Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Re: [Freesurfer] Tracula/ config file error
by Anastasia Yendiki 01 Jul '13

01 Jul '13

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:ayendiki@nmr.mgh.harvard.edu] > Sent: Monday, July 01, 2013 3:09 PM > To: Gundran, Andrew > Cc: freesurfer(a)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:ayendiki@nmr.mgh.harvard.edu] >> Sent: Monday, July 01, 2013 2:48 PM >> To: Gundran, Andrew >> Cc: freesurfer(a)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:ayendiki@nmr.mgh.harvard.edu] >>> Sent: Monday, July 01, 2013 2:34 PM >>> To: Gundran, Andrew >>> Cc: freesurfer(a)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 number for >>>> each of the # paths specified in pathlist # Default: 7 for the >>>> forceps major, 6 for the corticospinal tract, >>>> >>>> # 4 for the angular bundle, and 5 for all other paths >>>> >>>> # >>>> >>>> set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) >>>> >>>> >>>> >>>> # List of training subjects >>>> >>>> # This text file lists the locations of training subject directories >>>> # >>>> Default: $FREESURFER_HOME/trctrain/trainlist.txt >>>> >>>> # >>>> >>>> set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt >>>> >>>> >>>> >>>> # Number of "sticks" (anisotropic diffusion compartments) in the >>>> bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 >>>> >>>> >>>> >>>> # Number of MCMC burn-in iterations >>>> >>>> # (Path samples drawn initially by MCMC algorithm and discarded) # Default: >>>> 200 # set nburnin = 200 >>>> >>>> >>>> >>>> # Number of MCMC iterations >>>> >>>> # (Path samples drawn by MCMC algorithm and used to estimate path >>>> distribution) # Default: 7500 # set nsample = 7500 >>>> >>>> >>>> >>>> # Frequency with which MCMC path samples are retained for path >>>> distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 >>>> >>>> >>>> >>>> # Reinitialize path reconstruction? >>>> >>>> # This is an option of last resort, to be used only if one of the >>>> reconstructed # pathway distributions looks like a single curve. >>>> This is a sign that the # initial guess for the pathway was >>>> problematic, perhaps due to poor alignment # between the individual and the atlas. >>>> Setting the reinit parameter to 1 and # rerunning "trac-all -prior" >>>> and "trac-all -path", only for the specific # subjects and pathways >>>> that had this problem, will attempt to reconstruct them # with a different initial guess. >>>> >>>> # Default: 0 (do not reinitialize) >>>> >>>> # >>>> >>>> set reinit = 0 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> 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. >>> >>> >>> >> >> >> > > >

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manual editing
by Liane Hunter 01 Jul '13

01 Jul '13

I am new to FreeSurfer and have been tasked with running a large number of subjects through the pipeline. I wanted to inquire about the benefits of manually editing the output data at each step as outlined by the manual. Is there anything in the literature regarding the differences, if any, between data that is manually edited vs. not manually edited. Any guidance on this topic would be much appreciated. Thank you. -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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Re: [Freesurfer] Longitudinal Processing Error
by Jonathan Holt 01 Jul '13

01 Jul '13

I have tried to inspect the tal xfms that were created in the brief time this string was running recon-all -all -s <tpNid> -i path_to_tpN_dcm while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty. upon further inspection the log file is complaining about my nifty. WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > can you cc the list so that others can answer? > > On Mon, 1 Jul 2013, Jonathan Holt wrote: > > I have not and I am not certain how to do so >> >> >> >> On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote: >> >> Hi Jon >>> >>> have you visually inspected the results of the tal xform? >>> Bruce >>> On Mon, 1 Jul 2013, Jonathan Holt wrote: >>> >>> Log file indicates manual talairach alignment may be necessary. >>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>>> ***FAILED*** (p=0.0079, >>>> pval=0.0000 < threshold=0.0050) >>>> Manual Talairach alignment may be necessary >>>> Can anyone provide direction. Alternatively, the error indicates >>>> talairach alignment can be skipped >>>> with -notal-check flag. Is this step completely necessary? >>>> jon >>>> >>>> >>> >>> 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<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. >>> >> >> >> >> >>

