Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

Segmentation error at insula
by Angel Wong 06 Nov '09

06 Nov '09

Hi I have encountered an error for construction of white surface at insula (please see the attached image highlighting the segmentation error). Could anyone tell me how to fix this kind of error? Cheers Angel

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monkey data scripts
by Rosa Lafer-Sousa 06 Nov '09

06 Nov '09

Hello, I found the set of scripts Sebastian Moeller provided for processing monkey data in freesurfer (http://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData) which break down the steps of recon-all allowing for manual intervention (since the recon-all script is not setup to work for monkey data), but there are no instructions for how to run them. Does anyone have a guide to executing this set of scripts? thanks! Rosa ---- Rosa Lafer-Sousa Research Assistant, Bevil Conway Wellesley College - Neuroscience 106 Central Street Wellesley, MA 210-325-3185 rlaferso(a)wellesley.edu

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reslicing question
by Mehul Sampat 05 Nov '09

05 Nov '09

Hi Folks In my dataset each MRI exam is 256*256*180. I would like to convert wmparc.mgz back to 256*256*180. Since this is the segmentation output, I think I should use set the resample type to nearest and use a command like mri_convert -rl mri/orig/001.mgz -rt nearest mri/wmparc.mgz mri/wmparc.nii Does this look correct or is there anything else I need to specify? Thanks Mehul

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segmentation error
by Gonzalo Rojas 05 Nov '09

05 Nov '09

Hi: Which is the error of the volumes that appears in aseg.stats ?... are they quantifiable ?... Because I notice that the right-hippocampus (for example) that appears in aseg.auto.mgz is bigger than the right-hippocampus of T1.mgz image... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Visualize Supra-temporal Plane
by Oya, Hiroyuki 05 Nov '09

05 Nov '09

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mc-z sign
by Lars Tjelta Westlye 05 Nov '09

05 Nov '09

Hi, I have a couple of questions regarding mri_glmfit-sim (mc-z). 1. Is it correct that --sim-sign abs builds up a null distribution of max cluster sizes regardless of the direction of the effects in the simulated data while --sim-sign pos/neg only counts the largest positive/negative cluster for every iteration? Or is the sign only used in the subsequent correction procedure by mri_surfcluster and not affecting the null distribution? 2. Under which circumstances would it be advisable to choose --sim-sign abs instead of pos/neg and vice versa? Thanks a lot, Lars

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Re: [Freesurfer] Analysis using a custom template
by Bruce Fischl 05 Nov '09

05 Nov '09

Hi Cathy, no, I don't think so. You'll need to rerun the qcache stuff if you are using qdec to map the thickness and whatever else into the new common space, but I don't think you need to rerun autorecon3 Bruce On Thu, 5 Nov 2009, Cathy Scanlon wrote: > > > Hi, > > I have a question regarding group analysis using a custom template. > > I have created a custom template using mris_make_template as described > http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates > > I then registered all my study subjects (that have previously been run > through recon-all) to this new template using mris_register and named the > spherical registration ?h.sphere.reg for each subject. > > I want to conduct a group analysis of cortical thickness. So my question is > do I need to rerun autorecon3 or any subset of it (e.g. ?h.avg_curv) that > might affect my analysis or creation of the 'average subject'? > > All the best, > Cathy > >

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Analysis using a custom template
by Cathy Scanlon 05 Nov '09

05 Nov '09

Hi, I have a question regarding group analysis using a custom template. I have created a custom template using mris_make_template as described http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates I then registered all my study subjects (that have previously been run through recon-all) to this new template using mris_register and named the spherical registration ?h.sphere.reg for each subject. I want to conduct a group analysis of cortical thickness. So my question is do I need to rerun autorecon3 or any subset of it (e.g. ?h.avg_curv) that might affect my analysis or creation of the 'average subject'? All the best, Cathy

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multiple recon-all processes
by Ahmed, F, Me <fahmed＠sun.ac.za> 05 Nov '09

05 Nov '09

Hello, I know that FS can run multiple recon-all processes at one time, but I wanted to know how exactly one can do that. Is it just a matter of opening a terminal window for each recon-all process you wish to run? Thanks, Fatima

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RES: Single subject vs. group
by Pedro Paulo de Magalhaes Oliveira Jr 05 Nov '09

05 Nov '09

Our group published a paper with single subject vs group. The paper you can find in FreeSurfer's website article list: search by polymicrogiria If you want to discuss the results we published send me an e-mail. -----Msg original----- De: Tricia Merkley Enviado: 05/11/2009 00:15:17 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] Single subject vs. group Hi, I've seen similar questions posted to the list, but I haven't been able to find an answer. So sorry if this is a repeat. Is it possible (or even advisable) to create a map comparing cortical thickness for a single subject against a group? If so, how is the best way to go about doing that? Would I need to use z-score transformations? I would appreciate any suggestions for this. Thanks, Tricia Merkley

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Freesurfer November 2009