Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Contrast matrix for per-vertex regressor
by Elisa Scariati 04 Jul '13

04 Jul '13

Dear freesurfers, I'm currently making a per-vertex analysis using the --pvr flag of mri_glmfit. I already made within-group correlations between thickness and lGI correcting for age and gender that worked perfectly. However, when I tried to make a between groups comparison, I ran into an error and I'm wondering if I did it correctly. I want to compare the slope of the pvr between my groups, so I will use a DODS design. In my fsgd file I have the following columns: group, age, gender. So, counting my pvr, I should have in my contrast matrix 2*(3+1)=8 columns. I made my contrast this way : 0 0 0 0 0 0 1 -1 However, when running mri_glmfit, I get the following error: ERROR: dimension mismatch between X and contrast C22qVScon.txt X has 7 cols, C has 8 cols As my matrix file has 6 columns corresponding to what would be expected from my fsgd file (two for group, gender and age, that contain the correct values), it seems that there is only one column added for the pvr instead of two. Do anyone know if I made a mistake or is it not possible to compare pvr between groups this way? Thank you in advance for your answer, Best regards Elisa

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How to maximize the number of subjects on a machine?
by ye tian 04 Jul '13

04 Jul '13

Dear Freesurfers, I am currently running 4 subjects, each on a separate x11 window. With 19 subjects at hand and subsequent manual editing, I can't resist the temptation to open more x11 terminals and to submit more jobs. However, how do I know that I max out the machine's computing power? Hard drive info Processor Name: Intel Core i5 Processor Speed: 2.7GHz Number of Processors: 1 Total number of cores: 4 Memory: 16GB Thank you very much! Sincerely, Ye

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cerebellum
by clelia pellicano 04 Jul '13

04 Jul '13

Dear all, it is just a simple question. How reliable are the cerebellum WM and cortex volumes? There is any kind of manual editing for this structure? Thank you so much, Clelia

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Available post doc position
by Anders Martin Fjell 03 Jul '13

03 Jul '13

Available post doc/ PhD position At the Research group for lifespan changes in brain and cognition (LCBC) at the University of Oslo (Norway), we have an available post doc position on the project "Patterns and mechanisms of brain atrophy in healthy aging and dementia: Why is the aging brain susceptible to Alzheimer's Disease?" We will also consider applications from excellent PhD candidates. Deadline for applications is August 15th, and expected start date will be October 2013. The position is for three years. The position The successful candidate will work on the multi-center international project "Patterns and mechanisms of brain atrophy in healthy aging and dementia: Why is the aging brain susceptible to Alzheimer's Disease?" financed by the Norwegian Research Council. MRI, PiB PET/ CSF Abeta and cognitive data from large samples of elderly participants, MCI patients and AD patients will be analyzed. The candidate will be heavily involved in these analyses, as well as in writing papers on the results. The yearly salary for a post doc candidate will be equivalent of approximately 82.000-92.000 USD, while the yearly salary for a PhD candidate will be equivalent of approximately 71.000-80.000 USD. Requirements In addition to a formal background with a master or PhD in a relevant field, such as informatics/ physics/ mathematics, psychology, medicine, neurobiology/ neuroscience, the candidate needs excellent skills in neuroimaging. Expertise in FreeSurfer and preferably FSL will be important. Some programming skills, e.g. MatLab, Python etc, are also necessary. The candidate needs to be excellent in English, both oral and in writing. Interest and expertise in Alzheimer Disease research will also be an advantage. The research group The project is coordinated from Research Group for Lifespan Changes in Brain and Cognition (LCBC) at the Department of Psychology, University of Oslo, Norway. LCBC is a very active research group, and currently includes 16 full-time positions (faculty, post docs, PhD candidates). The project involves extensive collaborations with several AD centers and neuroimaging centers in the US and Europe. Bruce Fischl and Doug Greve from Harvard (FreeSurfer) and Steve Smith and Heidi Johansen-Berg from Oxford (FSL) are collaborators on the project and will participate in the neuroimaging analyses. The candidate will take active part in this collaboration. Link to the application form can be found here: http://uio.easycruit.com/vacancy/1001919/65775?iso=gb If you have questions or want more information, please contact PI Anders M Fjell (andersmf(a)psykologi.uio.no) -- Anders M Fjell Professor of cognitive psychology Research Group for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo www.oslobrains.no

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Tracts appear to be too large and malformed.
by Susan Kuo 03 Jul '13

03 Jul '13

Hi Anastasia, I am reviewing some of the subject's tracts - specifically looking at the uncinate fasciculus, and I noticed that some of the tracts look malformed. They look "chubby" and overgrown in some cases. Can you suggest a reason why this might be, and what I can do to control for this? Attached is a jpg showing the uncinate fasciculus in either hemisphere. As you can see, the right side is considerably larger and poorly defined. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

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Uncinate tract appears to be malformed
by Susan Kuo 03 Jul '13

03 Jul '13

Hi Anastasia, I am reviewing some of the subject's tracts - specifically looking at the uncinate fasciculus, and I noticed that some of the tracts look malformed. They look "chubby" and overgrown in some cases. Can you suggest a reason why this might be, and what I can do to control for this? Attached is a jpg showing the uncinate fasciculus in either hemisphere. As you can see, the right side is considerably larger and poorly defined. I'm also attaching a tgz file that contain all the files in <subject_dir>/dpath/rh.unc_AS_avg33_mni_bbr, for your perusal. Any help you can offer will be greatly appreciated by me! Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

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Re: [Freesurfer] Tracula/ config file error
by Anastasia Yendiki 03 Jul '13