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Re: [Freesurfer] Tracula/ config file error
by Anastasia Yendiki 01 Jul '13

01 Jul '13

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:ayendiki@nmr.mgh.harvard.edu] > Sent: Monday, July 01, 2013 2:48 PM > To: Gundran, Andrew > Cc: freesurfer(a)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:ayendiki@nmr.mgh.harvard.edu] >> Sent: Monday, July 01, 2013 2:34 PM >> To: Gundran, Andrew >> Cc: freesurfer(a)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 number for >>> each of the # paths specified in pathlist # Default: 7 for the >>> forceps major, 6 for the corticospinal tract, >>> >>> # 4 for the angular bundle, and 5 for all other paths >>> >>> # >>> >>> set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) >>> >>> >>> >>> # List of training subjects >>> >>> # This text file lists the locations of training subject directories >>> # >>> Default: $FREESURFER_HOME/trctrain/trainlist.txt >>> >>> # >>> >>> set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt >>> >>> >>> >>> # Number of "sticks" (anisotropic diffusion compartments) in the >>> bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 >>> >>> >>> >>> # Number of MCMC burn-in iterations >>> >>> # (Path samples drawn initially by MCMC algorithm and discarded) # Default: >>> 200 # set nburnin = 200 >>> >>> >>> >>> # Number of MCMC iterations >>> >>> # (Path samples drawn by MCMC algorithm and used to estimate path >>> distribution) # Default: 7500 # set nsample = 7500 >>> >>> >>> >>> # Frequency with which MCMC path samples are retained for path >>> distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 >>> >>> >>> >>> # Reinitialize path reconstruction? >>> >>> # This is an option of last resort, to be used only if one of the >>> reconstructed # pathway distributions looks like a single curve. This >>> is a sign that the # initial guess for the pathway was problematic, >>> perhaps due to poor alignment # between the individual and the atlas. >>> Setting the reinit parameter to 1 and # rerunning "trac-all -prior" >>> and "trac-all -path", only for the specific # subjects and pathways >>> that had this problem, will attempt to reconstruct them # with a different initial guess. >>> >>> # Default: 0 (do not reinitialize) >>> >>> # >>> >>> set reinit = 0 >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> >> 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. >> >> >> > > >

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Re: [Freesurfer] Tracula/ config file error
by Anastasia Yendiki 01 Jul '13

01 Jul '13

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:ayendiki@nmr.mgh.harvard.edu] > Sent: Monday, July 01, 2013 2:34 PM > To: Gundran, Andrew > Cc: freesurfer(a)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 number for >> each of the # paths specified in pathlist # Default: 7 for the forceps >> major, 6 for the corticospinal tract, >> >> # 4 for the angular bundle, and 5 for all other paths >> >> # >> >> set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) >> >> >> >> # List of training subjects >> >> # This text file lists the locations of training subject directories # >> Default: $FREESURFER_HOME/trctrain/trainlist.txt >> >> # >> >> set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt >> >> >> >> # Number of "sticks" (anisotropic diffusion compartments) in the >> bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 >> >> >> >> # Number of MCMC burn-in iterations >> >> # (Path samples drawn initially by MCMC algorithm and discarded) # Default: >> 200 # set nburnin = 200 >> >> >> >> # Number of MCMC iterations >> >> # (Path samples drawn by MCMC algorithm and used to estimate path >> distribution) # Default: 7500 # set nsample = 7500 >> >> >> >> # Frequency with which MCMC path samples are retained for path >> distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 >> >> >> >> # Reinitialize path reconstruction? >> >> # This is an option of last resort, to be used only if one of the >> reconstructed # pathway distributions looks like a single curve. This >> is a sign that the # initial guess for the pathway was problematic, >> perhaps due to poor alignment # between the individual and the atlas. >> Setting the reinit parameter to 1 and # rerunning "trac-all -prior" >> and "trac-all -path", only for the specific # subjects and pathways >> that had this problem, will attempt to reconstruct them # with a different initial guess. >> >> # Default: 0 (do not reinitialize) >> >> # >> >> set reinit = 0 >> >> >> >> >> >> >> >> >> > > > 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. > > >

