Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

PCA on PET / Thickness in Freesurfer
by Foo Keat Mak 01 Dec '16

01 Dec '16

Hi Freesurfer Team, For a given group, I want to look at the covariance patterns between thickness and PET. Within Freesurfer, what are some general workflow tips on how I could go about performing PCA (within modality) or joint ICA analyses looking at the covariance patterns across modalities? Is the -pca flag a good starting point? Any feedback is appreciated! Thanks a lot. Best Wishes, Elijah

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Demeaning variables
by Rodrigo Gonzalez Huerta 01 Dec '16

01 Dec '16

Hi Freesurfers, For obtaining my undergraduate degree I'm performing a study using Freesurfer. I'm stuck with the centering (de-meaning) issue. I have two discrete variables, gender, and patient-control, and a continuous variable which is age. The age population range goes from 20 to 55 years and is paired between patients and controls. Patient's disease affects cortical thickness over time and every patient has been presenting the disease for 6 years (no more, no less). I've runned QDEC and mri_glmfit using DODS obtaining the same results, the problem is that when I demean the age (I used the grandmean) the results are very differente. If I don't demean some clusters survive the monte-carlo multiple comparisons correction (p<0.05), but, when I demean no cluster survive. I have this questions: 1. Since most of my subjects are in the range of 20-35 years and only a few have more than 35 years, it is correct to use the mean? Wouldn't be better to use the median or some other value? 2. This is maybe a silly question, but why should I care about the intercept? I know that demeaning doesn't change the slope, just the intercept, but I don't understand why I should care, I read in some publications that demeaning is not always necessary. Other questions: 1. Most of my subjects are women (around 80%, N=18), Does it have an advantage to remove the males to get rid of the gender variable?, or should I continue as I've been doing, controlling for the effect of gender. 2. Since I don't know if this disease is more aggressive when is developed at some stage of life, I mean, if young patients are less affected than older patients after six years of presenting it, it is correct to control the effect of age? (Entering the variable as a nuisance factor), or should I search for an interaction between age and the condition variable? I only care about differences in cortical thickness. Any suggestion is very welcome, thanks in advance for your answer. Rodrigo

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DTI Multi band sequence?
by Martin Juneja 01 Dec '16

01 Dec '16

Hi, I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine whether the DTI data (in DICOM format) I have is multi-band sequence? I used dicominfo in MATLAB but couldn't find any information related to multi-band in the dicom header. Any help would be really appreciated.

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Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.
by Knut J Bjuland 01 Dec '16

01 Dec '16

Hi Anastasia If I want to use Tracula DTI files instead, which file do I choose: Is it FA_ditifit.nii? Best Knut Jørgen

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Pegasus workflows?
by Heiland, Randy 01 Dec '16

01 Dec '16

Hi, Somewhat off-topic, but are there Freesurfer users on this list who might use the Pegasus WMS for executing workflows? If so, I’d like to hear about your use cases. I’m part of an NSF-funded project to incorporate data integrity and security assurances into Pegasus for scientific workflows. thanks, Randy

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Postdoctoral position in early onset adolescent psychosis study
by Tiril Pedersen Gurholt 01 Dec '16

01 Dec '16

Dear All, At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, Norway, there is a position available as a postdoctoral student funded by the Research Council of Norway. The research area is psychiatric neuroimaging with focus on 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 neuroimaging, computer science, bioinformatics, psychiatry, 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 December 4th, 2016. For further information and to submit an application please see the University of Oslo’s website: http://uio.easycruit.com/vacancy/1719677/70331?iso=no . 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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Freesurfer December 2016