Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 gives the same error. Enclosed is the config file. Thank you so much Heidi
On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu> wrote: > >Hi Heidi - It knows where to find the freesurfer recons of the T1's from >SUBJECTS_DIR (see example config file). Based on your log file, it looks >like you haven't turned off the eddy current compensation, because it's >trying to run it. If you attach your config file, I'll take a look. > >Best, >a.y > >On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> Thanks! I tried to adapt the configuration file and it got a bit >>further, >> but then crashes again. Not sure why? I have added the log file, so that >> maybe you could have a look at what is happening? >> Also, how does the trac-all command knows where to find the T1 data? >> Thanks >> Heidi >> >> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>of >> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> ayend...@nmr.mgh.harvard.edu> wrote: >> >>> >>> No, it should be pointed to the DWI data, which can be corrected niftis >>> instead of the original dicoms. I would recommend turning off all the >>> corrections in the configuration file, and then running everything >>> without >>> skipping steps. This will create all the files that are expected to be >>> there for the registration. >>> >>> On Tue, 31 May 2016, Jacobs H (NP) wrote: >>> >>>> Dear Anastasia, >>>> >>>> Thanks for the feedback. So, does this mean that the dcm root should >>>>be >>>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in a >>>> different folder. >>>> Enclosed is the log file (of one subject) and the configuration file. >>>> You >>>> will see that I tried the inter and intra option, because I thought >>>>that >>>> for the inter it would not need anything else than the MNI template >>>>and >>>> the DTI images. >>>> >>>> Thanks >>>> >>>> Best >>>> Heidi >>>> >>>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>>> of >>>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>>>of >>>> ayend...@nmr.mgh.harvard.edu> wrote: >>>> >>>>> >>>>> Hi Heidi - The intra-subject registration step that you're trying to >>>>> run >>>>> registers your subject's DWI and T1 images. It expects to find those >>>>> images. It doesn't use the FA, MD, etc in any way. >>>>> >>>>> Did the log file get created in scripts/trac-all.log? If so, can you >>>>> please send that file and your configuration file? Thanks! >>>>> >>>>> a.y >>>>> >>>>> On Tue, 31 May 2016, Jacobs H (NP) wrote: >>>>> >>>>>> Dear FreeSurfers, >>>>>> >>>>>> The data I have is preprocessed, so I have the all the metrics (FA, >>>>>> MD, >>>>>> L1, L2, L3,..) in nifti format. >>>>>> On this data I would like to start tracula starting from step 1.3. >>>>>> >>>>>> I have organized the data as mentioned on the wiki: >>>>>> For example: >>>>>> <subjID>/<dmri> dtifit_FA.nii.gz >>>>>> >>>>>> I have also filled in the configuration file, canceling out the >>>>>>things >>>>>> I don¹t need and then I tried to run: >>>>>> Trac-all intra c <configuration file> >>>>>> >>>>>> Unfortunately, it does not work, it says: dcmlist: subscript out of >>>>>> range >>>>>> >>>>>> I do not have the original filesŠ is there a way that I can get the >>>>>> script working? >>>>>> >>>>>> Many thanks. >>>>>> Heidi >>>>>> >>>> >>
# # dmrirc.example # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2013/12/05 23:08:54 $ # $Revision: 1.12 $ # # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH" # # Terms and conditions for use, reproduction, distribution and contribution # are found in the 'FreeSurfer Software License Agreement' contained # in the file 'LICENSE' found in the FreeSurfer distribution, and here: # # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense # # Reporting: freesurfer@nmr.mgh.harvard.edu # # # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # #setenv SUBJECTS_DIR /path/to/recons/of/ducks # # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/dtifit/ # Subject IDs set subjlist = ` echo S_11XDXA S_1GQ9QV S_1OR6QC S_22ZHN3 S_2AL8RA S_2BB4H2 S_2C71QF S_2N88VA