Freesurfer

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19 participants
30088 discussions

define four major fiber tracts
by lujiao luo 14 Oct '13

14 Oct '13

Dear experts, I was trying to define the ILF(inferior longtitudinal fasciculus), IFOF(inferori fronto-occipital fasciculus), arcuate fasciculus, and corpus callosum (CC). But I am not very familiar with the structure of the cortex. So I am considering that if I can segment some roi files from freesurfer aseg+aparc.annot file and changing them into .nii.gz file, Then use these rois as the seed of fiber tracking. Would you mind teaching me which rois I choose for each fiber tract if this way is possible? Another question is about the meaing of labels with a wm- begining (e.g. wm-lh-G_frontal_superior) in the look-up table. Does it represent the white matter within the lh-G_ frontal_ superior or represent all white matter that passed through lh-G_frontal_superior? Thanks so much for your concern. Yours, Lulu

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Re: [Freesurfer] Tracula configuration error
by Anastasia Yendiki 14 Oct '13

14 Oct '13

Hi Michael - It doesn't look like the configuration file is the problem, or at least I cannot replicate it. I ran "trac-all -c dmrirc.txt -prep" on a mac and a linux machine and the only error I got was that the SUBJECTS_DIR doesn't exist (as expected since I don't have your directory structure). What system are you running this on? a.y On Mon, 14 Oct 2013, Michael Datko wrote: > Hi Anastasia,No log files were created, it seems like the program does not even begin to run. I get that > error immediately upon calling trac-all. I pasted the entire configuration file into the original > message, but I attach it here as well. > > Thanks, > Mike > > > > > On Mon, Oct 14, 2013 at 1:55 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Michael - It's hard to tell at which point it fails. Is there any output, is there a > trac-all.log? If so, can you please attach the entire file, as well as the entire > configuration file? > > Thanks, > a.y > > On Sat, 12 Oct 2013, Michael Datko wrote: > > Hello,I have been trying to set up a working Tracula configuration file and I keep > getting an error: > > set: Variable name must begin with a letter > I have searched previous message board questions and it seems that others have > seen this same error. I > have tried implementing some of their solutions, as well as searching my code for > a problem, but I cannot > find the source. Any advice? I am trying to get this working for a single > subject for now. I used the > dmrirc.example file as a template. I am calling trac-all from the tcsh command > line with the following: > trac-all -c dmrirc.example -prep > > The contents of my dmrirc file are below, I have deleted most of the options for > which I am just using the > default, to make things simpler. > > Thank you, > Mike > > # FreeSurfer SUBJECTS_DIR > # T1 images and FreeSurfer segmentations are expected to be found here > # > setenv SUBJECTS_DIR /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer > > # Output directory where trac-all results will be saved > # Default: Same as SUBJECTS_DIR > # > set dtroot = /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer > > # Subject IDs > # > set subjlist = (a226A) > > # 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 = /Users/mdatko/Desktop/tracula_tutorial/data/dti > set dcmlist = (a226A/226A/data.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 = > /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvecs.txt > > # Diffusion b-value table > # Must be specified if inputs are not MGH DICOMs > # Single-column format, one value for each volume in the diffusion data set > # Default: Read from DICOM header > # > set bvalfile = > /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvals.txt > > # Perform registration-based eddy-current compensation? > # Default: 1 (yes) > # > set doeddy = 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 > > # 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 > > > > > > 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] bvecs and bvals don't have the same number of entries
by Anastasia Yendiki 14 Oct '13

14 Oct '13

Hi Laura - I don't think the error "bvecs and bvals don't have the same number of entries" should have to do with interspersed zero b-values. When you run "wc -l" on the bvecs and bvals files, what do you get? a.y On Mon, 14 Oct 2013, Laura Christine Anderson wrote: > Hi Anastasia, the bval/bvec files were created on a Mac and not with > excel. I am not seeing the ^M character when I view the files in unix with > the more command or in gedit perhaps when I sent you the files, something > became corrupted? I am wondering if my issue has something to do with the > fact that there are 3 sets of 30 rows with a b0 image before each of the 3 > sets. In the examples I have seen, the b0 images all seem to be at the > beginning of the bvec and bval files. I am attaching a screenshot of the > bvec and bval files as I see them in case that is helpful. If you would > rather me send the actual files again, what is the best way to do that > without the formatting getting messed up? Before, I was using a free > fileshare program. > > Thank you! > Laura > > Laura C. Anderson, B.A. > Graduate Student > Clinical & Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > > > > > On 10/11/13 2:38 PM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > >> >> Hi Laura - Were these bval/bvec files created on windows or with excel by >> any chance? When you view them in unix (with the more command for >> example) >> you'll see an "^M" character instead of every end-of-line. Can you try >> editing these files in a unix editor to fix that? Let me know if this >> solves the problem. >> >> a.y >> >> On Fri, 11 Oct 2013, Laura Christine Anderson wrote: >> >>> Hi Anastasia, >>> Thanks so much for your help! Attached are bvec, bval and trac-all.log >>> files. >>> >>> I have been stuck at one of the preprocessing steps (trac all) for some >>> time and keep getting the >>> error: bvecs and bvals don't have the same number of entries. I saw a >>> couple blogs online about >>> this, but did not see any resolution. I am wondering if it is because >>> the B0 images are >>> interspersed? (see attached bvec file). If you have any insight, I >>> would love some feedback >>> whenever you get the chance. >>> >>> Laura >>> >>> >> >> >> 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 configuration error
by Michael Datko 14 Oct '13

