Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Questions regarding statistical analysis
by KimMJ 08 Jun '12

08 Jun '12

Dear FS experts I'm completely new to the world of freesurfer and apologize my silly queries. I'm trying to compare GM volume, cortical thickness, and mean curvature of 34 automatically parcellated cortical structures (data from 'aparcstats2table' command) between control and patient groups (N=32 for each) using SPSS. Here are my questions.1) It seems reasonable that statistical model of between-group comparison of each cortical GM volume should include age, sex, and intracranial (or cortical total GM volume) as covariates.But, should I also include intracranial volume (or cortical GMV) as a covariate in cases of cortical thickness and mean curvature ?? (Please note what I'm trying to do is NOT whole brain image analysis BUT MANCOVA using SPSS)When searching for the published articles containing cortical thickness analysis identical to what I'm doing, I found some use such a covariate, but some did not.Please let me know the better method. 2) My second questions is not directly related to FreeSurfer.From the above-mentioned analysis (MANCOVA: 2 groups, 34 dependent variables, 2 or 3 covariates), should I correct for multiple comparison problem using Bonferroni corrected P < 0.05/34=0.0014) or FDR-corrected P < 0.05 ?? Once again, apologies for my basic questions.Any comment would be greatly appreciated. Thank you in advance for your kind help. M. KimSouth Korea

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p-value of clusters
by Richter, Julia 08 Jun '12

08 Jun '12

Dear all, I am running a qdec analysis. When I press "Find clusters and Goto Max", all values of the significant clusters after FDR correcting appear except for the p values of the clusters. Any idea why this is happening and what I can do? Best, Julia

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total brain volume or intra crainal volume as estimated for total brain volume
by Knut J Bjuland 08 Jun '12

08 Jun '12

Hello, We would like to calculate a Total Brain Volume based on data in aseg.stat generated from version 5.1.0. Can I use intra crainal volume as estimated for total brain volume? Or should I just add total grey volume with subcortical grey volume with total white matter volume? Thanks, Knut Jørgen

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mri_fill problem
by Shay Ohayon 07 Jun '12

07 Jun '12

Hi, I am having problem getting mri_fill to run on one of my volumes (it did work with another monkey, so I assume I am running things right). I am using v5.0 (but it also happens on 5.1). The input is a monkey wm file with specified coordinates for the corpus callosum. The error I get is: "could not find corpus callosum" (see full log below). The input volume is available for download here <http://tsaolab.caltech.edu/sites/default/files/wm.mgz>( http://tsaolab.caltech.edu/sites/default/files/wm.mgz) Any takers? I tried various different coordinates and all of them fail. A hint may be this statement: "find_cutting_plane:seed point not in structure! Searching neighborhood..." which I don't fully understand as the point given is inside a connected component... Many thanks, Shay Tsao Lab Caltech --------------------------- reading input volume...done. searching for cutting planes...INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill: could not find corpus callosum /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill /space/data/shayo/cooked/test2/mri/wm.nii /space/data/shayo/cooked/test2/mri/filled.nii -CV 128 117 91: Signal 124

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loading surface in freeview
by Kushal Kapse 07 Jun '12

07 Jun '12

hi doug n fellow fs users, whenever we try to load a fsaverage surface in freeview, it shows me following message: "Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces" this message is limited only to fsaverage surfaces..... was just wondering if this is something to be worried about for further group analysis in qdec?.....any words on how to fix/avoid this message to reappear??? please let us know thanks kk

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Creating DMPFC ROIs in Freesurfer
by Wu, Paula (NIH/NIMH) [F] 07 Jun '12

07 Jun '12

I was wondering whether anyone here has used Freesurfer to create ROIs for the Dorsomedial Prefrontal Cortex, or if anyone knows citations of articles that have. Thanks, Paula Paula Wu Postbaccalaureate Intramural Research Training Associate Section on Functional Imaging Methods Laboratory of Brain and Cognition National Institute of Mental Health (301) 451-9582 wup2(a)mail.nih.gov<mailto:wup2@mail.nih.gov>

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fsgd
by Marie Schneider 07 Jun '12

07 Jun '12

Dear FreeSurfer experts, I am trying to start mris_preproc, but unfortunately it doesn't find my created fsgd file. I saved it in the foulder where you can find all subjects data. Shall I save it somewhere else? Thanks for your help, best Marie

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Re: [Freesurfer] How to avoid overlaps between volume labels?
by Cheol Han 07 Jun '12

07 Jun '12

Hi Yuko I think you can use multiple label tags when using mri_label2vol like below: mri_label2vol --subject $subject_name --hemi $hemi --label $label1 --label $label2 --label $label3 --temp $template --o $output --fillthresh 0.3 --proj frac 0 1 0.1 --identity The output volume would have non-zero voxels, marked with three different values. Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea

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FW: misalignment of aseg GM/WM and surface midway between pial and white
by Jeff Eriksen 06 Jun '12

06 Jun '12

I am wondering about how the pial and white surfaces are supposed to match up with the aseg file. I was expecting that when I created a new surface, usinfg mri_surf2surf, halfway between the pial and white surfaces (which I call the cortical ribbon), it would run right down the center of the GM. After creating that surface I converted it to voxel representation with mri_surf2vol. I found that it doesn't match everywhere. Are the pial and white surfaces not based on the aseg segmentation of G&WM? If they are, why the discrepancy? Thanks, -Jeff

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Creating a label from an .mgh file
by Ilia 06 Jun '12

06 Jun '12

Hello, How would one create a label (to be used as an input for "mris_anatomical_stats") based on a a statistical map generated by qdec (for example, the result of a Monte Carlo simulation such as "mc-z.abs.th23.sig.cluster.mgh"). The goal is to obtain average cortical thickness for regions where qdec detected significance. Thank you!!

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