Freesurfer

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30099 discussions

FSGD and contrast files for group analysis
by Kenza Drissi 02 May '14

02 May '14

Dear Marie,I want to run a group analysis on a set of subjects, correcting for gender(Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus inlh/focus in both h), age and IQ. Should my FSGD file look somewhat like thisbelow:GroupDescriptorFile 2Class NoFocus_MaleClass NoFocus_FemaleClass RhFocus_MaleClass LhFocus_MaleClass BhFocus_MaleClass RhFocus_FemaleClass LhFocus_FemaleClass BhFocus_FemaleVariables age IQIf so, considering that I want to investigate the effect of epilepsy on corticalgyrification, what should my contrast matrix look like?The hypothesis is that the gyrification index is diminished for epilepticpatients, probably more when there is bilateral focus.I know that we need as many number as regressors, so I expect there to be 10numbers, is it so?Thank you so very much for clarifying this point,Kenza

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effect size for conjunction analyses?
by Caspar M. Schwiedrzik 02 May '14

02 May '14

Hi! I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and I was wondering whether anyone can make a recommendation how to display effect sizes for this kind of analyses? Would you show the effect size estimate corresponding to the p-value that is chosen, an average, or anything else? Thanks, Caspar

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MICCAI PC workshop -- May 16 (fwd)
by Bruce Fischl 02 May '14

02 May '14

FYI ---------- Forwarded message ---------- Date: Fri, 2 May 2014 11:28:11 -0400 From: Polina Golland <polina(a)csail.mit.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: MICCAI PC workshop -- May 16 Hi Bruce, Can you please forward this around? Thanks, Polina. MICCAI PC Workshop May 16, 2014, 1-6pm, CSAIL Kiva and Star Conference rooms (32-D463, 32-G449). MICCAI program committee members will present their work in areas of Medical Image Computing and Computer Assisted Interventions. This is a great opportunity to hear about current research of 20 MICCAI groups from all around the world. Open to public; anyone interested in the topics of MICCAI is welcome to attend. Tentative Program can be found here: http://miccai2014.org/pc_workshop.html.

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per voxel regressor in LME toolbox?
by Marnie Shaw 02 May '14

02 May '14

Dear Freesurfers, Is there a way to include a per voxel regressor in an LME model within the matlab LME toolbox? Just like you can do with mri_glmfit? Cheers, Marnie

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Multi-echo FLASH
by Jon Houck 02 May '14

02 May '14

Hi all, I'm building a scan protocol for what is primarily a MEG study, which needs T1 information for co-registration and T1/T2 information to construct an accurate BEM from the inner skull surface. It seems like the two multi-echo FLASH sequences at 5 and 30 degrees would give me all of the information that I need without an MPRAGE, but I'm not sure how well the two MEFs work in the standard Freesurfer pipeline. Would it be reasonable to acquire no MPRAGE but two MEF sequences at 5 and 30 degrees, combine them following the method from https://surfer.nmr.mgh.harvard.edu/fswiki/MEF, and send the resulting T1 to recon-all? With my scan time constraints, the alternative would be to acquire a multi-echo MPRAGE and a single 5-degree MEF. Thanks for any help on what is probably a naïve question. Jon Houck

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Re: [Freesurfer] using multiple cores
by Lukas.Scheef＠ukb.uni-bonn.de 02 May '14

02 May '14

Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas > Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 > > Hi Luke > > what version of FS are you running? We see significant speedups. Try > running top in a unix terminal and seeing if the cpu usage of > mri_ca_register (during autorecon2, the longest single step) is morethan 100% > > cheers > Bruce > > On Fri, 2 May 2014, lukas.sch...(a)ukb.uni-bonn.de wrote: > > > > Hi folks! > > > > I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not > > see any accelartion when processing a single data set with or without the > > flag -openmp flag set. > > > > recon-all -s ernie_1 -all > > > > leads to ~6,4h processing time. > > > > Unfortunately > > recon-all -s ernie_2 -all -openmp 4 > > > > did not change anything. Do I miss anything? Do I have to prepare my system > > in a special way? Or run any scripts in advance? > > > > (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) > > > > Best wishes, > > > > Luke

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using multiple cores
by Lukas.Scheef＠ukb.uni-bonn.de 02 May '14

02 May '14

Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke

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Hippocampal subfields on 1.5 Tesla
by Alan Francis 01 May '14

01 May '14

Hi Bruce and FreeSurfers: I have received a manuscript to review for possible publication. The authors have used the subfields algorithm on 1.5T scans and obtained a parcellation with values. They have drawn some major conclusions on the basis of the findings. My understanding is that this method can only be done on 3T. Is the 1.5T results valid? Please advice. thanks, Alan Francis

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Plot Histograms
by Dídac Vidal 01 May '14

01 May '14

Hi! I would like to plot an histogram with values from sig.mgh across all cortical mantle (as represented in qdec or in tksurfer-overlay options). Which function would allow me to obtain/create histograms from *mgh files? I also would like to obtain a similar histogram, but restricted to a cortical label. How I could do that? Thanks in advance -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Faculty of Medicine University of barcelona

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Constraining fMRI data with a surface label generates a bfloat file?
by JacobML＠nmr.mgh.harvard.edu 01 May '14

01 May '14

Hello Freesurfer Experts, Using func2roi (in stable3), we constrained our functional data with specific surface labels and t thresholds, and over-threshold masks were outputted as .bfloat files. Does this mean these masks are in volume format and that the volumetric functional data was mapped to the surface but then back to the volume again when the mask was created? We would now like to project these masks onto the fsaverage brain (for viewing). Can you please let me know how this may be accomplished? It seems mri_convert can not transpose .bfloat to .label, but I imagine there is a way! Thank you again for the help. Jacob

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