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30084 discussions

Re: [Freesurfer] Tracula: trac-all prep badly formed if error
by Anastasia Yendiki 18 Dec '15

18 Dec '15

Hi Katherine - I believe that it's because you define bvecfile and bvalfile as lists of 2 file names each. Both bvecfile and bvalfile accept a single file name. In bveclist you can enter as many gradient tables as input volumes. Best, a.y On Thu, 17 Dec 2015, Katherine Damme wrote: > Here is all of the output to the terminal. > > On Thu, Dec 17, 2015 at 5:12 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Katherine - I don't see this error in the log file, but the > last > command that it ran before it stopped was this: > > mri_probedicom --i > /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR. > Temple.9.1.20140521.105357.1f9ykdm.dcm > > > /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dcminfo.dat > > Does this .dat file exist? If so the error probably happened > after this > command. Can you send the exact error message that you see on > your > terminal? > > Thanks! > > a.y > > On Tue, 15 Dec 2015, Katherine Damme wrote: > > > Hello Everyone! > > > > I am getting a badly formed number error in my trac-all any > ideas? > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > -- > > Kate Damme | Affective and Clinical Neuroscience Lab | Northwestern > University > > (847) 491-4069 | 2029 Sheridan Rd. | 226 Swift Hall | > email | LinkedIn | Academic > > > >

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Re: [Freesurfer] question BrainMap
by Thomas Yeo 18 Dec '15

18 Dec '15

Hi Joost, This is a good question and something I should have anticipated. I am cc-ing the freesurfer list (since it might be helpful for others). I am attaching a zip file. If you unzip the zip file, the folder YeoBrainmapFreeSurfer/Specialization/ contains 10 csv files corresponding to 10 to 14 components, left and right hemispheres, i.e., 5 x 2 = 10 files. Each csv file consists of two columns. First column corresponds to ROI number and second column corresponds to top component. For example, for 12 components, the ROI in the superior temporal lobe corresponds to ROI #2 and is specialized for component 3 (auditory). So the csv file (rh.YeoSpecialization_12comp_top.csv) has a row with first column corresponding to 2 and second column corresponding to 3. Let me know if this makes sense. Regards, Thomas On Thu, Dec 17, 2015 at 8:49 PM, Joost Janssen <joost.janssen76(a)gmail.com> wrote: > Dear Prof. Yeo, > > Frame 2 of lh.Yeo_Brainmap_10to14Comp_SpecializationROI.mgz > > contains all the numbered ROIs of the 12-component specialization map, but > the ROIs are not categorized in each of the 12 components - i think. Goal: I > have results on fsaverage and want to quantify the overlap (# vertices) with > each of the 12 components and for this i need the ROIs to be categorized > into components (e.g. ROI #1 - component X, ROI #2 - component Y, etc.), i > think. > > advice? > > thanks! > -joost

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WM Hyperintensities
by Junjie Wu 17 Dec '15

17 Dec '15

Hello all, I have a quick question. As we know, T2 FLAIR can be used in Freesurfer to refine the pial surfaces. I am wondering if T2 FLAIR can also be used to improve the detection of white matter hyperintensities? Thanks, Junjie

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annot file to volume mask in the subject folders
by Woo, Jonghye 17 Dec '15

17 Dec '15

Hi Freesurfers, What would be the best way to convert annot to volume mask (like nifty format) from fsaverage atlas? Thanks,

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average cortical thickness measure?
by Maria Kharitonova 17 Dec '15

17 Dec '15

Hi, in response to the average thickness measure (see below). In ?h.aparc.stats, I see a variable ThickAvg, is that it? And then to get the average thickness across the *entire* cortex, I average across the couple of dozen regions that it provides? Thanks! Maria > > >Message: 7 >Date: Fri, 11 Dec 2015 13:49:23 -0500 >From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] average cortical thickness measure? >To: freesurfer(a)nmr.mgh.harvard.edu >Message-ID: <566B1AB3.9090309(a)nmr.mgh.harvard.edu> >Content-Type: text/plain; charset=windows-1252; format=flowed > >In ?h.aparc.stats, you'll find a line like > ># Measure Cortex, MeanThickness, Mean Thickness, 2.40617, mm > >You'll have to get the value for each hemi and compute the mean > > >On 12/11/2015 01:38 PM, Maria Kharitonova wrote: >> I know that the aseg atlas provides a number of voume measures >> (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a >> variable for an average cortical thickness? I?d like to see if >> thickness in some of the regions is associated with a variable of >> interest over and above an overall main effect, so would like to >> control for the average thickness, but can?t figure out a good way to >> do that. >> >> Thanks! >> Maria >> >> ? >> Maria Kharitonova, PhD >> Research Assistant Professor >> Department of Medical Social Sciences >> Northwestern University Feinberg School of Medicine >> 625 N. Michigan Ave, Suite 2700 >> Chicago, IL 60611 >> Phone: (312) 503-6503 >> Email: maria.kharitonova(a)northwestern.edu >> <mailto:maria.kharitonova@northwestern.edu> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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 >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/ > > > >------------------------------

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gyrification and longitudinal processing
by Bernardoni, Fabio 17 Dec '15

