Hi Deryk , Thanks for checking...As Anastasia mentioned, If FSL's bedpostx runs well then that should work as well...I'm not exactly sure about why the error is coming up and I can't replicate it on my computer either. Can you check one more thing in your terminal? In your dmri.bedpostX directory there will be a commands.txt file which contains commandline arguments for each of the slices seperately...It should be something like this:
/usr/pubsw/packages/fsl/current/bin/bedpostx_single_slice.sh /autofs/cluster/freesurfer/subjects/diffusion_tutorial/Diff001/dmri 2 1 1000 1250 25 1 0 If you copy paste one of these lines, does it give you the same error? If not we can take a look at it if you upload the data to see if we can replicate the error. Thanks, Priti > Hi Priti > > In addition, if I run bedpostx from the command line as follows: > > bedpostx /usr/local/freesurfer/subjects/C001/dmri > > it works just fine without errors. > > 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. > > > On Mon, Jun 13, 2011 at 1:51 PM, Deryk S. Beal, Ph.D. <dsb...@bu.edu> wrote: > >> Hi Priti >> Thank you for your quick replay. The following files / folders are listed >> in my dmri.bedpostx directory: >> ************************************************************** >> /usr/local/freesurfer/subjects/C001/dmri.bedpostX$ ls >> commands.txt diff_slices logs monitor xfms >> ************************************************************** >> I am able to call bedpostx from the command line without error. It is worth >> noting that I am running Ubuntu 10.10 and the Neurodebian distro of FSL4.1. >> However, FSL and bedpostx appear to be sourced properly: >> ********************************************************************** :/usr/local/freesurfer/subjects/C001/dmri.bedpostX$ bedpostx >> 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) >> **************************************************************** 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 Mon, Jun 13, 2011 at 1:25 PM, <rspr...@nmr.mgh.harvard.edu> wrote: >>> 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
