Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

help
by Aditya P Singh 18 May '17

18 May '17

> On May 18, 2017, at 11:29 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Freesurfer white matter outer edge to volume (Gamaliz) > 2. Re: Freesurfer white matter outer edge to volume (Gamaliz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 18 May 2017 12:16:46 -0400 > From: Gamaliz <gliza002(a)fiu.edu> > Subject: Re: [Freesurfer] Freesurfer white matter outer edge to volume > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CALei8e7=HH+Y8DoHLgUDLOci2BOrceA6b8XqqASSteMnN_AX+w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Douglas, > > I am looking at them in freeview and mango. They are not aligned. I am able > to align them using flirt, and they come out perfect. I have tried 5 cases. > 3 of them they are aligned, two were not. I am loading below the wm and > lh.wm. They are supposed to be aligned (wm is aligned with T1). > > I got a surface by using Bruce's method, but it's much more irregular than > the one obtained from mri_surf2vol. I wonder why the inconsistency. I guess > I can create the surface and flirt using a solid transform to the T1. It > takes longer, but it works. > > Gabriel > > [image: Inline image 1] >

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Questions about FreeSurfer
by Alliey-Rodriguez, Ney [PSY] 18 May '17

18 May '17

Dear FreeSurfers, I received FreeSurfer structural MRI brain data to analyze, but there are some questions about specific FreeSurfer variables that I could not find answered on your wiki or in the mail archive: 1.- "Non-White Matter hypointensities": 1.a - Are these the same thing as "gray matter hyperintensities"? 1.b - Are these scanned from the whole brain gray matter or only sub-cortical? 1.c - Are these also considered traumatic markers? (literature would be appreciated) 2.- 5th Ventricle: is this variable encompassing the Cavum Septum Pellucidum only, or does it also include the Cavum Vergae? 3.- Are there published analysis about FreeSurfer accuracy for CSF volumes? Thanks and will look forward, Ney __________________________ Ney Alliey-Rodriguez, M.D. Research Assistant Professor - Gershon Lab Department of Psychiatry and Behavioral Neuroscience University of Chicago 5841 S Maryland Ave Room M344 (MC3077) Chicago, IL 60637 Phone: 1(773)702-0599

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mri_mcsim for individual subjects and references {Disarmed}
by Kevin Aquino 18 May '17

18 May '17

Hi all, First of all, Freesurfer V6 is working like a dream, my 0.7 mm segmentations are running really well and in comparisons to hi-resrecon in 5.3 and early beta, I'm having to do fewer manual corrections! Now for my questions, 1. I'm running mri_mcsim in order to correct for multiple comparisons via the FS-FAST stream. I'm wondering how many iterations are advised, and how can one check for convergence in an automatic fashion. I've run the simulations with 1000 and 10,000 iterations on a 1mm segmentation with the FWHM simulations at 8mm. (i.e. using mri_mcsim --o . --base mc-z --save-iter --surf subject lh/rh --nreps 10000 --fwhm 8) and I can't see many differences between the two when correcting for multiple comparisons (i.e. using cluster-sess -analysis myanalysis -thresh 3 -cwp .05 -s SESSION -sign pos). 2. I'm trying to find some references that detail the simulations and form the corrections, does anyone have advice which list I can read/start off with, as well as some key papers that use it (esp on a single subject level). I really like this approach and It does look to circumvent (I think...) a lot of the problems of cluster-wise corrections described with Eklund et al. (Cluster failure paper). Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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manuel edits
by Caroline Beelen 18 May '17

18 May '17

Dear FS team, I have two questions regarding manuel editing. We were looking at inter-rater reliability, but noticed it was not too high... However, during editing we used different criteria. Therefore I would like to ask: 1. Does the order of pial correction, topological deficit, wm corrections and control points editing matters? You seem to assume on your website for instance that pial corrections would come before wm corrections/control points, but is this necessarily the case? 2. When the wm intensity value is below 110, voxel inclusions might be needed. On the website is written: "when you feel like there is wm underneath you can add control points (...)". How to make a decision on this matter: based on sight or on wm intensity values? For instance, often the WM values are either 0 or 80 or above... Would it be good to assume that wm intensity values above 80 are actually wm, regardless of how it visually would look like? Likewise, would it be good to assume that areas where it says the wm intensity value is 0, that these areas are actually not wm, regardless of whether it might look like wm? So, basically, it is correct to make your decision only based on wm intensity values? Thank you for your reply. Kind regards, Caroline Beelen

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Mean gray-white contrast for each ROI
by Yaakub, Siti Nurbaya 18 May '17

18 May '17

Hi, I read from a previous post that the "{lh,rh}.w-g.pct.stats files in $SUBJECTS_DIR/subject/stats … will have the mean gray-white contrast for each ROI in the aparc." I've looked at the lh.w-g.pct.stats file and am not sure which values I should be looking at if I am interested in the ratio of grey to white matter averaged over each of the ROIs? What are the area in mm2 and the SNR in this w-g context? Thank you, Siti

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Re: [Freesurfer] Question of longitudinal processing
by jahanvi patel 18 May '17

