External Email - Use Caution Hi Anastasia,
I think there are some misunderstandings here. I have created one configuration file for each subject and it works processing longitudinal data. And since all my subjects are stored following /subjects/ in one directory, I assumed adding individual 'SUBJ1/' to the file would work. Here attached my individual and multiple subjects' configuration file. Can you help take a look? From what you say, I have some suspicion that my individual configuration could also have some problem. Thank you so much ! Best, Qi On Thu, Apr 30, 2020 at 4:41 PM Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote: > You cannot have multiple SUBJECTS_DIR's. It is supposed to be the base > directory under which all subjects' dirs are saved. You could have a > different configuration file for each subject if you want each of them to > have a different SUBJECTS_DIR, but this hack won't work for longitudinal > analyses as all the time points from the same subject have to be defined in > the same config file. If you must have subjects saved in different > locations, you can create a "mock" SUBJECTS_DIR and in it create symlinks > to the dirs of every individual subject (this includes both *.long.* and > base dirs). > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < > qi.z...@icahn.mssm.edu> > *Sent:* Thursday, April 30, 2020 3:40 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] longitudinal dmrirc script error with the baselist > > > External Email - Use Caution > > Hi, > > I have my trac-all up and running with no error with individual subjects > when I set the subject directory to individual subjects. > as follow: > set SUBJECTS_DIR=/*/subjects/SUBJ1 > set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2) > set baselist = (SUBJ1_base SUBJ1_base) > > However, when I put subjects together and set the directory to multiple > subjects as follow: > set SUBJECTS_DIR=/*/subjects > set subjlist = (SUBJ1/SUBJ1_ses-1 \ > SUBJ1/SUBJ1_ses-2 \ > SUBJ2/SUBJ2_ses-1 \ > SUBJ2/SUBJ2_ses-2 \ > etc. ) > set baselist = (SUBJ1/SUBJ1_base \ > SUBJ1/SUBJ1_base \ > SUBJ2/SUBJ2_base \ > SUBJ2/SUBJ2_base \ > etc.) > > It has a problem finding the baselist file: > "cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should > I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it > not happening with the subject individual? > > Best, > Qi > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ph.D. candidate Icahn School of Medicine at Mount Sinai
# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # set SUBJECTS_DIR=/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects # output directory (same as SUBJECTS_DIR) set dtroot = /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects # Subject IDs (one per time point per subject) set subjlist = (003_S_4288/003_S_4288_ses-1 003_S_4288/003_S_4288_ses-2 029_S_4385/029_S_4385_ses-1 029_S_4385/029_S_4385_ses-2 029_S_4652/029_S_4652_ses-1 029_S_4652/029_S_4652_ses-2 029_S_5166/029_S_5166_ses-1 029_S_5166/029_S_5166_ses-2 098_S_0896/098_S_0896_ses-1 098_S_0896/098_S_0896_ses-2 098_S_4275/098_S_4275_ses-1 098_S_4275/098_S_4275_ses-2 098_S_4506/098_S_4506_ses-1 098_S_4506/098_S_4506_ses-2 126_S_5214/126_S_5214_ses-1 126_S_5214/126_S_5214_ses-2) # Longitudinal base template subject IDs (one for each time point above) set baselist = (003_S_4288/003_S_4288_base 003_S_4288/003_S_4288_base 029_S_4385/029_S_4385_base 029_S_4385/029_S_4385_base 029_S_4652/029_S_4652_base 029_S_4652/029_S_4652_base 029_S_5166/029_S_5166_base 029_S_5166/029_S_5166_base 098_S_0896/098_S_0896_base 098_S_0896/098_S_0896_base 098_S_4275/098_S_4275_base 098_S_4275/098_S_4275_base 098_S_4506/098_S_4506_base 098_S_4506/098_S_4506_base 126_S_5214/126_S_5214_base 126_S_5214/126_S_5214_base) # Default: Run analysis on all time points and subjects set runlist = (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16) # Input diffusion DICOMs (file names relative to dcmroot) set dcmroot = /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects set dcmlist = (003_S_4288/DTI/DTI_ses-1/003_S_4288.nii.gz 003_S_4288/DTI/DTI_ses-2/003_S_4288.nii.gz 029_S_4385/DTI/DTI_ses-1/029_S_4385.nii.gz 029_S_4385/DTI/DTI_ses-2/029_S_4385.nii.gz 029_S_4652/DTI/DTI_ses-1/029_S_4652.nii.gz 029_S_4652/DTI/DTI_ses-2/029_S_4652.nii.gz 029_S_5166/DTI/DTI_ses-1/029_S_5166.nii.gz 029_S_5166/DTI/DTI_ses-2/029_S_5166.nii.gz 