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30132 discussions

Import FS data to FSL
by stdp82＠virgilio.it 25 Sep '13

25 Sep '13

Hi list, I have 2 questions, please. 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)? 2-I'd like to export cortical masks from FS to FSL. An option is mri_binarize but this way failed in probtrackx (fsl).FSL list have advised me that I should use label2surf command to convert label to surface files. Where could find the .label (according to FreeSurferColorLUT.txt) to build mask of frontal, parietal, motor, sensor, temporal and occipital lobes? Do you have other ways that you advise me? Thanks, Stefano

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Technical position available at Columbia/NYPH MRI Unit
by Andrew Gerber 25 Sep '13

25 Sep '13

Direct link: http://rfmh.iapplicants.com/ViewJob-499585.html Please email me with any questions. Best, Andrew Andrew J. Gerber, M.D., Ph.D. Interim Director, MRI Unit Assistant Professor of Clinical Psychiatry New York State Psychiatric Insitute / Columbia University Division of Child and Adolescent Psychiatry Phone: (212) 543-5104 Fax: (917) 522-9588 Email: gerbera(a)nyspi.columbia.edu Research Foundation for Mental Hygiene, Inc. - Jobs<http://rfmh.iapplicants.com> ________________________________ * Senior Computer System Analyst I, Grade 21 Job #499585 - New York, NY Senior Computer System Analyst I, Grade 21 Job #499585 - New York, NY<http://feedproxy.google.com/~r/ResearchFoundationForMentalHygieneInc-Jobs/~…> Posted: DESCRIPTION The MRI Unit and IT Department are jointly seeking applicants for a Senior Computer System Analyst who would serve as a specialist in the design, maintenance, and training for computers and other technical devices required for research using the NYSPI MRI Unit. Specifically, this individual will be responsible for (a) computers and associated software which store and back up MRI acquired data, (b) computers and associated software which present functional stimuli to MRI research participants and record behavioral and psychophysiological responses from participants, and (c) electronic peripherals responsible for presenting and recording functional stimuli and behavioral/psychophysiological responses. This individual will also be responsible for training staff, investigators, and personnel who use the MRI Unit/Core in the use and maintenance of these devices. This individual will be asked to be available on a rotating schedule for emergencies during MRI scanning hours (8 am to 8 pm, 7 days a week but not including holidays) related to the computers and peripherals listed above. Finally, this individual may be trained in operation of the MRI console to serve as a backup operator when the technologists are sick or on vacation. DUTIES - Design, maintain, and train personnel in computers and associated software for storage and back up of MRI data - Design, maintain and train personnel in computers, associated software, and peripheral devices involved in presenting functional stimuli to MRI research participants and recording behavioral and psychophysiological responses. - Be available for emergency maintenance on a rotating schedule with other staff - Train and backup operation of MRI console QUALIFICATIONS - Possesses knowledge of installation and maintenance of systems running Windows, Mac, and Linux operating systems, including experience as a sys admin. - Has at least intermediate programming knowledge include familiarity with shell scripting - Has at least intermediate level skills in building simple electronic circuits, including soldering, building basic circuitry (Arduino or equivalent), and troubleshooting and repairing existing circuits. - An undergraduate or master's level degree in electrical engineering or a related field would be ideal, as well as the skills of an advanced hobbyist. - Must be able to think independently and creatively about solutions to electronic and computer problems, yet also work as part of a team in designing and implementing these tools. - Ideally would have at least some experience in image processing, advanced digital photography - Mandatory evening/weekend coverage as scheduled on a rotating basis. - Participation in medical surveillance required. The Research Foundation is a private not-for-profit corporation and is not an agency or instrumentality of the State of New York. Employees of the Research Foundation are not state employees, do not participate in any state retirement system and do not receive state fringe benefits. Excellent benefits package, AA/EEO Employer. Applications will only be accepted through website at: http://corporate.rfmh.org then click on Employment Opportunities. Applications will be accepted only during the posting dates as listed at the top of the job announcement.