14 Oct '13

Hello, I have been trying to set up a working Tracula configuration file and I keep getting an error: set: Variable name must begin with a letter I have searched previous message board questions and it seems that others have seen this same error. I have tried implementing some of their solutions, as well as searching my code for a problem, but I cannot find the source. Any advice? I am trying to get this working for a single subject for now. I used the dmrirc.example file as a template. I am calling trac-all from the tcsh command line with the following: trac-all -c dmrirc.example -prep The contents of my dmrirc file are below, I have deleted most of the options for which I am just using the default, to make things simpler. Thank you, Mike # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer # Subject IDs # set subjlist = (a226A) # 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 = /Users/mdatko/Desktop/tracula_tutorial/data/dti set dcmlist = (a226A/226A/data.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 = /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvecs.txt # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvals.txt # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 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 # 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

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QA in Tracula
by Garikoitz Lerma-Usabiaga 14 Oct '13

14 Oct '13

Dear Anastasia, I am visually inspecting the output of Tracula, and checking the stats on pathstats.overall. For example, in the following image (S_23_...) it can be seen that the rh.slfp is missing (there is just a very small piece of it). The rest of the tracts seem to be ok. In the stats the four xx_Avg_Center values are a NaN, and the value of the volume and Len_xx are the same, excepting Len_Center, which is zero. Although there are more statistics, I understand we should convert the whole line to NaN and not include the data of this specific subject/tract in the statistics, right? (and should I script it to make it happen always? - I mean, always that there is Len_Center=0, make everything NaN - ). [image: Inline image 5] I did freeview dpath/rh.slfp_PP_avg33_mni_bbr/path.pd.nii.gz as recommended in a the email list, and the path looks exactly like in this image. In the next image (S_13_...) there are more problems. -- rh.slft missing (not showing in the image). Len_Center=0 again. -- fmajor almost not there, but Len_Center=1 -- lh.ccg much shorter than the rh.ccg -- very strange looking rh.cab [image: Inline image 6] Should I consider all those tracts out of the statistics? Is there any way to mend those? (if yes, where can I find documentation?) And last question: I understand that I could control the volume of the tracts with ICV as it is done for other volumes, but, should I control for the FA values? What exactly is FA_Avg_Weighted? (sorry, couldn't find any documentation on that while searching). Thank you very much again and sorry for long post! Gari PS note that I plotted the hippocampus as well because I am analyzing it in the same study.

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Fwd: OHBM 2014 Call for Council Nominations
by Douglas Greve 14 Oct '13

