Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Watershed Errors - Multiple attempts tried
by Christian Lambert 06 Jul '10

06 Jul '10

Hi all, I'm assissting with an aging study and a good handful of their scans are coming up with watershed errors. My assumption was errors with the skull strip leading to empty brain volumes. I have read through all the lists and tried the following: - Manually corgistering to MNI to improve Talairich alignment; Same error - Using a range of -wsthresh (from 30-55) with the -no-wsgcaatlas -wsthresh command in recon all; these all had very bad skull strips but avoided watershed error. They all crashed later on at register_mri: find_optimal_transform - Rescaling the voxel intesity ranges to be closer to "successful" scans (watershed error again) I'm not entirely sure what to try next. I'm using Magnetic Transfer Images that I've multiplied the voxel intesities by 1000 (as normally 0.6-1.5) in order to freesurefer (which works well in most subjects). Other images I have available are T1, T1w, PDw,MTw. I'm avoiding the weighted scans due to coil induced bias. I have tried the T1 with identical results. WM values=~1800-1900 GM Values= 900 CSF = 50 Out of brain ~300 Cheers for any help you can provide, - Chris

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Regression analysis on files produced with the -osgm flag
by Jürgen Hänggi 06 Jul '10

06 Jul '10

Dear FS experts We have done a one-sample-group-mean (osgm) analysis and now we would like correlate a behavioural measure with the difference maps produced by the -osgm analysis. Is this possible? Or do we have to compute the difference of each subject again, the running mri_surf2surf to register the difference files and then running the regression? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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position announcement: Research Program Coordinator/MRI Data Analyst
by Julie E McEntee 05 Jul '10

05 Jul '10

The Division of Psychiatric Neuroimaging in the Department of Psychiatry, Johns Hopkins University School of Medicine (Baltimore, MD), is seeking a Research Program Coordinator/MRI Data Analyst. The position will oversee all facets of research activities, data management and administrative aspects for research projects involving multimodal imaging (structural, fMRI, DTI, MRS) on the 3 T and 7 T Philips systems at the F. M. Kirby Center for Functional Neuroimaging, imaging systems at JHH, or other imaging systems. Current research projects include studies of Huntington’s Disease, schizophrenia, anorexia nervosa, other neuropsychiatric conditions and healthy control populations. The primary duties and responsibilities include: Assist development of fMRI neuropsychological protocols, recruit and enroll participants, administer clinical neuropsychological tests and research tasks, assist (with MRI technician) in image acquisition, enter research data, conduct data and image analysis. Essential job functions: Maintaining and monitoring supply of testing materials, monitoring the control of data quality and research integrity. The duties also include organizing and maintaining research files and maintaining study databases. Responsible for the development of IRB applications as well as IRB compliance. Master’s degree in psychology, neuroscience or related discipline relevant to imaging is strongly preferred. Advanced experience with personal computers, Windows 7 and Mac OS operating systems and Microsoft Office 2007/2010 applications (particularly Excel and Access) required; experience with UNIX preferred. Knowledge of univariate and multivariate statistics required; experience with statistical analysis software (e.g., SPSS, SAS, Stata) preferred. Knowledge of imaging analysis software (e.g., SPM, FSL, AFNI, FreeSurfer, MIPAV) preferred. Clinical research experience with neuropsychiatric populations and database management required; experience with completing Case Report Forms (CRF’s) and creating source documents a plus. Must be extremely well organized, precise and detail oriented. Must have the excellent interpersonal skills, ability to problem solve and work independently. Please send statement of interest and CV to Julie McEntee at jmcentee(a)jhmi.edu and Graham Redgrave at gwr(a)jhmi.edu. Julie E. McEntee, M.A., C.C.R.P. Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./ Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676

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Postdoctoral Fellowship - Neuroimaging of Langauge
by Rutvik Desai 05 Jul '10

