Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

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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Dummy Scans and Paradigm Files
by Dave Brohawn 01 Jul '10

01 Jul '10

Hello, My name is David Brohawn, and I am one of Dr. Roffman's research assistants. We run the SIRP and N-Back memory tests with our subjects. We have specified for 3 dummy scans to take place at the beginning of each of these protocols, which takes 6 seconds of scanning time, respectively. When writing paradigm files in freesurfer, should we include a 6 second period to account for these dummy scans, or do we write the paradigm files not making any reference to the time elapsed during these dummy scans? Thanks, Dave

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Qdec default design
by Dankner, Nathan (NIH/NIMH) [F] 01 Jul '10

01 Jul '10

Hello all, I'm running a cortical thickness group analysis in qdec with two groups and one covariate (age). By default, does qdec use the DODS option, or DOSS?

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writing out a transformed fmri volume
by Hansen, Kathleen (NIH/NIMH) [F] 01 Jul '10

01 Jul '10

Hi, We have had several naive questions about registration recently, and thank you all very much for your patience. Here is another one. We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate that subject's surface. We are happy with the accuracy of this process and understand that the registration file records the transformation parameters between the original fmri volume and the anatomical. Is there also a way to write the transformed fmri volume itself to disk? Thank you, Kathleen

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Fwd: postdoctoral imaging position
by Susanna Carmona Cañabate 01 Jul '10

01 Jul '10

Applications are invited for a position at the Unitat de Recerca en Neurociència Cognitiva (http://dpsiquiatria.uab.cat/en/grupRecerca_2.php) at the Fundació IMIM- Hospital del Mar, Barcelona, Spain. (www.imim.es) The position is full-time for 18 months. It entails working mainly on a grant entitled: “MR Structural and functional neuroimaging of cognitive and motivational executive functions in ADHD” (SAF2009- 10901), but also in other neuroimaging projects of the group. The postholder will be responsible for analyzing functional, structural, and diffusion tensor data as well as writing up the results. Essential skills include knowledge of fMRI and/or structural MRI techniques, a proficient management of SPM and other programs, and a strong interest in psychiatric diseases. The position is available for a start as soon as October 1st 2010. Salary will be around and gross annual income of €26,200 (plus social security, health and unemployment benefits). The position will be located in Barcelona city, at the Hospital del Mar. Please send enquiries or applications (which must include a covering letter detailing professional objectives and interests, CV, and the names and email addresses of three references, all together in one pdf file) to Dr. Oscar Vilarroya, (ovilarroya1(a)imim.es) with the subject line "Postdoctoral imaging position".

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how to filp Fa maps
by Morita, Marcia E. 01 Jul '10

01 Jul '10

Hi, I would like to know if there is a way to flip FA maps (the FA.nii.gz file) before running TBSS. Many Thanks, Marcia

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Reenviar: signal dropouts in 7T scanners
by Jose Luis Cantero Lorente 01 Jul '10

01 Jul '10

I would be very grateful to receive your comments. Thanks in advance, --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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Freesurfer July 2010