17 Dec '15

dear freesurfer enthusiasts, does it makes sense to compute the local Gyrification Index (lGI) on longitudinally preprocessed subjects? thanks fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Tel. +49 (0)351 458-5245 Fax +49 (0)351 458-7206 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Merge both hemispheres in cortical parcellations
by Carme Uribe Codesal 17 Dec '15

17 Dec '15

Dear FreeSurfer users, I've been looking for an appropiate way to merge both hemispheres in the Desikan parcellations but I can't find it in the list. Which formula do I need to use to consider, for example, the bilateral posterior cingulate as an only measure (not lh and rh separated)? I'm not sure if I can just add them in a mean... Thank you very much for your help! Carme

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Position Available: Director of Machine Learning Core
by Thomas, Adam (NIH/NIMH) [E] 17 Dec '15

17 Dec '15

The NIMH is starting up a Machine Learning core facility and needs a director. Apply now! Title 42 Staff Scientist / Director Machine Learning Core National Institute of Mental Health, National Institutes of Health Department of Health and Human Services, Bethesda, MD The National Institute of Mental Health (NIMH), a major research component of the National Institutes of Health (NIH), and the Department of Health and Human Services (DHHS), is seeking exceptional candidates for the Director position in the Division of Intramural Research Programs (DIRP) of the newly created Machine Learning Core (MLC). The NIMH DIRP represents one of the largest concentrations of neuroimaging researchers in the world with experts in cognitive neuroscience, mental health, neurological disorders, functional MRI methods and technology, DTI, high field imaging, parallel imaging, spectroscopy, and molecular imaging, among others. The NIH also hosts a world class high performance computing cluster with 20,000+ computing nodes and over a petabyte of storage (http://hpc.nih.gov <http://hpc.nih.gov/>). The new Machine Learning Core will be responsible for developing, facilitating, and supporting machine learning approaches to analyzing human neuroimaging data collected within the NIMH IRP as well as the currently growing number of functional and anatomic imaging databases worldwide. The MLC will also be responsible for assisting investigators in their own research for the search for biomarkers to help diagnose mental health and neurologic disorders in individual subjects. Lastly, MLC will provide extensive education and outreach efforts to help NIMH IRP investigators learn more about machine learning approaches and effectively collaborate with machine learning experts. Candidates must have a Ph.D. in a STEM discipline, post doctoral experience in machine learning approaches, and a passion for applying computational analysis to imaging data towards the goal of deriving biomarkers. Skill and experience in fMRI and MRI acquisition and analysis methods will be considered very favorably. The director’s role will include hiring and supervising junior machine learning specialists, maintain the core’s budget, managing an educational series focused on machine learning for NIMH IRP staff, developing novel and generally useful machine learning approaches, and providing support to investigators in machine learning analyses. Salary will be commensurate with education and experience. Application deadline is March 1, 2016. Applicants should send curriculum vitae and three letters of recommendation to: Peter A. Bandettini, Ph.D. MLCORE-JOBSEARCH(a)mail.nih.gov bandettini(a)nih.gov Building 10, Room 1D80 10 Center Drive Bethesda, MD 20892-1148, 301-402-1333 TTY: MD Relay Operator at 1-800-735-2258. The National Institutes of Health is an equal opportunity employer. http://bit.ly/Machine_Learning_Core_Director

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Fwd: error in long_mri_slopes
by Nabin Koirala 17 Dec '15

17 Dec '15

Hi all, I am doing longitudinal analysis (recon-all) and while running the long_mri_slopes using the following command, I am getting different errors for each run and its driving me crazy. The command I am running : long_mris_slopes --qdec ./qdec/long.qdec.Sub_7_t0t1.dat --meas thickness --hemi lh --do-avg --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /home/nk/freesurfer/subjects/ I could not make any sense as the errors as they are different every time and sometimes it gets completed aswel. The various errors are : ERROR 1 : mri_convert splitting qcache stack did not work? ERROR 1 : mris_label_calc intersect did not work? ERROR 1 : mri_glmfit did not work? These are for the same subject and for the same hemisphere. And once it completed for left hemisphere but threw similar error for right hemisphere. Your suggestions would be very much appreciated. PS This is not only for one subject but for most of them. Thank you. Regards, Nabin

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freeview automatization not working nicely
by BAUTISTA-PERPINYA Maximilià 17 Dec '15

17 Dec '15

Hi FS experts, I have an script (screenshots.txt) that takes screenshots of freeview of several scans: It looks like this: -v scan1/mri/T1.mgz ; -v scan1/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; -viewport sagittal -slice 80 127 127 -ss sag1_scan1 ; -v scan2/mri/T1.mgz ; -v scan2/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; -viewport sagittal -slice 80 127 127 -ss sag1_scan2 ; ... and so on Then I run freeview -cmd screenshots.txt and it gives me this error: MRIread failed: Unable to read from /home/freesurfer/Desktop/test005/subjects/; This path is my cwd. The scan folders (scan1, scan2, and so on) are contained within the above mentioned cwd, but the cwd is not mentioned in the script. I tried specifying the complete path (/home/freesurfer/Desktop/test005/subjects/scan1 and so on) but gives the same error. As well, the only output from this is the screenshot from the last scan (sag1_scan2 in this case). The other ones before are missing. Anybody knows a way around this? Any help would be much appreciated Best regards, Max Bautista btw: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 ---------------------------------------------------------------------

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