Hi Deryk, Is bedpostx properly installed in your computer? Can you just type bedpostx in your terminal to see if it gives this message?
############################################################################ Usage: bedpostx <subject directory> [options] expects to find bvals and bvecs in subject directory expects to find data and nodif_brain_mask in subject directory options: -n (number of fibres per voxel, default 2) -w (ARD weight, more weight means less secondary fibres per voxel, default 1) -b (burnin period, default 1000) -j (number of jumps, default 1250) -s (sample every, default 25) ############################################################################ Also can you let us know if any files are created after this error in /usr/local/freesurfer/subjects/C001/dmri.bedpostx directory ? This looks like an error with the bedpostx itself...I've used the trac-all -bedp on my local machine (instead of a cluster) and it seems to work fine. Priti > Dear Tracula Users > > I completed trac-all -prep -c without difficulty or errors. However, > without > any changes to my director structure or my Tracula config file I am > receiving the following errors when running trac-all -bedp -c. I will copy > and past my config file contents below the error messages. Please advise. > > trac-all -bedp -c > /media/5424CE1A24CDFECC/UofT/data/Tracula/tracula_config.txt -debug > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > INFO: Diffusion root is /usr/local/freesurfer/subjects > Actual FREESURFER_HOME /usr/local/freesurfer > ln -sf > /usr/local/freesurfer/subjects/C001/dlabel/diff/anat_brain_mask.bbr.nii.gz > /usr/local/freesurfer/subjects/C001/dmri/nodif_brain_mask.nii.gz > ln -sf /usr/local/freesurfer/subjects/C001/dmri/dwi.nii.gz > /usr/local/freesurfer/subjects/C001/dmri/data.nii.gz > WARN: Running FSL's bedbost locally - this might take a while > WARN: It is recommended to run this step on a cluster > bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri > subjectdir is /usr/local/freesurfer/subjects/C001/dmri > Making bedpostx directory structure > Queuing preprocessing stages > [: 223: NONE: unexpected operator > [: 314: NONE: unexpected operator > [: 327: xbedpostx_pre: unexpected operator > [: 486: x: unexpected operator > [: 486: -le: argument expected > Queuing parallel processing stage > [: 223: NONE: unexpected operator > [: 327: xbedpostx: unexpected operator > [: 486: x53: unexpected operator > 0 slices processed > Queuing post processing stage > [: 223: NONE: unexpected operator > [: 314: NONE: unexpected operator > [: 327: xbedpostx_post: unexpected operator > [: 486: x: unexpected operator > [: 486: -le: argument expected > > CONFIG FILE CONTENTS: > # > # 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: 2011/05/24 06:47:12 $ > # $Revision: 1.3.2.3 $ > # > # 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 /usr/local/freesurfer/subjects > > # Output directory where trac-all results will be saved > # Default: Same as SUBJECTS_DIR > # > set dtroot = /usr/local/freesurfer/subjects > > # Subject IDs > # > set subjlist = (C001 C002 C003 C004 C005 C006 C007 C008 C009 C010 C011 > S001 > S002 S003 S004 S005 S006 S007 S008 S009 S010 S011) > > # In case you want to analyze only Huey and Louie > # Default: Run analysis on all subjects > # > set runlist = (1) > # 2 3 4 5 6 7 8 9 10 11) > #12 13 14 15 16 17 18 19 20 21 22) > > # Input diffusion DICOMs (file names relative to dcmroot) > # If original DICOMs don't exist, these can be in other image format > # but then bvecfile, bvalfile, and nb0 must be specified (see below) > # > set dcmroot = /media/5424CE1A24CDFECC/UofT/data/Tracula > set dcmlist = (C001_merged.nii.gz \ C002_merged.nii.gz \ > C003_merged.nii.gz > C004_merged.nii.gz \ C005_merged.nii.gz \ C006_merged.nii.gz \ > C007_merged.nii.gz \ C008_merged.nii.gz \ C009_merged.nii.gz \ > C010_merged.nii.gz \ C011_merged.nii.gz \ S001_merged.nii.gz \ > S002_merged.nii.gz \ S003_merged.nii.gz \ S004_merged.nii.gz \ > S005_merged.nii.gz \ S006_merged.nii.gz \ S007_merged.nii.gz \ > S008_merged.nii.gz \ S009_merged.nii.gz \ S010_merged.nii.gz \ > S011_merged.nii.gz) > > # Diffusion gradient table > # Must be specified if inputs are not MGH DICOMs > # Three-column format, one row for each volume in the diffusion data set > # Default: Read from DICOM header > # > set bvecfile = /media/5424CE1A24CDFECC/UofT/data/Tracula/bvecs.txt > > # Diffusion b-value table > # Must be specified if inputs are not MGH DICOMs > # Single-column format, one value for each volume in the diffusion data > set > # Default: Read from DICOM header > # > set bvalfile = /media/5424CE1A24CDFECC/UofT/data/Tracula/bvals.txt > > # Number of low-b images > # Must be specified if inputs are not DICOM > # Default: