Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

re conversion
by Linn Mittlestein 11 Feb '13

11 Feb '13

Dear freesurfer experts, I have a question. I am trying to complete the longitudinal tutorial, and in freeview tutorial it states: "In order to analyze your longitudinal data, you have different options. You could, e.g., open the stats text files in each tpN.long.templateID/stats/ dir, containing statistics such as volume of subcortical structures or thickness averages for cortical regions. These statistics can be fed (after conversion) into statistical packages to run whatever analysis you are interested in" I am wondering what exactly "after conversion" refers to ( I encountered the same phase in the other recon option (ie cross-sectional). I was under the impression that the values from the stats files are the ones to use; thus what does after conversion refer too? Kind Regards, Linn

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thickness and area in aparc.stats and mri_glmfit
by Wolff Schlotz 11 Feb '13

11 Feb '13

Dear Freesurfer experts, I tested associations between a continuous predictor and thickness and area in qdec (and command line mri_glmfit, which gives the same results) and found a cluster being negatively associated with thickness orbitofrontal, but nothing for area orbitofrontal. After exporting mean thickness and area values from aparc.stats into Stata, consistent with my expectation I found a significant negative correlation with my predictor for thickness. However, I also found a significant positive association between birth weight and area. To check what might be wrong I tested correlations between mean medialorbitofrontal thickness from rh.aparc.thickness and thickness in qdec and did the same for area. As expected, large average thickness values were positively associated with thickness in medialoribotfrontal and adjacent areas (see attached qdec screenshot thickness.png), but there were no associations using area (see attached qdec screenshot area.png). My expectatioin was that there should be positive area associations similar to those for thickness. Hence my question: Is this expectation correct? If yes, why this discrepancy between thickness and area? Thank you. Wolff

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surface morphology
by Fred Sanders 09 Feb '13

09 Feb '13

Hi All, Is there an approach within freesurfer (or related software) for examining surface morphology of subcortical structures? WIth freesurfer I'm able to examine the total volume of various subcortical structures, but if my participants differ in volume of a subcortical structure, I can't determine where in that structure the difference is located. I'd love to do a surface analysis of these structures, similar to what's done with the cortical surface. Is this possible? Thanks!

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the mid point slide bar doesn't come back to 0 by manually entering 0 in the freeview
by Glen Lee 08 Feb '13

08 Feb '13

Hi freesurfer experts, I'm a newbie for the free surfer and am playing around with the freeview GUI. I'm having trouble moving the slide bar back to '0' by manually entering '0' right next to the Mid point slide. Interestingly, the slide bar moves when I entered other values like -2 or 2, but it doesn't when I entered 0. I wonder if it happens to my computer or a minor bug in the GUI. Glen

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Re: [Freesurfer] mrisReadTriangleFile failed
by Jonathan Holt 08 Feb '13

08 Feb '13

OK, good deal! The first time I ran recon-all it exited with errors. That must be the issue. thanks, jon > >> Hi Jon >> >> that means that one of the surfaces is out of date, usually because you >> edited and reran but not to completion. Try running >> >> recon-all -s <subject> -make all >> >> cheers >> Bruce >> >> p.s. ignore the "can't find file" thing. It really means it tried to read >> it, but found it wasn't the same topology as the other surface and that's >> what it is complaining about >> >> On Fri, 1 Feb 2013, >> Jonathan Holt wrote: >> >>> Experts, >>> >>> Having an issue with this error. It's complaining about rh.pial not matching rh.white, indicates there's no such file or directory and that mrisReadTriangleFile failed, and then proceeds to load without rh.pial. I tried loading rh.pial manually, but upon loading it immediately removes every surface on the LH. Wasn't an issue before I ran recon-all. Worth noting this brain was generated from a particularly low contrast MRI scan, and freesurfer had trouble generating correct surfaces from the get go. >>> >>> Jon >>> >>> _______________________________________________ >>> 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. >> >> >> >

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Large differences in subcortical structure volume between native and FreeSurfer space
by Seán Froudist Walsh 08 Feb '13

08 Feb '13

Dear experts, I would like to ask for help in explaining an unexpected difference in volume in subcortical structures between orig.mgz space and rawavg.mgz space scans. I used FreeSurfer (v5.1, Mac 10.7.5) on a group of subjects in order to extract subcortical segmentation volumes. I then changed the wmparc.mgz file to nifti format and used fsl tools to extract the hippocampus and other structures. I then used tkregister2 to produce the orig-to-rawavg matrix and applied this to each of the subcortical structure volumes individually to get these segmentations in the original native T1 space. On visual inspection this seemed to work fine, but when I compared the volumes of the orig.mgz space subcortical structures to the rawavg.mgz space structures there was a large difference (e.g. left hippocampus is in the range of 5000mm3 in the orig.mgz space and in the range of 7000mm3 in rawavg.mgz space). I wasn't expecting differences of this magnitude as I thought the rawavg-to-orig transformation only involved reorienting and reslicing? I compared volumes using fsl's "fslstats image -V" command. Can anybody please explain these differences and recommend a way to move forward? Ideally I would like to use the rawavg.mgz space subcortical structures for further analysis but I would like to know that I can trust them first! Many thanks in advance! Sean