18 May '17

Hi Martin, Do you mean by creating this long.testretest.qdec file, one can then perform the stats for the longitudinal2StageModel? So for a 2 timepoints analysis, eg. TP1 & TP2. the long.testretest.qdec will be looking like this ? fsid fsid-base tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC . . . Thanks, Jahanvi tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh Hi Jahanvi, > > long.testretest.qdec is a qdec table in the longitudional format (with the > fsid-base as the second column). > > For test-retest (e.g. same session with subject removal), you usually > don't need a time column, that is why --generic-time is specified. the qdec > table would just look like > > fsid fsid-base > > me me_test > > me me_retest > > you you_test > > you you_retest > > ... > > > Best, Martin > > > On 05/08/2017 04:10 PM, jahanvi patel wrote: > Hello list, > > I have a simple question about the LongitudinalTwoStageModel tutorials on > freesurfer website. > > It is from this link > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel > > > long_mris_slopes --qdec long.testretest.qdec \ > --meas thickness \ > --hemi lh \ > --sd $SUBJECTS_DIR \ > --do-pc1 --do-label \ > --generic-time \ > --fwhm 15 \ > --qcache fsaverage \ > --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ > --isec-labels lh.testretest.fsaverage.cortex.label > > My question is, what is the content of long.testretest.qdec ? > I understood till 1st stage was done, we got only one file which is > long.qdec.table.dat. > > Could anyone help to clarify my question? > > Thanks a lot > Jahanvi > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 6

Postdoctoral position in psychosis studies - Oslo, Norway
by Tiril Pedersen Gurholt 18 May '17

18 May '17

Dear All, At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital and Diakonhjemmet Hospital, Norway, there is a position available as a postdoctoral student with employment at Diakonhjemmet hospital. The research area is psychiatric neuroimaging with focus on obstetric complications and the analysis of structural and functional, DTI and ASL MR imaging datasets with regard to developmental trajectories and genetic, environmental and phenotypic variation. Applicants should have a doctoral degree (PhD) in psychiatry or a related medical discipline, neuroimaging, computer science, bioinformatics, psychology, or equivalent. Applicants who have handed in their dissertation for evaluation are also encouraged to apply, caveat the dissertation is approved. Application deadline is June 15th, 2017. For further information and to submit an application please see the website of Diakonhjemmet Hospital, Oslo, Norway: https://www.webcruiter.no/WcMain/advertviewpublic.aspx?oppdragsnr=342027797… Best regards, Tiril Gurholt --- Tiril Gurholt Postdoctoral Fellow Psychosis Research Centre, NORMENT Institute of Clinical Medicine, University of Oslo, Norway http://www.med.uio.no/norment/ [cid:image001.png@01D21DA0.544E82D0]

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ExploreDTI Workshop - it is still possible to register
by Szabolcs David 18 May '17

18 May '17

*ExploreDTI* Workshop - A course on processing, analyzing, and visualizing diffusion MRI data When: 10-12 July, 2017 Where: Utrecht, Netherlands *Registration deadline: 15th June* Details: http://www.exploredti.com/workshop Hope to see you in the Dutch summer ;) Cheers, Szabolcs

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longitudinal analysis or cross-sectional anslysis of the subfield of hippocampus
by Jinsong Tang 17 May '17

17 May '17

Dear all, I have 2 groups (patients and controls), and I want to analysis the subfields of the hippocampus. Some of the subjects have 2 scans (before treatment and post treatment) and some subjects only have one scan(before treatment). aim 1: I want to compare the subfied volume of the hippocampus between patients and control using the before treatment data. aim 2: I also want to calculate the treatment effects on the subfield volume of the hippocampus. Do I need to use longitudinal analysis ? or cross-sectional analysis is fine? If use longitudinal analysis, for the aim 1, only part of the subjects have 2 scans. I still need to use the cross-sectional data to calculate the groups' difference in order to include all subjects. What your suggestions? Thank you so much! Best Jinsong

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Research Assistant Position in Clinical Neuroscience Laboratory
by Herring, Elizabeth J. 17 May '17

17 May '17

Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, starting June 1st, 2017, in the Clinical Neuroscience Laboratory<http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> of Dr. Ruchika Prakash at the Ohio State University. The laboratory is currently conducting several randomized controlled trials, designed to look at the effects of lifestyle interventions, such as mindfulness training and exercise intervention in improving cognitive and emotional control in older adults and in individuals with multiple sclerosis. This position is designed for individuals who are interested in building on the research experience that they already have and learn about the new field of health neuroscience. Applications are solicited from individuals with considerable programming experience, as well as experience in neuroimaging data analyses. Knowledge of matlab and an existing software package, such as FSL, AFNI, or SPM is desired. Responsibilities will include active involvement in all aspects of research, facilitating recruitment efforts between the laboratory and community partners, and overseeing day-to-day operations of the laboratory. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com, job listing number 428162 and submit a current CV, a brief statement of interest, and names of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at Prakash.30(a)osu.edu Contact Website: http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.

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