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[FSL] Microstructural Imaging Jobs in CUBRIC, Cardiff (fwd)
by Bruce Fischl 12 Nov '17

12 Nov '17

FYI ---------- Forwarded message ---------- Date: Mon, 13 Nov 2017 01:38:46 +0000 From: Derek Jones <JonesD27(a)CARDIFF.AC.UK> Dear All, Please find below links to three jobs in microstructural imaging at CUBRIC, Cardiff University (available immediately). Obviously, a large part of this will be exploring the benefits of using the ultra-strong gradients on the Connectom scanner, but we’re also interested to see what 7T offers in terms of microstructure. As an update, we’re pretty pleased with the current performance of the Connectom scanner and getting some really nice results out, so I think there is a really good opportunity for people that want to explore cutting edge diffusion / multi-contrast approaches with ultra-strong gradients. Anyway, I’d be very happy to discuss any of these with you. Please feel free to pass on the details to other people that you think may be interested. Here’s the links: Research Associate: https://goo.gl/a6bRVe Research Fellow: https://goo.gl/ZqgMKY Thanks for reading! Derek Jones __________________________________________ Derek Jones Director CUBRIC Cardiff University +44-29-2087-9412 [IMAGE] http://sites.cardiff.ac.uk/cubric Yr Athro Derek Jones Cyfarwyddwr Canolfan Delweddu Prifysgol Caerdydd er Ymchwil yr Ymennydd (CUBRIC) Coleg Y Gwyddorau Biofeddygol Prifysgol Caerdydd Ffôn: + 44(0)2920879412

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Re: [Freesurfer] Creating cached versions of Xhemi registrations
by Mehta, Chintan 12 Nov '17

12 Nov '17

Dear Doug, I'm performing a linear regression over one sample with a design matrix including columns for one continuous-valued predictor whose effect on neural measures I'm interested in testing, several covariates to adjust for (continuous- or binary-valued such as age, sex, total intracranial volume, and other demographic groupings), and an intercept. The contrast matrix I'll be testing will have 1 in the column corresponding to the column in the design matrix containing the predictor of interest and zeros in all other columns. In addition, I was interested in performing the same linear regressions over subsets of the group to determine whether the pattern associated with the predictor-of-interest is persistent. That's why I want to stack surfaces for different sets of subjects (without recreating surfaces registered to fsaverage_sym for each subjects' laterality indices for each instance). This way I could repeat the same contrast, except subsetting rows of the design matrix for subjects in the given sample. Thank you. Best, Chintan >Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Fri, 10 Nov 2017 11:28:52 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> > That looks right, though I'm not sure what is in the design matrix. Is it a column of +1 and -1?

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mean cortical thickness map
by John Anderson 12 Nov '17

12 Nov '17

Dear Freesurfer community, I want to visualize the mean cortical thickness map of 20 subjects. I ran the command recon-all on the the T1 images. How can I visualize the mean cortical thickness of one group. Thanks for any advice John

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Reference on measures computed by dt_recon
by Mehta, Chintan 11 Nov '17

11 Nov '17

Dear FreeSurfer users, I'm using FS 6.0 and have computed summary statistics for different measures including adc, ivc, volume ratio, and radial diffusivity. Is there a reference on how the FreeSurfer software computes these measures (i.e. mathematical formulas)? Thank you. Best, Chintan

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Destrieux (aparc2009) atlas in MNI 2mm space?
by Daya P 11 Nov '17

11 Nov '17

Hi All, How can I get the aparc2009 atlas in MNI 2mm space? I want the labels to be in MNI 2mm space. Are there Destrieux labels in 2mm space already somewhere? I could only find them in 1mm ... Thank you, Daiana

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QDEC
by Kinzel, Phillipp 10 Nov '17

10 Nov '17

Hi, I have problems loading project files in QDEC. I get the following error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I would be greatful for any advice. Best, Philipp

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Re: [Freesurfer] dt_recon and Tracula
by Mehta, Chintan 10 Nov '17

10 Nov '17

Dear Doug, I figured out the mistake I was making, which was that I ran: > freeview -v orig.mgz wmparc2diff.mgz:colormap=lut lowb.nii.gz:reg=register.dat -f lh.white:edgecolor=green rh.white:edgecolor=green -viewport coronal & Here the lowb, orig, and white surfaces were consistent. Since wmparc2diff.mgz is in diffusion space, it was bound to be mismatched with the lowb & white surface lines. When replacing wmparc2diff.mgz with wmparc.mgz, it is no surprise that there is a much better match between the white matter parcellation & lowb. There is a very good match between lowb and wmparc2diff, when running, per the documentaiton, > freeview -v lowb.nii.gz wmparc2diff.mgz:colormap=lut -f lh.white:edgecolor=green rh.white:edgecolor=green -viewport coronal & However, the lh.white and rh.white surfaces do not change. I suppose this is because those surfaces are not for volumes registered to the diffusion space. Does that make sense? Or would the lh.white and rh.white automatically adjust to diffusion space? Thank you. Best, Chintan