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Tracula/ config file error
by Gundran, Andrew 01 Jul '13

01 Jul '13

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 single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0

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Longitudinal Processing Error
by Jonathan Holt 01 Jul '13

01 Jul '13

Log file indicates manual talairach alignment may be necessary. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates talairach alignment can be skipped with -notal-check flag. Is this step completely necessary? jon

3 2

Re: [Freesurfer] Problem with FS-FAST, mkcontrast (Douglas N Greve)
by O'Shea,Andrew 01 Jul '13

01 Jul '13

I have matlab installed. I have the following lines in my ~/matlab/startup.m file %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% Is there a way check to see if the path is set correctly? Message: 9 Date: Mon, 01 Jul 2013 09:46:39 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Problem with FS-FAST, mkcontrast To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <51D1883F.5050103(a)nmr.mgh.harvard.edu<mailto:51D1883F.5050103@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed doyou have matlab installed and in your path? doug On 07/01/2013 08:55 AM, O'Shea,Andrew wrote: Hello, I am trying to work through the FS-FAST tutorial on my data. I am using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I run ' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 ' I get the following output error: " phhp-jcraggs-mb:Project aoshea$ mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 INFO: Found 1 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o test/pain-v-rest.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile test/pain-v-rest.mat nconds 1, wcond 1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o test/pain-v-rest.mat -wdelay 1 -no-octave Mon Jul 1 08:51:02 EDT 2013 " It is not creating a .mat file in the analysis directory. Any suggestions would be greatly appreciated. Thanks! -Andrew _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 1

Re: [Freesurfer] Fwd: DTI questions
by Anastasia Yendiki 01 Jul '13

01 Jul '13

Hi Rotem - No problem. Were these scans by any chance acquired with a coronal slice prescription? In the axial views that you sent, the artifact that you're pointing to looks like misalignment between consecutive coronal slices, which could be due to head motion. a.y On Tue, 25 Jun 2013, Rotem Saar wrote: > Dear Anastasia, > > I tried several times to upload these images in a non-compressed way, but > they were too big and my posts were rejected, with no opportunity for any > other upload way. > Is there any other way for me to upload it so that everyone can see it ? > > Attached are the images in a non-compressed fashion. I will be very happy if > u will have a look, and post your answer to me and the list to save some > time, until I will be able to consider another way to upload them. > > I know that we should write to all the list, but at the moment if the images > are not visible this won't help - so I will really appreciate if u will have > a look but also tell me what is the best way to upload them so that all list > members will be able to see them. > > Thank u very much for your help. > > Rotem > > 2013/6/25 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Sorry, can't open the image. > > On Sun, 23 Jun 2013, Rotem Saar wrote: > > Hi there, > > Long time:). Well I wrote to the list several times > regarding high FA values > I got when performing DTI analysis. > Today we know that the problem was an additional > direction (we had 17 > directions instead of 16 - we used a Philips > scanner,1.5T). So we deleted > the additional slices and the high values indeed > disappeared, but then > another problem came up (tried several subjects so > the problem is not > specific to a subject) - > > I noticed an artifact that I can't explain - please > see the attached > pictures. > > This artifact existed even before I deleted the > additional slices, also - I > see the artifact also when loading the masked > volume...It is cyclic - run > over all slices... > > any ideas ? > > I'm using version 5.2 and I know the command lines > are correct (send it to u > in the past). > > Thanks for your help > > Rotem > > > > > 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. > > > >

2 2

Pial surface consistently misplaced
by Jonathan Holt 01 Jul '13

01 Jul '13

Hi all, I'm having a bit of trouble with one particular subject for which we brains for 4-5 different time points. The pial surface is consistently misplaced in the same area, see attached main/aux volume images. I'm hesitant to manually replace the white matter myself as I fear it wouldn't be as accurate. Suggestions on other methods to fix this? The problem is always in the LH temporal right around the lateral inferior ventricle and the fusiform and other subcortical structures.

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Freesurfer July 2013