03 Jul '13

What is the trac-all command line that you're running? On Wed, 3 Jul 2013, Gundran, Andrew wrote: > I dont seem to have a trac-all.log file in the scripts directory. I do however have a recon-all.log. I'll attach > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: Wednesday, July 03, 2013 2:42 PM > To: Gundran, Andrew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Tracula/ config file error > > Can you please send the trac-all.log file from the scripts directory? > > On Wed, 3 Jul 2013, Gundran, Andrew wrote: > >> That'd be a yes to both your questions. >> >> -----Original Message----- >> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >> Sent: Wednesday, July 03, 2013 2:33 PM >> To: Gundran, Andrew >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] Tracula/ config file error >> >> >> You're very welcome. Is your freesurfer recon-all output for this subject under /home/baileype/Desktop/JG005/freesurfer? Does the file mri/aparc+aseg.mgz exist? >> >> I'm cc-ing the freesurfer list so that our conversation is archived, other users benefit from it, and we avoid replication of questions. >> >> On Wed, 3 Jul 2013, Gundran, Andrew wrote: >> >>> I've reattched the actual file so it might be easier. >>> Thanks for all the help. >>> ________________________________________ >>> From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] >>> Sent: Monday, July 01, 2013 3:38 PM >>> To: Gundran, Andrew >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: 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: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. >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] Tracula/ config file error
by Anastasia Yendiki 03 Jul '13

03 Jul '13

You're very welcome. Is your freesurfer recon-all output for this subject under /home/baileype/Desktop/JG005/freesurfer? Does the file mri/aparc+aseg.mgz exist? I'm cc-ing the freesurfer list so that our conversation is archived, other users benefit from it, and we avoid replication of questions. On Wed, 3 Jul 2013, Gundran, Andrew wrote: > I've reattched the actual file so it might be easier. > Thanks for all the help. > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: Monday, July 01, 2013 3:38 PM > To: Gundran, Andrew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: 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: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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Volume ROI statistics
by Garikoitz Lerma-Usabiaga 03 Jul '13

03 Jul '13

Hi, I want to obtain volume statistics from a ROI in fsaverage. I have register.dat and a .nii file (the ROI), but I don't now how to get to the .label. The last try has been: mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/ROI.nii --o $SUBJECTS_DIR/fsaverage/label/ROI.mgh --reg $SUBJECTS_DIR/fsaverage/mri/transforms/my_own_register_created_with_bbregister.dat --targ fsaverage (but it is failing, error: corRead(): can't open file $SUBJECTS_DIR/fsaverage/COR-.info) My next steps were: cor2label (in fsaverage) mri_label2label (per every subject) mri_segstats (per every subject) Is there any simpler method to accomplish the same? Or at least that it works? many thanks, Gari

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Re: [Freesurfer] [tracula] running into trouble with nifti data
by Anastasia Yendiki 03 Jul '13

03 Jul '13

Hi Satra - What you're showing in the screenshots would be consistent with a L-R flip of the gradient directions, which is what my comparison of your gradients to the original Siemens gradients indicated. (Assuming the data was acquired with the standard Siemens 60 gradient directions.) a.y On Tue, 2 Jul 2013, Satrajit Ghosh wrote: > hi ay, > i'll look into the orientations a little later tonight, but here is V1 > overlaid on FA for preflip and postflip execution of dtifit. > > cheers, > > satra > > > On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What > flip4fsl will do is convert it to LAS, and perform the same > conversion on the gradient table that you provide. This of > course assumes that dwi_orig.nii.gz and your gradient table are > consistent as they come out of your custom preprocessing. Is > there any chance that they're not? > > Looking at the sample data set that you sent me, I can only see > what came out of your preprocessing and not what went in. I'm > assuming that this is from the standard Siemens 60 direction > sequence, and it has 57 directions b/c 3 of them were thrown out > by your preprocessing. I don't know which directions were thrown > out obviously, but the first 2 directions in your gradient table > are: > -0.99699027939850948 -0.057720153020443053 0.051758263409041924 > 0.63287878858184599 0.066164234845749903 0.77141869630019422 > > The first two directions in the Siemens 60 direction gradient > table are: > 1.0000000000 0.0000000000 0.0000000000 > 0.5867917880 -0.3765825401 -0.7168409782 > > There's not only a small adjustment of the direction but also a > sign change there. So I'd look into that. > > Let me know if any of my assumptions about your original data is > wrong. > > a.y > > On Tue, 2 Jul 2013, Satrajit Ghosh wrote: > > hi anastasia, > i'm trying to debug a seg fault that some folks are > seeing deep into a > tracula run. > > process: > > 1. feed dicoms to a script that runs DTIPrep and > outputs a nifti file, bvec, > bval > > (among checking for many artifacts, this reduces the > b=0 volumes to a single > registered mean volume, runs eddy correction, > discards bad directions, > reorients the gradients appropriately and generates > a report of the quality) > > 2. run tracula on this nifti file > > observation: > > when i run fsl/dtifit on the same nifti file + bvec > + bval, i get the proper > orientation for eigvec1 lines. however, when i feed > this into tracula, the > output of the dtifit step looks terrible - i.e. the > lines are not oriented > as how one might expect water to diffuse. > > suspicion: > > although i have not reached the crash yet, i believe > it might be related to > this fact that the gradients are not oriented > properly relative to the > volume. > > i also suspect that this has something to do with > the flip4fsl step inside > tracula, which is possibly unnecessary because fsl > already likes the input > files. but it seems this step is encoded quite > heavily within the trac-all > scripts. > > questions: > > a. is there a quick way to turn the flip4fsl step > off? > b. alternatively do you have any suggestions for > what to do here? > > the whole point of running through DTIPrep is to > clean up the data before > giving it to tracula or other programs, so i would > really like to keep that > step. > > cheers, > > satra > > > > > > 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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Freesurfer