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Flux Satellite Conference
by Margaret Sheridan 10 Nov '17

10 Nov '17

*UNC Chapel Hill, in association with The Flux Society, *will host a conference highlighting research using large, representative, or publicly available datasets to investigate developmental cognitive neuroscience. This conference will address the unique ability of larger, more representative datasets–and particularly those with multiple time points–to ask questions about brain development that have historically been impossible to address with the smaller, cross-sectional samples utilized in most neuroimaging research studies. The focus will be on research leveraging large datasets to understand functional and structural brain development in the context of connectomics, environmental influences on brain development, and typical and atypical trajectories of brain development. The conference will take place at UNC Chapel Hill May 6 – May 8, 2018. Abstract submission deadline: 1/22/18 Registration opens: 2/1/18 For more information and to submit your abstract, visit: http://fluxsatellite.web.unc.edu/ You may also sign up for the conference listserv on the site to receive future announcements.

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Re: [Freesurfer] Trans. : VBM question
by Douglas N Greve 10 Nov '17

10 Nov '17

Hi Mohamed, please remember to post to the list. As for your question, what aparc files are you looking at? Those measures are in, eg, lh.aparc.stats On 11/06/2017 04:05 AM, Mohamed Ali Bahri wrote: > > Dear Douglas, > > Many thanks for your answer! > > We are interested on one region belonging to the Brodmann areas > "Perirhinal". Cortical thickness as well as volume values appear on > the BA stat list and not on the aparc or aseg lists. Does the > ROI-based analysis could be used for this BA region? > > Best regards, > > Mohamed > > > On 05/11/2017 18:46, Douglas Greve wrote: >> >> Do you just want to do an ROI analysis? Or do you want to do a >> voxel-based analysis? If ROI-based, then follow the steps on the ROI >> tutorial (ie, aparcstats2table and mri_glmfit with --table input). >> >> >> On 11/3/17 4:08 PM, Bruce Fischl wrote: >>> Hi Mohamed >>> >>> Doug is away this week and can give you a more details answer next >>> week. Certainly you could use mris_anatomical_stats -l <BA label >>> file name> to compute the volume/thickness/area for each subject >>> then do whatever GLM analysis you want outside of FS. >>> >>> cheers >>> Bruce >>> >>> >>> On Fri, 3 Nov 2017, m.bahri(a)uliege.be wrote: >>> >>>> Dear All, >>>> Does anyone have an answer to the following VBM question? >>>> >>>> Many thanks in advance, >>>> Regards >>>> >>>> -----Mail original----- >>>> De: "Mohamed Ali Bahri" <m.bahri(a)uliege.be> >>>> À: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM >>>> Objet: [Freesurfer] VBM question >>>> >>>> Dear Freesurfer users, >>>> >>>> I would like to study the between groups changes of volume/cortical >>>> thickness of one region (Perirhinal) belonging to the Brodmann >>>> areas. I >>>> tried to do that with Qdec tool but unfortunately Qdec does not >>>> load the >>>> Brodmann areas stat list. I am wondering if I could use the GLM >>>> formalism with of course regressing out the ITV. Any suggestion/advice >>>> will be very welcome. >>>> >>>> Many thanks in advance, >>>> >>>> Best regards, >>>> >>>> Mohamed >>>> >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> 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. > > -- > Dr. Mohamed Ali Bahri, > 1er Logisticien de Recherche, > Cyclotron Research Centre, > University of Liège, Belgium > m.bahri(a)uliege.be -- 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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Re: [Freesurfer] Optseq and de convolution for rapid designs
by fmri2013 10 Nov '17

10 Nov '17

Many thanks Douglas If I optimise my design using Optseq, do you know if this de convolution process is implemented in SPM or any other software? and it is part of the processing behind th3 scenes? Or do I have to account for this using a specific software. Aser Sent from my Samsung Galaxy smartphone. -------- Original message --------From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Date: 10/11/2017 19:24 (GMT+00:00) To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Optseq and de convolution for rapid designs It is because the random jitter creates differential amounts of overlap. Imagine if you have A=C+D and B=C-D. You know A and B, but you want C and D. You have two equations and two unknowns, so you can solve for C and D from A and B eventhough C and D "overlap" in A and B and you never see C or D by themselves. This is a type of deconvolution On 11/10/17 11:38 AM, Aser A wrote: Hi all I used Optseq to optimize rapid event designs with multiple conditions . I have a theortical question : how it is possible to distingwoh the close by trials ? Is it by de convoution ? How is it possible to deal with overallped trials ? Is it because the conditions are random so that when averaging them the distingwoh is possible? Many thanks Aser _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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