098_S_0896/DTI/DTI_ses-1/098_S_0896.nii.gz 098_S_0896/DTI/DTI_ses-2/098_S_0896.nii.gz 098_S_4275/DTI/DTI_ses-1/098_S_4275.nii.gz 098_S_4275/DTI/DTI_ses-2/098_S_4275.nii.gz 098_S_4506/DTI/DTI_ses-1/098_S_4506.nii.gz 098_S_4506/DTI/DTI_ses-2/098_S_4506.nii.gz 126_S_5214/DTI/DTI_ses-1/126_S_5214.nii.gz 126_S_5214/DTI/DTI_ses-2/126_S_5214.nii.gz) # Diffusion gradient tables (if there is a different one for each scan) set bvecroot=/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects set bveclist = (003_S_4288/DTI/DTI_ses-1/003_S_4288.bvec 003_S_4288/DTI/DTI_ses-2/003_S_4288.bvec 029_S_4385/DTI/DTI_ses-1/029_S_4385.bvec 029_S_4385/DTI/DTI_ses-2/029_S_4385.bvec 029_S_4652/DTI/DTI_ses-1/029_S_4652.bvec 029_S_4652/DTI/DTI_ses-2/029_S_4652.bvec 029_S_5166/DTI/DTI_ses-1/029_S_5166.bvec 029_S_5166/DTI/DTI_ses-2/029_S_5166.bvec 098_S_0896/DTI/DTI_ses-1/098_S_0896.bvec 098_S_0896/DTI/DTI_ses-2/098_S_0896.bvec 098_S_4275/DTI/DTI_ses-1/098_S_4275.bvec 098_S_4275/DTI/DTI_ses-2/098_S_4275.bvec 098_S_4506/DTI/DTI_ses-1/098_S_4506.bvec 098_S_4506/DTI/DTI_ses-2/098_S_4506.bvec 126_S_5214/DTI/DTI_ses-1/126_S_5214.bvec 126_S_5214/DTI/DTI_ses-2/126_S_5214.bvec) # Diffusion b-value tables (if there is a different one for each scan) set bvalroot=/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects set bvallist = (003_S_4288/DTI/DTI_ses-1/003_S_4288.bval 003_S_4288/DTI/DTI_ses-2/003_S_4288.bval 029_S_4385/DTI/DTI_ses-1/029_S_4385.bval 029_S_4385/DTI/DTI_ses-2/029_S_4385.bval 029_S_4652/DTI/DTI_ses-1/029_S_4652.bval 029_S_4652/DTI/DTI_ses-2/029_S_4652.bval 029_S_5166/DTI/DTI_ses-1/029_S_5166.bval 029_S_5166/DTI/DTI_ses-2/029_S_5166.bval 098_S_0896/DTI/DTI_ses-1/098_S_0896.bval 098_S_0896/DTI/DTI_ses-2/098_S_0896.bval 098_S_4275/DTI/DTI_ses-1/098_S_4275.bval 098_S_4275/DTI/DTI_ses-2/098_S_4275.bval 098_S_4506/DTI/DTI_ses-1/098_S_4506.bval 098_S_4506/DTI/DTI_ses-2/098_S_4506.bval 126_S_5214/DTI/DTI_ses-1/126_S_5214.bval 126_S_5214/DTI/DTI_ses-2/126_S_5214.bval) # Perform registration-based eddy-current compensation? set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? 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 = 0.3 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) set doregflt = 0 # 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 = /hpc/packages/minerva-common/fsl/6.0.0/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) set doregcvs = 0 # 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) # 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
# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # set SUBJECTS_DIR=/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288 # output directory (same as SUBJECTS_DIR) set dtroot = /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288 # Subject IDs (one per time point per subject) set subjlist = (003_S_4288_ses-1 003_S_4288_ses-2) # Longitudinal base template subject IDs (one for each time point above) set baselist = (003_S_4288_base 003_S_4288_base) # Default: Run analysis on all time points and subjects set runlist = (1 2) # Input diffusion DICOMs (file names relative to dcmroot) set dcmroot = /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects set dcmlist = (003_S_4288/DTI/DTI_ses-1/003_S_4288.nii.gz 003_S_4288/DTI/DTI_ses-2/003_S_4288.nii.gz) # Diffusion gradient tables (if there is a different one for each scan) set bveclist = (/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/DTI/DTI_ses-1/003_S_4288.bvec /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/DTI/DTI_ses-2/003_S_4288.bvec) # Diffusion b-value tables (if there is a different one for each scan) set bvallist = (/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/DTI/DTI_ses-1/003_S_4288.bval /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/DTI/DTI_ses-2/003_S_4288.bval) # Perform registration-based eddy-current compensation? set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? 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 = 0.3 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) set doregflt = 0 # 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 = /hpc/packages/minerva-common/fsl/6.0.0/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) set doregcvs = 0 # 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) # 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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