Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

longitudinal processing
by Catherine Bois 09 Jan '13

09 Jan '13

Sorry, another question about longitudinal processing; just realized that my institution has been using version 5.0, so all the cross sectional processing has been done with this version, is it ok to go ahead and do base and long with version 5.1 once I have managed to get this installed? Thanks, ----- Forwarded message from C.Bois(a)sms.ed.ac.uk ----- Date: Wed, 09 Jan 2013 13:35:12 +0000 From: Catherine Bois <C.Bois(a)sms.ed.ac.uk> Subject: longitudinal processing To: freesurfer(a)nmr.mgh.harvard.edu Hi, just to clarify, When beginning longitudinal analysis, the first step is the same as cross-sectional processing, eg just the "normal" recon-all command, for each subject, and each individual time point? Then the norm.mgz files are used? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ----- End forwarded message ----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Postdoctoral Position at Harvard Medical School/Boston Children's Hospital
by Gaab, Nadine 09 Jan '13

09 Jan '13

The Gaab Labhttp://www.childrenshospital.org/research/gaablab and (www.babymri.org<http://www.babymri.org>)) at the Laboratories of Cognitive Neuroscience at Children's Hospital Boston (Developmental Medicine Center) invites applications for a NIH funded post-doctoral associate in the area of developmental cognitive neuroscience/pediatric fMRI. Available resources include a 3.0T MRI scanner, a child-friendly Mock scanner and analysis platforms based in MATLAB/UNIX. The candidate will be expected to design, organize and conduct pediatric and infant (f)MRI experiments, analyze behavioral and fMRI data, prepare manuscripts for publication, and participate in conferences. The NIH and foundation funded projects will focus on neural and behavioral pre-markers of developmental dyslexia in infants and pre-reading children as well as typical reading and language development. The successful applicant should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, developmental psychology, medicine or psychology). Individuals with a background in electrical engineering, biomedical engineering or computer science will also be considered, as appropriate. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and statistical analysis of functional brain-imaging experiments. Experience with SPM, FSL, Freesurfer, UNIX/LINUX/ and/or programming skills (MATLAB, C++; Python) are desirable and experience with MVPA or connectivity analyses a plus. Experience with pediatric functional neuroimaging and language and reading research are useful. Approximate start date is Spring/Summer 2013 (the earlier the better). Successful applicants will be appointed at Children's Hospital Boston and Harvard Medical School. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Nadine Gaab, PhD (nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu>). The search will continue until the position is filled. -- "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Assistant Professor of Pediatrics Harvard Medical School Faculty Affiliate Program in Neuroscience, Harvard Medical School Member of the Faculty of Education Harvard Graduate School of Education Children's Hospital Boston Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience 1 Autumn Street (Office 643) Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: (857)-218-3021 Main Lab: 617-355-0400 fax: 617-730-0518 http://www.childrenshospital.org/research/gaablab www.babymri.org<http://www.babymri.org/>

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freesurfer question
by Catherine Bois 09 Jan '13

09 Jan '13

Hi, I am currently editing some scans (ie adding control points etc), however I keep finding that after the editing often the brains look "worse" than they did before; especially the medial temporal lobe area. I have taken care not to put too many control points in/made sure not to place them in partial volume areas, and only in areas that are clearly excluded white matter. This problem has happened repeatedly, yet looking at scans that my colleagues have edited (some with up to 2000 control points) this problem does not occur. Has this happened before, is it the software "malfunctioning" in some way? Thank you very much for your reply, -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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unable to download updated mri_segstats
by Salil Soman 09 Jan '13

09 Jan '13

Hi, The link ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.… from the release notes for freesurfer 5.1 ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) appears broken. I also checked the anonymous ftp site and found only the directories bbr-papers and growth-curves within the /transfer/outgoing/flat/greve directory. Could someone please direct me to the correct download link for the updated file? Also, is there an updated version of mri_segstats for mac? Thank you. Salil Soman, MD, MS

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Re: [Freesurfer] QA Tools Snaps Scrambled - Clairification
by Irwin, William 09 Jan '13

09 Jan '13

Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having problems with any of the other apps running on my system. Obviously I'm not asking you to help diagnose the health of my system, but though you might have some thoughts/suggestions. Regards, Wil -----Original Message----- From: Irwin, William Sent: Wednesday, January 09, 2013 5:37 AM To: Louis Nicholas Vinke Cc: freesurfer(a)nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -----Original Message----- From: Louis Nicholas Vinke [mailto:vinke@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: > > Hi- > > > > I’ve come across a peculiar behavior with recon_checker, and am hoping > someone can shed some light on this. > > > > I have used it 100’s of times in the past, but not for about 2 months. > I recently processed a large set of cases I wanted to QC. When I ran > it, some, but not all, of the snaps were corrupted. Specifically the > talairach, aseg, surfs, and all the ‘detailed snaps’, which are > basically additional instances of the aforementioned types. The > inflated, curv, and parc are all just fine. As the process runs, all > images are being displayed in the pop-up windows, and the html page is created. > > > > While there have been no system changes which should affect this, I > upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the > problem. The problem remains. And the problem remains w/ or w/o the > flag for detailed snaps. > > > > If all of the images were corrupted, I would have certainly concluded > something has gone awry with my system. The fact that only some of the > images are corrupted makes me scratch my head. > > > > Thoughts? Suggestions? > > > > Thanks, > > Wil > > > 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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creating picture using 3D slicer
by L. Koenders 09 Jan '13