14 Oct '13

-------- Original Message -------- Subject: OHBM 2014 Call for Council Nominations Date: Mon, 14 Oct 2013 09:50:14 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu <mailto:info@humanbrainmapping.org> Dear OHBM Member: Strong leadership is the key component to setting and accomplishing OHBM’s strategic goals and in anticipating future needs. The OHBM Nominating Committee will continue to work diligently to develop a slate of candidates for election on the Council, but *we need your participation now in identifying candidates.* The Nominating Committee is pleased to invite OHBM members to nominate individuals to serve on the OHBM Council. Open positions include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program Chair-Elect and Education Chair-Elect. The term of service begins in June 2014, and each term is for three years. Please make your nominations by completing the Call for Nominations form <http://www.humanbrainmapping.org/i4a/forms/index.cfm?id=25> no later than *Friday, November 22^nd at* *11:59 PM US CST*. Self-nominations are welcome and encouraged. The OHBM By-Laws <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3292>, Article 5 provides the framework and process for the election of new Council members. *OHBM Nominating Committee:* Simon Eickhoff, Secretary Doug Greve, Secretary-Elect Thomas Nichols, Past Secretary Steve Smith, Chair Susan Berman, Chair-Elect Susan Bookheimer, Past Chair You must, when making your nominations, specify a position you want the person to fill (Chair Elect, Treasurer Elect, Secretary Elect, Program Chair Elect, Education Chair-Elect) *AND *be sure to check with this person before you make the nomination to be sure they would be interested in serving. Once the final slate is prepared and distributed, members will be able to see a brief bio on each candidate and vote online via the OHBM website. The results of these elections will be announced during the Town Hall Meeting, Wednesday, June 11, 2014, during the OHBM Annual Meeting in Hamburg, Germany. All candidates identified on the ballot will be informed of the results prior to the Annual Meeting. *Current OHBM Councilors:* * Steve Smith, Chair * Karen Berman, Chair-Elect * Susan Bookheimer, Past Chair * Jia-Hong Gao, Treasurer * Jeanette Mumford, Treasurer-Elect * Julien Doyon, Past Treasurer * Simon Eickhoff, Secretary * Doug Greve, Secretary-Elect * Thomas Nichols, Past Secretary * Pedro Valdes Sosa, Program Chair * Jack Van Horn, Program Chair-Elect * Peter Bandettini, Past Program Chair * Jack Van Horn, Education Chair * Niko Kriegeskorte, Education Chair-Elect * Klaas Enno Stephan, Education Past Chair Councilors are not eligible for re-election for three years after serving one term. Individuals who are currently ineligible as nominees due to service on Council within the past 3 years are listed below. * Maurizio Corbetta, 2011-2012 Chair * Christian Beckmann, 2011-2012 Treasurer * Hugh Garavan, 2011-2012 Secretary * Katrin Amunts, 2011-2012 Program Chair * Michael Beauchamp, 2011-2012 Education Chair * Heidi Johansen-Berg, 2010-2011 Chair * Vince Calhoun, 2010-2011 Treasurer * Jean-Baptiste Poline, 2010-2011 Secretary * Alain Dagher, 2010-2011 Program Chair * John Ashburner, 2010-2011 Education Chair We look forward to your involvement in the identification and election of your association’s leadership. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) ------------------------------------------------------------------------ *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org <http://www.humanbrainmapping.org> info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>.

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regions in FreeSurferColorLUT.txt and the atlas
by Xinyang Liu 14 Oct '13

14 Oct '13

Dear all, In the "FreeSurferColorLUT.txt", what brain regions are represented by "right-vessel" and "left-vessel", respectively? Is there a file or document that explains the definition of regions listed in "FreeSurferColorLUT.txt"? Also, the atlas for subcortical segmentation is in $FREESURFER_HOME/average/RB_all_2008-03-26, which is a ".gca" file. What is this format? Is there a way that I can "see" this atlas in 3D? Can it be transferred to a ".nii" file? Thanks, Xinyang

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bvecs and bvals don't have the same number of entries
by Laura Christine Anderson 11 Oct '13

11 Oct '13

Hi Anastasia, Thanks so much for your help! Attached are bvec, bval and trac-all.log files. I have been stuck at one of the preprocessing steps (trac all) for some time and keep getting the error: bvecs and bvals don't have the same number of entries. I saw a couple blogs online about this, but did not see any resolution. I am wondering if it is because the B0 images are interspersed? (see attached bvec file). If you have any insight, I would love some feedback whenever you get the chance. Laura

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atlases labels coordinates
by maria estanqueiro 11 Oct '13

11 Oct '13

Dear all, I need the center coordinates of the anatomical labels from the desikan and destrieux atlases. I saw a similar post a while ago in which it was recommended the following: #1 Convert the annotation to a set of labels. This is for the Desikan atlas, but you can spec the destrieux instead mri_annotation2label --subject fsaverage --hemi lh --outdir ~/tmp/aparc # For each label, run mri_surfcluster to get the centroid mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel lh.pericalcarine.label --sum sum.lh.pericalcarine --centroid --thmin 0 --hemi lh --subject fsaverage I did the last step step for 2 different labels, one in the temporal and the other in the occipital cortex. However, the coordinates that were generated in the sum files were the same. Does anyone know why? Is this the right procedure for what I want to do? Thanks!

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Normalization for brain/head size differences in a pediatric population
by David O Kamson 11 Oct '13

11 Oct '13

FreeSurfers, I have a couple of questions regarding normalization for brain/head size. We are trying to analyze a pediatric population with subjects between age 4 and 16 with variable brain (and head) sizes. We are mainly interested in measuring cortical thickness in these children, but not sure whether volumetric normalization should be performed or the output of the recon-all -all script is already comparable among subjects with different ages and brain sizes. As per the eTIV page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV) of the FreeSurfer website, cortical thickness information cannot be normalized using volumetric information. Does this mean it doesn't have to be normalized in our population at all? If normalization for cortical thickness is necessary, what approach at what stage would you suggest to use? For volumetric information, is there any data suggesting normalization to the estimated intracranial volume does not work in children? Your help is much appreciated! David Olayinka Kamson, MD Research Associate PET Center Children's Hospital of Michigan 3901 Beaubien, Detroit, MI 48201 Phone: 313-745-0668 FAX: 313-966-9228 david.kamson(a)pet.wayne.edu

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