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Monte Carlo Simulation in Qdec
by Tara Ann Miskovich 24 Sep '13

24 Sep '13

Hello, I am conducting group analyses with LGI data in qdec, and I am having an issue with the monte carlo simulation I am hoping to get help with. Under design I leave the Smoothing (FWHM) at 10, and when I try to run the monte carlo simulation after running the analysis I get this error: Error in Monte Carlo simulation: Error running mri_surfcluster. Plus in the terminal I get an error: mri_surfclusterfwhm.dat: 37.226284, rounded to 38 Error: fwhm out-of-range (< 1 or > 30)! Should I be using fwhm0 for LGI data? Thank you for your help! Tara

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Effects of age on different parameters (thickness, lGI...)
by Daniel Klein 24 Sep '13

24 Sep '13

Dear FreeSurfer experts, I want to test linear, square and cubic effects of age on different parameters (thickness, lGI....) with qdec. I add age (square) and age (cubic) as column in my qdec table. Am i right to see only the square effects: Add Age square as continous factor and age (maybe age cubic too?) as nuisance factor in the model. Best wishes and thanks a lot. Daniel

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Malloc(): memory corruption
by ye tian 24 Sep '13

24 Sep '13

Dear freesurfers, I am trying to run clusterwise correction for multiple comparisons. The command line executed smoothly if I run mri-glmfit-sim with --sim mc-z 5 4 mc-z.positive, but it throws the follow error glibc detected *** mri_segstats: malloc(): memory corruption 0x30050bf0 *** I searched the archive, but haven't found a readily executable solution. I have freesurfer 5.3 and my computer ram is 4.0GB. Thank you very much! Sincerely, Ye

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Loading control points into freeview from command line
by Jonathan Holt 24 Sep '13

24 Sep '13

Is there a way to do this? jon

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Re: [Freesurfer] Viewing auxiliary and main volumes simultaneously
by Jonathan Holt 24 Sep '13

24 Sep '13

Never mind, page up/page down are separate from arrow keys. thanks bruce On Sep 24, 2013, at 1:09 PM, Jonathan Holt <whatsdac(a)umich.edu> wrote: > forgot to cc list > >> You'd think that was it, but that simply moves the brain around in it's box, it doesn't change slices. The only way i can go through slices is by grabbing them with the cursor in the 3D view, but I can't navigate slice by slice that way >> >> >> On Sep 24, 2013, at 12:50 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> >>> Hi Jon >>> >>> try page up/page down >>> >>> cheers >>> Bruce >>> >>> >>> On Tue, 24 Sep 2013, Jonathan Holt wrote: >>> >>>> Thanks bruce >>>> >>>> I'm realizing free view is a ton more powerful than tkmedit. I can't figure out how to navigate through the brain slice by slice like I could in tkmedit. >>>> >>>> jon >>>> On Sep 24, 2013, at 12:22 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> there is an opacity slider in freeview you can use for this >>>>> >>>>> cheers >>>>> Bruce >>>>> On Tue, 24 Sep 2013, Jonathan Holt wrote: >>>>> >>>>>> Is there any way to accomplish this? >>>>>> >>>>>> Jon >>>>>> _______________________________________________ >>>>>> 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. >>>>> >>>> >>>> >>>> >>>> >> >

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Re: [Freesurfer] Viewing auxiliary and main volumes simultaneously
by Bruce Fischl 24 Sep '13

24 Sep '13

Hi Jon try page up/page down cheers Bruce On Tue, 24 Sep 2013, Jonathan Holt wrote: > Thanks bruce > > I'm realizing free view is a ton more powerful than tkmedit. I can't figure out how to navigate through the brain slice by slice like I could in tkmedit. > > jon > On Sep 24, 2013, at 12:22 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> there is an opacity slider in freeview you can use for this >> >> cheers >> Bruce >> On Tue, 24 Sep 2013, Jonathan Holt wrote: >> >>> Is there any way to accomplish this? >>> >>> Jon >>> _______________________________________________ >>> 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. >> > > > >

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complex repeated measure model
by Jacobs H (NP) 24 Sep '13

24 Sep '13

Dear FreeSurfers, I am struggling with how to set the fsgd-file and contrast file for a probably complex model. I have two groups: old and young participants. For each participant, I have one T1-weighted image, on which I would like to perform the cortical thickness analyses. This T1 image was collected at baseline. The variable of interest is cognitive performance defined on three different occasions (during which we applied an intervention). We want to investigate susceptibility for this intervention over time, as reflected in this cognitive outcome score. The idea is to investigate whether susceptibility for this intervention is associated with different cortical thickness patterns in old versus in young persons. Is there a way to capture this in one test and then do posthoc pariwise comparisons? Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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LME toolbox for VBM-style data?
by Seán Froudist Walsh 24 Sep '13

24 Sep '13

Dear FreeSurfers, I was wondering if anyone had tried to use the MATLAB LME toolbox that you kindly developed for volume based VBM-style data? Either way would you be able to impart some initial advice as to considerations that should be made etc? Best wishes and many thanks, Sean

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