Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

aparcstats2table
by Dana W. Moore 06 Nov '09

06 Nov '09

Hi, I was very excited to read in the release notes that the aparcstats2table command had been updated so that the output will always be in the same order. This is an issue for me, as I have a spreadsheet that I like to paste new subjects into. However, I have just tried to do so, and was disappointed to find that the output was in a different order from my original spreadsheet. (This has all been done with v4.5.0, so it's not that I switched versions and then expected it to be in the same order.) Is there a command I can use to make it come out in the same order? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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(no subject)
by Zaman, Arshad 06 Nov '09

06 Nov '09

Please can you remove me from the email listing thanks, Arshad Zaman

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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

3 2

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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