S_38ZNK5 S_3RSPPP S_3VZEQN S_46JBNZ S_4MPQCY S_4WJ2CR S_556CFT S_591HTP S_5KA3RS S_65UK1S S_693X4P S_6D51EY S_6FWKZD S_6FZL4U S_6SB9KZ S_6YRT6A S_71GPF7 S_7HSOBN S_7KFHPW S_7NOX7M S_7WP6BG S_82FZ4L S_8BWFJ6 S_9737MM S_9EUNFD S_9K8SLX S_9N8KQW S_9P3JR7 S_9ZVDZV S_A1F2CM S_ALV5CB S_AUL7R4 S_BZ4FBH S_CCCMW3 S_CMM2WL S_CTY2ER S_CU4FZA S_CURLLB S_DL4N2Q S_DNQ9KU S_DQ1ZSG S_DTW7J6 S_DWA2LP S_DXM9JK S_EHDWX1 S_ENG47C S_F4PH5M S_F8P42D S_FCBAMR S_FDJ6UU S_FMSJER S_FQHJWH S_FSK1HD S_FWFNC5 S_G7KP27 S_H7YAA1 S_HCFNSF S_HW7R19 S_HWGXLJ S_J9HY8A S_JY5M58 S_K1K5LS S_K8ZC3B S_KBGJQU S_KCT9S6 S_KL5Q3P S_KMUW5L S_L33YSL S_LABYUQ S_LJ1GWN S_LLPPCW S_MEEDAH S_MFUFDS S_MX83QU S_NE58SM S_NIQUVD S_P4K6DM S_PE9J6U S_Q9A2UG S_QS6SFY S_R3BPAK S_RANV43 S_RFDRD6 S_RHXWND S_SO63PR S_SVAQUY S_T1LVDV S_T8CBM1 S_TJIU8X S_TMNXYB S_TNS7IM S_U2V5FD S_U98RJE S_U9U9QL S_UHC6WM S_V36DLL S_VTMXMZ S_WA1CLD S_WDVBAY S_X69RWA S_XFNM9K S_XRZQKV S_XTDEMR S_XXMGFN S_XY62WP S_Y97L76 S_YANQMX S_YEFGQ2 S_ZASXXZ S_ZNUP4E S_ZPBHLL TAU_001 TAU_024 TAU_029 TAU_064 TAU_074 TAU_122 TAU_151 TAU_154 TAU_156 TAU_157 TAU_160 TAU_161 TAU_169 TAU_175 TAU_178 TAU_180` # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # #set runlist = (1 3) # # 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/MACPRO1/EXPLORE_DTI_analyses/mytbss/OnlyFA set dcmlist = `echo S_11XDXA.nii S_6YRT6A.nii S_DL4N2Q.nii S_K1K5LS.nii S_SO63PR.nii S_YEFGQ2.nii S_1GQ9QV.nii S_71GPF7.nii S_DNQ9KU.nii S_K8ZC3B.nii S_SVAQUY.nii S_ZASXXZ.nii S_1OR6QC.nii S_7HSOBN.nii S_DQ1ZSG.nii S_KBGJQU.nii S_T1LVDV.nii S_ZNUP4E.nii S_22ZHN3.nii S_7KFHPW.nii S_DTW7J6.nii S_KCT9S6.nii S_T8CBM1.nii S_ZPBHLL.nii S_2AL8RA.nii S_7NOX7M.nii S_DWA2LP.nii S_KL5Q3P.nii S_TJIU8X.nii TAU_001.nii S_2BB4H2.nii S_7WP6BG.nii S_DXM9JK.nii S_KMUW5L.nii S_TMNXYB.nii TAU_024.nii S_2C71QF.nii S_82FZ4L.nii S_EHDWX1.nii S_L33YSL.nii S_TNS7IM.nii TAU_029.nii S_2N88VA.nii S_8BWFJ6.nii S_ENG47C.nii S_LABYUQ.nii S_U2V5FD.nii TAU_064.nii S_38ZNK5.nii S_9737MM.nii S_F4PH5M.nii S_LJ1GWN.nii S_U98RJE.nii TAU_074.nii S_3RSPPP.nii S_9EUNFD.nii S_F8P42D.nii S_LLPPCW.nii S_U9U9QL.nii TAU_122.nii S_3VZEQN.nii S_9K8SLX.nii S_FCBAMR.nii S_MEEDAH.nii S_UHC6WM.nii TAU_151.nii S_46JBNZ.nii S_9N8KQW.nii S_FDJ6UU.nii S_MFUFDS.nii S_V36DLL.nii TAU_154.nii S_4MPQCY.nii S_9P3JR7.nii S_FMSJER.nii S_MX83QU.nii S_VTMXMZ.nii TAU_156.nii S_4WJ2CR.nii S_9ZVDZV.nii S_FQHJWH.nii S_NE58SM.nii S_WA1CLD.nii TAU_157.nii S_556CFT.nii S_A1F2CM.nii S_FSK1HD.nii S_NIQUVD.nii S_WDVBAY.nii TAU_160.nii S_591HTP.nii S_ALV5CB.nii S_FWFNC5.nii S_P4K6DM.nii S_X69RWA.nii TAU_161.nii S_5KA3RS.nii S_AUL7R4.nii S_G7KP27.nii S_PE9J6U.nii S_XFNM9K.nii TAU_169.nii S_65UK1S.nii S_BZ4FBH.nii S_H7YAA1.nii S_Q9A2UG.nii S_XRZQKV.nii TAU_175.nii S_693X4P.nii S_CCCMW3.nii S_HCFNSF.nii S_QS6SFY.nii S_XTDEMR.nii TAU_178.nii S_6D51EY.nii S_CMM2WL.nii S_HW7R19.nii S_R3BPAK.nii S_XXMGFN.nii TAU_180.nii S_6FWKZD.nii S_CTY2ER.nii S_HWGXLJ.nii S_RANV43.nii S_XY62WP.nii S_6FZL4U.nii S_CU4FZA.nii S_J9HY8A.nii S_RFDRD6.nii S_Y97L76.nii S_6SB9KZ.nii S_CURLLB.nii S_JY5M58.nii S_RHXWND.nii S_YANQMX.nii` # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if inputs are not MGH DICOMs # 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 = (/path/to/huey/bvecs.txt \ # /path/to/dewey/bvecs.txt \ # /path/to/louie/bvecs.txt) # Diffusion gradient table (if using the same one for all scans) # Must be specified if inputs are not MGH DICOMs # The table 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 = /Volumes/MACPRO1/EXPLORE_DTI_analyses/Diffusion_HighRes_20.mghdti.bvecs # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header set bvalfile = /Volumes/MACPRO1/EXPLORE_DTI_analyses/Diffusion_HighRes_20.mghdti.bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # #set dob0 = 1 # # 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) # # 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 = 0 # # 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 = 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 = /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
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