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 dsbeal@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. dsbeal@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 < ayendiki@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 dsbeal@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.
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 dsbeal@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. dsbeal@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 < ayendiki@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 dsbeal@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
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 dsbeal@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, rspriti@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
-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 dsbeal@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. dsbeal@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 < ayendiki@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 dsbeal@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
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 dsbeal@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. dsbeal@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
-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 dsbeal@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, rspriti@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
-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 dsbeal@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. dsbeal@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 < ayendiki@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 dsbeal@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
Hi Deryk - Trac-all doesn't call the version of bedpostx under the FSL dir but a specially modified version in the freesurfer distribution (called bedpostx_seychelles for historical reasons).
It's fine to run bedpostx directly since that works for you. You can also upload the data set for us to try to replicate the error.
Sorry for the confusion, a.y
On Mon, 13 Jun 2011, Deryk S. Beal, Ph.D. wrote:
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 dsbeal@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. dsbeal@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 dsbeal@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, rspriti@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. PritiDear 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 dsbeal@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.
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 < ayendiki@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 dsbeal@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
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 dsbeal@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. dsbeal@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
-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 dsbeal@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, rspriti@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
-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
dsbeal@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.
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 < ayendiki@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
> dsbeal@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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Deryk S. Beal, Ph.D. -
rspriti＠nmr.mgh.harvard.edu