[Freesurfer] Tracula/Config file error
I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter Its become very annoying. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Tracula/ config file error
I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter It has become very, very annoying. PLEASE SOMEONE HELP!!! Andrew -- # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 # Subject IDs # set subjlist = (freesurfer) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.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 = /home/baileype/Desktop/JG005/bvecs # 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 = /home/baileype/Desktop/JG005/bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1 # 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 = 0.2 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = (lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of sticks (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a
Re: [Freesurfer] Tracula/ config file error
Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go. More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system? a.y On Mon, 1 Jul 2013, Gundran, Andrew wrote: I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter It has become very, very annoying. PLEASE SOMEONE HELP!!! Andrew -- # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 # Subject IDs # set subjlist = (freesurfer) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.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 = /home/baileype/Desktop/JG005/bvecs # 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 = /home/baileype/Desktop/JG005/bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1 # 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 = 0.2 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = (lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of sticks (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path
Re: [Freesurfer] Tracula/ config file error
Can you see that this is all one line? # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) On Mon, 1 Jul 2013, Gundran, Andrew wrote: Yes, the text was saved on a unix system -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:34 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula/ config file error Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go. More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system? a.y On Mon, 1 Jul 2013, Gundran, Andrew wrote: I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter It has become very, very annoying. PLEASE SOMEONE HELP!!! Andrew -- # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 # Subject IDs # set subjlist = (freesurfer) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.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 = /home/baileype/Desktop/JG005/bvecs # 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 = /home/baileype/Desktop/JG005/bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1 # 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 = 0.2 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = (lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) # Number of path control points # It can be a single number for all paths or a different
Re: [Freesurfer] Tracula/ config file error
What program are you viewing it in? If you add a line at the end of config.txt that says echo $dcmlist (without the quotation marks) and then run source config.txt on the command line, does it print out DKI.nii.gz? On Mon, 1 Jul 2013, Gundran, Andrew wrote: It reads like # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:48 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula/ config file error Can you see that this is all one line? # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) On Mon, 1 Jul 2013, Gundran, Andrew wrote: Yes, the text was saved on a unix system -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:34 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula/ config file error Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go. More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system? a.y On Mon, 1 Jul 2013, Gundran, Andrew wrote: I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing set: Variable name must begin with a letter It has become very, very annoying. PLEASE SOMEONE HELP!!! Andrew -- # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 # Subject IDs # set subjlist = (freesurfer) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /home/baileype/Desktop/JG005 set dcmlist = (DKI.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 = /home/baileype/Desktop/JG005/bvecs # 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 = /home/baileype/Desktop/JG005/bvals # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1 # 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 = 0.2 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used
Re: [Freesurfer] Tracula/ config file error
That probably means you're not running a C shell. That's fine, can you
instead try running trac-all and see if it prints out the value of
dcmlist now that you've added that line?
I'll repeat my other question: What program are you using to view the text
file?
On Mon, 1 Jul 2013, Gundran, Andrew wrote:
Whoops. It doesn't read like that every # is a new line along with each set
I did that and the error was
Line13: syntax error near unexpected token `('
Line 13: `set subjlist = (freesurfer)
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 3:09 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula/ config file error
What program are you viewing it in? If you add a line at the end of config.txt that says echo
$dcmlist (without the quotation marks) and then run source config.txt on the command line,
does it print out DKI.nii.gz?
On Mon, 1 Jul 2013, Gundran, Andrew wrote:
It reads like
# Input diffusion DICOMs (file names relative to dcmroot) # If
original DICOMs don't exist, these can be in other image format # but
then bvecfile and bvalfile must be specified (see below) # set dcmroot
= /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 2:48 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula/ config file error
Can you see that this is all one line?
# Input diffusion DICOMs (file names relative to dcmroot) # If
original DICOMs don't exist, these can be in other image format # but
then bvecfile and bvalfile must be specified (see below) # set dcmroot
=
/home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)
On Mon, 1 Jul 2013, Gundran, Andrew wrote:
Yes, the text was saved on a unix system
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 2:34 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula/ config file error
Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep
breath and let it all go.
More to the point, when I view the text file that you sent, I see that several
of the lines are joined together, so both the dcmroot and dcmlist variables
appear commented out. Is this intentional? Was this text file saved on a unix
system?
a.y
On Mon, 1 Jul 2013, Gundran, Andrew wrote:
I have been trying to run tracula with a config file but keep
getting the same error message when I use the trac-all command for
pre-processing
set: Variable name must begin with a letter
It has become very, very annoying. PLEASE SOMEONE HELP!!!
Andrew
--
# FreeSurfer SUBJECTS_DIR
# /home/baileype/Desktop/JG005/freesurfer/mri
#
setenv SUBJECTS_DIR /home/baileype/Desktop/JG005
# Output directory where trac-all results will be saved # Default:
Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005
# Subject IDs
#
set subjlist = (freesurfer)
# In case you want to analyze only Huey and Louie # Default: Run
analysis on all subjects # set runlist = (1)
# Input diffusion DICOMs (file names relative to dcmroot) # If
original DICOMs don't exist, these can be in other image format #
but then bvecfile and bvalfile must be specified (see below) # set
dcmroot =
/home/baileype/Desktop/JG005 set dcmlist = (DKI.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 =
/home/baileype/Desktop/JG005/bvecs
# 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 =
/home/baileype/Desktop/JG005/bvals
# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
# set dob0 = 1
# Input B0 field map magnitude DICOMs (file names relative to
dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist =
(huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)
# Input B0 field map phase DICOMs (file names relative to dcmroot) #
Only used if dob0 = 1 # Default: None # # set b0plist =
(huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1
# 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