05 Jul '10

A postdoctoral fellowship is available immediately at the Medical College of Wisconsin, Milwaukee, in the laboratory of Dr. Rutvik Desai, which is affiliated with the Language Imaging Laboratory (www.neuro.mcw.edu<https://owamail.mcw.edu/owa/redir.aspx?C=3b718d6eb18f4a7ead52886096b52157&U…>). The research in our lab focuses on language and speech processing. The NIH-funded project will emphasize semantics and embodiment of meaning, using neuroimaging techniques and patient studies. Close collaborators include Drs. Jeffrey Binder, Einat Liebenthal, Sylvain Baillet (MCW), Mark Seidenberg ,and Tim Rogers (UW Madison). State-of-the-art facilities include two 3T scanners, MEG, TMS, and EEG systems. A Ph.D. or equivalent in neuroscience, psychology, or a related field is required. Experience with language research using neuroimaging, TMS, computational modeling, or machine learning is highly desirable. The fellow will have an exciting opportunity to receive training, depending on their interest, in fMRI, TMS, MEG, EEG, and/or in conducting patient studies, and to pursue collaborative and self-directed projects. MCW has been ranked consistently as one of the “Best Places to Work” for postdoctoral fellows. Please email a CV, a statement of research background and interests, contacts of three references, and copies of relevant publications to Dr. Rutvik Desai at rhdesai(a)mcw.edu<https://owamail.mcw.edu/owa/redir.aspx?C=3b718d6eb18f4a7ead52886096b52157&U…> .

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How can I make aparc.2009 from aparc.2005
by Shahin 02 Jul '10

02 Jul '10

Hi everyone For my old subjects I already have aparc.2005 atlas file in the label directory but not the 2009a version. I want to know how can I make 2009 version for these subjects without doing the recon-all for them. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard University

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Skullstrip Delay
by Riskin-Jones, Hannah 02 Jul '10

02 Jul '10

Hi, I am attempting to run an fMRI data set through the freesurfer workflow and the skullstripping step seems to be delayed. It has been stuck on the following command line for an inordinate amount of time. First Search limited to translation only. using real data threshold=28.0 Found translation: (-1.1, -8.0, -23.9): log p = -22300.7 Nine Parameter search. iteration 0 nscales = 0 ... without an error message, I have no clues as to how to fix this problem. Any suggestions would be much appreciated! Thank you so much, Hannah

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Fwd: Plotting functional data on surface
by Corey Keller 02 Jul '10

02 Jul '10

Hi Bruce, Thanks for the info. I am trying to register a resting state functional nifti file. I ran bbregister but it was not well aligned (pictures are attached). Our thought is that the contrast was not strong enough for freesurfer to detect enough common points with the anatomical volume. If we feed another example functional file with better contrast, could we then use that register file to apply to our data? Any thoughts on how we can do this betterwithout manually aligning? Thanks again. Best, Corey On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Corey, > > yes, or you can try bbregister to do it automatically. > > cheers > Bruce > On Fri, 2 Jul 2010, Corey Keller wrote: > >> Hi Freesurfers, >> >> I know this is probably an easy question, but I am having some trouble >> with it. I am trying to plot functional data (in nifti format) onto a >> pial or inflated surface in matlab. I am uring mri_vol2surf but am >> missing the register file. Do I find this from registering the >> functional data to the anatomical surface via tkregister? Thanks. >> >> -Corey >> _______________________________________________ >> 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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Plotting functional data on surface
by Corey Keller 02 Jul '10

02 Jul '10

Hi Freesurfers, I know this is probably an easy question, but I am having some trouble with it. I am trying to plot functional data (in nifti format) onto a pial or inflated surface in matlab. I am uring mri_vol2surf but am missing the register file. Do I find this from registering the functional data to the anatomical surface via tkregister? Thanks. -Corey

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Error in SubCort Seg.
by Hui Zheng 01 Jul '10

01 Jul '10

Hi freesurfers, I have a few subjects failed at SubCort Seg step. The error message is: not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.03 x + 0.0 Left_Pallidum too bright - rescaling by 0.984 (from 1.025) to 105.9 (was 107.6) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux compute-08-09.cbdc.rhhpc.cluster 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux Please advice any solution. Thanks, Zheng Hui

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Methods doubt
by Gabriel Go.Es. 01 Jul '10

01 Jul '10

Hello freesurfers Does anyone knows wich is the method in which the FS makes an average of 2 images, in the autorecon1 step when doing the motion correction?. I mean how can I explain it? Thanx Gabriel _________________________________________________________________ Accede a tu Hotmail en un solo clic ¡Descárgate Internet Explorer 8 y empieza a disfrutar de todas las ventajas! http://www.ayudartepodria.com/

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