09 Jan '13

Dear FreeSurfer people, I have a problem creating a picture with my FreeSurfer volumetric data, for which I have been using 3D Slicer. First, let me explain what I am trying to do. We have a list with cortical and subcortical grey matter areas that were significantly different between our patient and control group. I want to make one picture showing all these areas, and the 3D model as can be made with 3D Slicer with a part of the surface 'clipped out' would be perfect. I tried to do this by loading the surfaces and parcellation map in Slicer. I could successfully load the volumes (mri.mgz, aseg.mgz) and the surfaces (lh.pial and rh.pial). But when I load the parcellation map (aparc.annot) as a scalar overlay for the already loaded model, slicer crashes. I emailed the 3D slicer helpdesk with this problem, but I hope you might have some ideas as well. My question is if there is a way to fix this problem, and if not; if there's another way to get the type of picture I want? I really hope you can help me, thanks in advance! Kind regards, Laura ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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QA Tools Snaps Scrambled
by Irwin, William 09 Jan '13

09 Jan '13

Hi- I've come across a peculiar behavior with recon_checker, and am hoping someone can shed some light on this. I have used it 100's of times in the past, but not for about 2 months. I recently processed a large set of cases I wanted to QC. When I ran it, some, but not all, of the snaps were corrupted. Specifically the talairach, aseg, surfs, and all the 'detailed snaps', which are basically additional instances of the aforementioned types. The inflated, curv, and parc are all just fine. As the process runs, all images are being displayed in the pop-up windows, and the html page is created. While there have been no system changes which should affect this, I upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The problem remains. And the problem remains w/ or w/o the flag for detailed snaps. If all of the images were corrupted, I would have certainly concluded something has gone awry with my system. The fact that only some of the images are corrupted makes me scratch my head. Thoughts? Suggestions? Thanks, Wil

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longitudinal processing
by Catherine Bois 09 Jan '13

09 Jan '13

Hi, just to clarify, When beginning longitudinal analysis, the first step is the same as cross-sectional processing, eg just the "normal" recon-all command, for each subject, and each individual time point? Then the norm.mgz files are used? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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ask about demean in GLM model setup
by chenchunhuichina 09 Jan '13

09 Jan '13

Dear experts, I am confused by demean during GLM model setup and would like someone here can help me. Thanks! Suppose I have a continuous behavior data and I want to find out which brain region(s) correlated with it. The simple way is to calculate correltation between brain data and behavior data, or in GLM to set up a model Y=AX+B+e, A is slope, B is constent and e is error, Y is brain data and X is beahvior data. So this design matrix have two collumns: behavior data and ones. or we can think of demean that dX=X-mean(X), dY=Y-mean(Y) Y=A'dX+B'+e', A' should be the same a A and B' differed from B, and B' maybe more interpretatable. I was told that -D opion in FSL randomise will demean X and Y at the same time. one can set up models like dY=A1dX+B1+e1, or dY=A2dX+e2. I simulated a data in SPSS and confirmed that A1,A2 is the same as A, B1 is 0. but t test for A1 A2 differed a little, A1 is the same as above models. So it seems to me that include a constent in the model is always right, right? My confusion is why Y also need to demean and how was it done in randomise? when one says "demean" or "mean centering", he/she means demean X only or demean X and Y both? Thanks for any clarification! 2013-01-09 Chunhui Chen _________________ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875

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Matching stats in SPSS and QDEC
by Maleki, Nasim 08 Jan '13

08 Jan '13

Hi list, I have done an analysis using QDEC and now I would like to do set up similar statistical analysis in SPSS on some parcellated structures. I have the following setup in QDEC: 2 cohorts (patients, healthy control subjects) Continuous variable : demeaned Age Nuisance Factor: demeaned intracranial volume DODS I'm interested in the effect of age i.e. "differences in the thickness-age correlation between the patients and healthy subjects" . Now my question is if I the following set up would be correct for doing the stats on slopes in SPSS: Univariate General Linear Model Dependent variable: ROI Fixed Factor: group (i.e. patient or healthy control) Covariate: demeaned age AND demeaned intracranial volume and then I also add an interaction term of demeaned_age*group to be the equivalent to the difference between thickness-age correlation in patients vs. healthy subjects that I have in QDEC. Is this correct? Thanks, Nasim

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Freesurfer January 2013