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public MRI dataset, alzheimer's and controls, MIRIAD
by Ian Malone 08 Feb '13

08 Feb '13

Dear FreeSurfer users, We are happy to announce the release of a new publicly available dataset of volumetric brain MRI of Alzheimer's patients and age-matched controls: MIRIAD (Minimal Interval Resonance Imaging in Alzheimer's Disease). MIRIAD complements existing datasets such as ADNI by providing a high number of scans for each subject over a range of intervals from 2 weeks up to 2 years and back-to-back scans, enabling reproducibility, symmetry and transitivity assessment of longitudinal measures. You can find further information and download links at <http://miriad.drc.ion.ucl.ac.uk/>, and an accompanying publication providing an overview of the study and previous publications at <http://dx.doi.org/10.1016/j.neuroimage.2012.12.044> (Malone et al., NeuroImage Vol 70, P33–36) Registration is required so we can assess impact and notify users of any updates. Please take the time to read the Data Use Agreement at <https://www.ucl.ac.uk/drc/research/miriad/Database>. Instructions for downloading the entire dataset and demographic and psychology data can be found at <https://www.ucl.ac.uk/drc/research/miriad/Downloading>. The release of this data was made possible through the support of the UK Alzheimer's Society and the kind permission of the original study participants and funders. Full acknowledgements can be found at <https://www.ucl.ac.uk/drc/research/miriad/Acknowledgements>. Best wishes for your future research, Ian Malone Dementia Research Centre, UCL Institute of Neurology MIRIAD Team: Dementia Research Centre, UCL Institute of Neurology, UK Centre for Medical Image Computing, UCL, UK NMR Research Unit, UCL Institute of Neurology, UK Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, UK

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Pixels left after manual correction of subcortical regions.
by Elin Allzén 08 Feb '13

08 Feb '13

Dear FreeSurfer, When i manually have corrected some areas of subcortical structures (ex Caudate) i still get some pixels left of other regions (NAcc for ex) in the corrected area after I again have run recon-all -autorecon2 and -autorecon3. It seems like the program does not read my alterations correct. Why is this? Is there anything i can do to prevent this? I have off course saved segmentation after my corrections before i re-run them. Kind regards, Elin Allzén

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Postdoctoral Fellow position: UNSW SYDNEY AUSTRALIA
by Alana Shepherd 08 Feb '13

08 Feb '13

Postdoctoral Fellow UNSW Faculty of Medicine School of Psychiatry REF. 9160NET FIXED TERM: - Salary: (Level A Step 6-8) A$78K – A$84K per year (plus up to 17% employer superannuation plus leave loading.) The School of Psychiatry, Faculty of Medicine, The University of New South Wales, invites applications for the position of Postdoctoral Fellow. This is a research position funded by the National Health and Medical Research Council (NHMRC), located within the Research Unit for Schizophrenia Epidemiology at St Vincent’s Hospital, Darlinghurst. The successful applicant will contribute to multimodal studies of neuroimaging and genetics using a national schizophrenia cohort (the Australian Schizophrenia Research Bank) for which clinical, cognitive, neuroimaging, and genetic data has already been collected over the past six years. The successful applicant will hold a PhD in neuroscience, psychology, biomedical science, bioinformatics or relevant discipline, and will have demonstrated skills in structural neuroimaging analyses, and/or machine learning techniques for analyses of multidimensional data sets. The successful applicant will also have a very good track record of research productivity relative to opportunity, excellent communication and interpersonal skills. The successful applicant will be expected to demonstrate an interest in biological mechanisms of psychosis. This is a full time fixed term position for a period of 1 year, with a possibility of renewal depending on performance. The successful applicant may be required to undergo pre-employment checks prior to being offered this position. Applicants should systematically address the selection criteria in their application. Having read all the documentation, applicants may then direct any enquiries to Dr Melissa Green on (61 2) 8382 1584 or melissa.green(a)unsw.edu.au<mailto:melissa.green@unsw.edu.au> Apply at: http://www.hr.unsw.edu.au/services/recruitment/jobs/01021302.html Applications close : 22 February 2013

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Download v. 5.0 on Mac Lion 10.7.5
by krista kelly 07 Feb '13

07 Feb '13

Hello, I need to download an older version of freesurfer (Version 5.0) on a Mac Lion 10.7.5. In the archives I don't see a file for Lion, just Leopard and Tiger. Is it possible that either of these will work for Lion? Also, are there any step by step instructions on how to install? Thanks! Krista

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Freesurfer February 2013