present in the DICOM header of the phase image as suggested by the meta data in the OSIRIX DICOM viewer, and therefore I would rather use NIFTI files and define dTE in the config file as it has been suggested that this is possible in TRACULA in FS 7.2. writing to /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz... mri_probedicom --i /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm > /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.dat ERROR: Need dTE for field map /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm However, if I try to use DICOM files and "set dTE = 2.46“ in the config file, the same error occurred as when not setting dTE in the config file. Thanks in advance for any advice Best regards Jürgen
trac-all.log
Description: trac-all.log
# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/01_TRACULA_Results_NIFTI_FS720 # Subject IDs (n = 130 incl. IPS_SZ_024, excl. IPS_SZ_028 & IPS_SZ_068 due to missing fieldmap) # set subjlist = (IPS_CO_007 IPS_CO_009) # 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/Datenspeicher/01_IPS/04_C_DTI_TRACULA/01_TRACULA_Prepared_NIFTI_FS720 set dcmlist = (IPS_CO_007/DTI/data.eddy_outlier_free_data.nii.gz IPS_CO_009/DTI/data.eddy_outlier_free_data.nii.gz) # 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 bveclist = (IPS_CO_007/DTI/data.eddy_rotated_bvecs IPS_CO_009/DTI/data.eddy_rotated_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 bvallist = (IPS_CO_007/DTI/bvals.bval IPS_CO_009/DTI/bvals.bval) # Perform correction for B0 inhomogeneity distortions? # 0: No correction (default) # 1: Perform correction based on a field map # Requires additional inputs (see below): b0mlist, b0plist, echospacing # 2: Perform correction based on reverse-polarity images # Requires additional inputs (see below): echospacing, pedir, epifactor # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names can be relative to dcmroot) # Only used if dob0 = 1 # Default: None # set b0mlist = (IPS_CO_007/B0_map/rmagnitude.nii.gz IPS_CO_009/B0_map/rmagnitude.nii.gz) # Input B0 field map phase DICOMs (file names can be relative to dcmroot) # Only used if dob0 = 1 # Default: None # set b0plist = (IPS_CO_007/B0_map/fieldmap_rads.nii.gz IPS_CO_009/B0_map/fieldmap_rads.nii.gz) # Echo spacing (this is found in the scanner protocol printout) # Only used if dob0 = 1 or 2 # Default: None # set echospacing = 0.28999 set dTE = 2.46 # Perform correction for eddy-current distortions? # 0: No correction # 1: Perform registration-based correction with eddy_correct # 2: Perform model-based correction with eddy (default) # set doeddy = 0 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 or 2 # Default: 1 (yes) # set dorotbvecs = 1 # Intra-subject (diffusion-to-T1) registration method # 1: Affine with a correlation ratio cost # 2: Affine with a mutual information cost # 3: Affine with a boundary-based cost (default) # set intrareg = 3 # Degrees of freedom for intra-subject registration # Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine) # Default: 6 for infants, 9 otherwise # set intradof = 6 # Maximum rotation angle (degrees) for intra-subject registration # Default: 3 for infants, 90 otherwise # set intrarot = 90 # Inter-subject registration method # 1: Affine T1-to-T1 with a correlation ratio cost # 2: Affine T1-to-T1 with a mutual information cost # 3: Affine T1-to-T1 with a robust cost (default for infants) # 4: Nonlinear T1-to-T1 with CVS # 5: Nonlinear FA-to-FA with SyN (default) # set interreg = 5 # Target brain for inter-subject registration # Default for affine T1-to-T1: # $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Default for nonlinear T1-to-T1: # $FREESURFER_HOME/subjects/cvs_avg35/ # Default for nonlinear FA-to-FA: # $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # set intertrg = $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # Whole-brain segmentation used to extract the anatomical neighborhood priors # of the pathways of interest # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/$segname.mgz # Default: aparc+aseg # set segname = aparc+aseg # Use the thalamic nuclei segmentation? # This is highly recommended to use for any pathways that terminate in # or neighbor the thalamus # When used, it is merged with the whole-brain segmentation above # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz # Default: 1 (yes) # set usethalnuc = 1 # 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 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.3 # Paths to reconstruct # Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # #set pathlist = ( lh.cst_AS rh.cst_AS ) # 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 (recommended, with more points for longer paths) # Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # #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/hcp/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
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