Freesurfer August 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
75 discussions

Number of voxels that intersect with inflated brain surface
by raij＠nmr.mgh.harvard.edu 08 Aug '07

08 Aug '07

Dear FreeSurfers, Is there a way to estimate the number of fMRI voxels that intersect with the FreeSurfer anatomical inflated surface space? -"- for a given surface label? We need this as N for calculations of statistical significances (to correct for the oversampling of the orginal 3D voxel space by very densely spaced vertex points on the surface). For this purpose, the voxel size was 3.125 x 3.125 x 4.4 mm, the FOV covered the entire brain, and the anatomical brain is "fsaverage". Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Question about aseg.mgz
by jorge luis 08 Aug '07

08 Aug '07

Hello all Are the norm.mgz and aseg.mgz volumes already aligned to talairach standard space ? I have read on the freesurfer tutorial that the transformation is computed and stored in transforms/talairach.ita but it is no applied to the initial volume. I would like to get the segmentation results aligned to talairach space. In advance thank you very much ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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Question about functional analysis on freesurfer
by lan lin 07 Aug '07

07 Aug '07

I know in freesurfer, the functional statistical analysis is performed on fsl. Could I use freesurfer to analysis the functional data instead of fsl?

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(no subject)
by Lisa Ronan 07 Aug '07

07 Aug '07

Hi All, I am interested in creating a surface label for the temporal lobe. I have tried running the mri_annotation2label calling the aparc.a2005s annotations, then merging the appropriate labels. The process sees to work fine except no label is made for S_temporal_superior. I understand from the --help that "if there are no points in the annotation file for a particular index, no label file is created", but I'm not quite sure what this means. There are stats generated for this region so I'm not sure what's going wrong. I would be grateful for any help on this. Kind regards, Lisa Ronan

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help
by whblqh＠mail.ustc.edu.cn 07 Aug '07

07 Aug '07

Hello, I setup FC6 system, and download freesurfer-Linux-centos4-stable-pub-v3.0.4-full.tar.gz. Now FS is installed on my computer, tkmedit work successfully. however, tksurfer work abnormally, its interface cann't display.I think it may be problem of nvidia driver . curr ently I cann' t find tksurfer related to FC6,would you like help me? Wang Hai-bao

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dev version of mri_glmfit for intel macs
by Catherine Hartley 06 Aug '07

06 Aug '07

Hi, I'm getting a bus error when I run mri_glmfit on my Intel Mac. When I had this problem before, I got a development version of mri_glmfit which solved the problem. Unfortunately I've reinstalled a newer version of Freesurfer since then and overwrote that binary file and it's no longer on the public distribution server. If someone could repost the latest version of mri_glmfit for Intel Macs (10.4.9), that would be great. The same problem is described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04632.html Thanks, Cate

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determining sizes of clusters at given CWP cutoff
by Robert Levy 06 Aug '07

06 Aug '07

Hi, I was trying to figure out if there is any way to determine the exact size at which clusters becomes significant given a specified significance, and it appeared from the mc-corrected overlay that in this overlay the clusters do not continously change in size but appear discretely at a given threshold and are the same size at higher thresholds in an all-or-nother sort of way. I take this to mean that because the monte carlo simulation was performed at a given threshold, the clusters at that threshold size are corrected for mutiple comparisons based on the probability distribution of the chance data (though I don't know the details). Because it is done in this way, it seems I would either have to run several monte carlo simulations, at successively higher minimum thresholds, in order to arrive at the critical cutoff sizes for significance. This is impractical, so I guess my question is, does the way in which the monte carlo simulations are done preclude the possibility of getting the cluster sizes at which they will have a certain CWP value, or is there some way of doing this? Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Thickness standard deviation map
by Burmicz, Ryszarda 06 Aug '07

06 Aug '07

Hi Freesurfers, I have tried looking this up on the list, but I don't understand exactly what to do in this scenario: I have a group of subjects (all controls). I want to create a surface map of the standard deviations of the thickness values (i.e. to show how the thicknesses vary across subjects). I am not sure what is the easiest way to go about this - can I: 1) simply convert the ?h.thickness files to .asc and calculate the deviations at each vertex (I am under the impression that this is not correct as they need to be registered to a common surface first), then convert back to .thickness and load into tksurfer 2) use mris_preproc then mris_glmfit? I don't necessarily want to calculate any stats, but I wouldn't mind a pretty picture :) If I have 4 groups of 10 subjects each, so if I churn these all through glm_fit will I be able to access separate thickness files for each group? And how can I map standard deviations for each group in this scenario? Many thanks, Rysia

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editing labels
by Sarah J Greene 06 Aug '07

06 Aug '07

Hi all, I just wanted to ask about editing labels in tksurfer. I have converted my annot files to labels using mri_annotation2label, and now have all of the labels in the label directory. However when I edit the labels, and then save them using save selected label (highlighting the label and choosing the correct label in the correct hemisphere), nothing is saved when I pull up the image again. I have tried to convert the labels to annot files using mris_label2annot, but this isn't working either. I'm not sure what I am doing incorrectly. Thanks, sarah

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mris_anatomical_stats question
by Morgan Hough 06 Aug '07

06 Aug '07

I am reporting thickness values from subjects native space constrained by mask labels using mris_anatomical_stats. I am currently getting the average of the unsmoothed estimates. I would like to be able to get smoothed values but the usage reports the smoothing option as -nsmooth <#> where the # is the # of smoothing iterations. If we are using 10mm FWHM smoothing for the group results can I estimate the number of smoothing iterations to obtain something equivalent? Would it be easier to use mri_surf2surf and create a smoothed thickness file for each subject? Thanks again. Cheers, -Morgan

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Freesurfer August 2007