Freesurfer August 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
82 discussions

fsl ROIs become smaller after registered to freesurfer
by Wang, Xin 28 Aug '08

28 Aug '08

Hello, Group, I tried to registered the fsl average of one subject .gfeat to his freesurfer surface. After manual correction of register files, the ROIs of ,gfeat become much smaller on the freesufer surface (including less cortical areas). please help me with this problem. Thank in advance, Xin

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Recommended workflow
by Martin Kavec 28 Aug '08

28 Aug '08

Greetings to all, I have several pathological subjects, which need substantial editing involving removing of dura reminders, filling WM due to the lesions, and adding control points due to the WM atrophy. I ran "recon-all -all" first to have initial reconstruction, which helps me to focus on correcting the earlier mentions problems. I have corrected brainmask, wm, and created control points, and now I wonder if re-running "recon-all -autorecon2-cp -autorecon3" would be sufficient to get correct results, or should better run separately "recon-all -autorecon2-cp" followed by "recon-all -autorecon2-wm -autorecon3"? Thanks in advance, Martin

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Classifying cortical thickness
by Sebastian Gluth 28 Aug '08

28 Aug '08

Hi, I'm planning to analyze cortical thickness data and read about this classification and permutation approach by Golland et al. (2002) and Golland & Fischl (2003) in order to account for multivariate effects. Is this classification procedure included in FreeSurfer (in form of a tool or a Matlab script or so)? Thanks, Sebastian

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mri_glmfit full Monte Carlo simulation run time on tutorial data
by Silviu Podariu 28 Aug '08

28 Aug '08

Hello! I was running the full Monte Carlo simulation on the 40 subjects tutorial data (following the Group Analysis tutorial, with mri_glmfit from command line) and I see the simulation is still running after 10 days... I was wondering if this was normal or something is wrong. (using a single 2GHz dual-core Intel Xeon processor on an 8GB Mac workstation). What would be an expected time for that simulation, with exactly the same options/parameters as given in the tutorial command (shown below)? mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 10000 2 lh.gender_age.glmdir/csd1Thank you very much, Silviu Podariu U.Nebr.Med.Cent. Omaha, NE

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Configure Overlay display
by Nicola Hobbs 28 Aug '08

28 Aug '08

Hi all, We've noticed that the min threshold value in the configure overlay display toolbar doesn't correpond to the value displayed on the scale bar. Could someone explain this difference please? Thanks for your help. Nicola -- Nicola Hobbs Dementia Research Centre National Hospital for Neurology and Neurosurgery Queen Square London WC1N 3BG +44 (0)845 155 5000 ext. 723839

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(no subject)
by Xie, Hong 28 Aug '08

28 Aug '08

Hello, group, I am running longitudinal process step by step following the wiki page of 12 differences between longitudinal and recon-all process. But some needed files are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz, wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz, fill.mgz, brain.finalsurfers.mgz, ?h.smoothwm, ?h.inflated, ?h.sulc, and ?h.aparc.annot. Should I use recon-all commands to create these files or just copy ( or transform) them from tp1 to tp2? Thank you for help. Hong

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(no subject)
by Xie, Hong 28 Aug '08

28 Aug '08

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how to locate the auditory cortex?
by bin.lv 27 Aug '08

27 Aug '08

Hi all, After getting the cortical surface with Freesurfer,could I identify the location of the auditory cortex in each individual, and further then calculate the surface area , or the volume of it? In the paper of Cerebral Cortex " Cortical Folding Patterns and Predicting Cytoarchitecture", it seems that there is no auditory cortex yet. Thanks in advance, Bin Lv 2008-08-27 bin.lv

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FDR correction
by Manja Lehmann 27 Aug '08

27 Aug '08

Hi, We've noticed that FDR correction produces different p-values for the left and right hemispheres. We found that this issue was observed previously and an email was sent to the mailing list (see below), however, no answer was received. We wondered if anybody has noticed this problem before and if there are any suggestions on how best to deal with it. Thanks Manja Hi, FDR correction for multiple comparisons gives you different p-values for the left and right hemispheres. It seems really weird to report in a paper: a) that you've corrected for the right and left hemispheres separately and b) that the p-value that gave rise to a corrected probability of .05 was different for each. How do people deal with this issue? Take the most stringent p-value and use it for both hemispheres? Just report that FDR adjusted the p- value to .05? Also, correcting for right and left hemispheres separately assumes that they are independent observations. Unless you're studying callosotomy patients (and maybe even if you are) this doesn't seem justified. Are we supposed to be adjusting p-values accordingly? Thanks, Dara -- Manja Lehmann Research Assistant Dementia Research Centre University College London Institute of Neurology Queen Square London WC1N 3BG lehmann(a)drc.ion.ucl.ac.uk Tel: 020 7837 3611 ext. 3962 P Please consider the environment before printing this e-mail

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dPSD in RPER
by Britta Holzel 27 Aug '08

27 Aug '08

For a rapid event-related design, how do I choose my dPSD, i.e. the delay of onset? I have a TR of 2 seconds and 45 trials for one stimulus type. Can I divide 2 seconds by 45 in order to get the maximum fine grained resolution? Or would it be better to have a larger dPSD, to make sure that I can average over several trials? Thanks! Britta -- Dr. Britta Hoelzel Massachusetts General Hospital Psychiatric Neuroscience Program 149 13th Street Charlestown 02129 MA USA https://www.nmr.mgh.harvard.edu/~britta

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Freesurfer August 2008