Read from DICOM header > # > set nb0 = 2 > > # 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) > > # 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 = 0.3 > > # Perform diffusion-to-T1 registration by flirt? > # Default: 1 (yes) > # > set doregflt = 0 > > # Perform diffusion-to-T1 registration by bbregister? > # Default: 0 (no) > # > set doregbbr = 1 > > # MNI template (the only option for inter-subject registration in this > version) > # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > # > set mnitemp = /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz > > # 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 > # Default: 5 > # > set ncpts = 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 > > # Use long (more descriptive) directory hierarchy for saving path > distributions? > # By default, paths distributions are saved directly under > $subjectname/dpath > # Default: 0 (no) > # > set dopathsubdirs = 0 > > # 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: 5000 > # > set nsample = 5000 > > # Frequency with which MCMC path samples are retained for path > distribution > # Default: 5 (keep every 5th sample) > # > set nkeep = 5 > > > > Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO > Speech-Language Pathologist > C.I.H.R. Post Doctoral Research Fellow > Department of Cognitive and Neural Systems Speech Laboratory > Boston University, 677 Beacon Street, Boston, MA 02215 > dsb...@bu.edu > http://blogs.bu.edu/dsbeal/about/ > ************************************************************************* > This email may contain confidential and/or privileged information for the > sole use of the intended recipient. Any review or distribution by others > is > strictly prohibited. If you have received this email in error, please > contact the sender and delete all copies. Opinions, conclusions or other > information expressed or contained in this email are not given or endorsed > by the sender unless otherwise affirmed independently by the sender. > > > On Fri, Jun 10, 2011 at 3:28 PM, Deryk S. Beal, Ph.D. <dsb...@bu.edu> > wrote: > >> Hi Anastasia >> >> If I have T1 data available in my FS subject directory and I have >> >> 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 >> >> then will the B0 brain mask we spoke of below be used? >> >> Deryk >> >> >> On Fri, Jun 10, 2011 at 10:46 AM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> wrote: >> >>> >>> Hi Deryk - This variable is only used to average lowb images to create >>> a >>> mask, so in your case you can set it to 2 and it'll just use the first >>> 2 >>> volumes from your nii file. Sorry for the confusion! >>> >>> a.y >>> >>> >>> On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote: >>> >>> Dear Tracula Users >>>> >>>> Does Tracula assume that the number of B0 scans, specified in Step 7.3 >>>> of >>>> the config file tutorial (below), are the first X number of volumes in >>>> the >>>> 4Dnii.gz file or will the Tracula routines know from the bvals file >>>> where >>>> the B0 scans are ordered in the file? For example, I have two runs of >>>> 16 >>>> directions + 2 B0s each for each of my subjects. I have merged the two >>>> runs >>>> together and the resulting file has the volumes ordered such that the >>>> bvals >>>> are entered into Tracula as follows: >>>> >>>> 0 >>>> 0 >>>> 1000 >>>> 1000 >>>> 1000 >>>> etc >>>> 0 >>>> 0 >>>> 1000 >>>> 1000 >>>> 1000 >>>> etc >>>> >>>> My question pertains to the following part of the Tracula config file: >>>> >>>> Step7.3: Specifying Number Of low-b Images The last step to set up if >>>> not >>>> using original DICOMs would be to specify the number of low-b images >>>> with >>>> the following variable: >>>> >>>> set nb0 = *No. of low-b images* >>>> Thank you in advance for your help. >>>> Cheers, >>>> Deryk >>>> >>>> Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO >>>> Speech-Language Pathologist >>>> C.I.H.R. Post Doctoral Research Fellow >>>> Department of Cognitive and Neural Systems Speech Laboratory >>>> Boston University, 677 Beacon Street, Boston, MA 02215 >>>> dsb...@bu.edu >>>> http://blogs.bu.edu/dsbeal/about/ >>>> ************************************************************************* >>>> This email may contain confidential and/or privileged information for >>>> the >>>> sole use of the intended recipient. Any review or distribution by >>>> others >>>> is >>>> strictly prohibited. If you have received this email in error, please >>>> contact the sender and delete all copies. Opinions, conclusions or >>>> other >>>> information expressed or contained in this email are not given or >>>> endorsed >>>> by the sender unless otherwise affirmed independently by the sender. >>>> >>>> >>>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
