Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

using mri_glmfit-sim
by Chris Hyatt 02 Feb '11

02 Feb '11

I've read both Hagler et al 2006 Neuroimage (Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data) and B. Douglas Ward's description of AlphaSim that both describe clusterwise correction for multiple comparisons. I recently found, however, an MGH Freesurfer presentation that mentioned that after synthesizing Gaussian noise and smoothing (Monte Carlo), the rows of the design matrix were permuted. Does the mri_glmfit-sim clusterwise correction method permute rows of the design matrix? I'm still a bit confused about the exact method the clusterwise correction for multiple comparisons work in Freesurfer. Thanks for your help. Christopher Hyatt, PhD IOL/Olin Neuropsychiatry Research Center Hartford, CT

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Jacobian values
by Larissa Stanberry 02 Feb '11

02 Feb '11

Afternoon greetings, upon inspection of ?h.jacobian_white files, I realized the values are all positive. I was expecting to see some negative determinants, perhaps I'm missing something. Any input is appreciated. Cheers Larissa

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transform to original mri
by Seok Lew 02 Feb '11

02 Feb '11

Dear all, I am trying to transform the reconstructed surface like rh.pial into the original mri's (like 001.mgz) coordinate. I found some matrices in the ./transform directory, but not sure of which one (or a set of matrices) would do the transform? Seok slew(a)nmr.mgh.harvard.edu

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error during autorecon2-wm routine
by Larissa Stanberry 02 Feb '11

02 Feb '11

Dear experts, after correcting WM, I got the following error running recon-all - autorecon-wm -subjid XXX ERROR: _FindFacePath: could not find path! It happens in the middle of the correcting topology routine. I'd appreciate any input on as to why it happens and how to fix it. Cheers Larissa

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One Way Anova and multiple comparisons
by marco battaglini 02 Feb '11

02 Feb '11

Hi to everybody, I am a very inexperienced users of FreeSurfer. I have 3 groups of subjects and I have run recon-all and checked the results for all the subjects (very good results). Now what I need to do, is to calculate the differences in the regional cortical thickness between these 3 groups (using age and gender as covariates) and to perform multiple comparisons, in order to detect possible local differences in cortical thickness. Is it possible to perform this kind of analysis also for comparing surfaces between different groups? Could you give me a short "pipeline" about the steps I need to do, or redirect me to some focused documentation? Thank's. Marco

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Segmentation problems
by Tetiana Dadakova 02 Feb '11

02 Feb '11

Dear FreeSurfer users, I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction? Thank you, Tetiana.

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Surface area intepretation problem
by Jürgen Hänggi 02 Feb '11

02 Feb '11

Dear FS experts We divided the superior temporal sulcus derived from the aparc.a2009s.annot into parcellations of 300mm2 (using mris_divide_parcellation) and computed the mean cortical thickness within each parcellation. So far so good. But we noticed that each parcellation has a unique surface area that deviates largely from 300mm2 (96-480mm2). We defined the parcells on the fsaverage template and transformed them back into the native space of each individual. Therefore, we expected some variation in the surface area, but not such large differences. How to explain it? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Manual editing of skull strip and mri_segstats
by Cheryl McCreary 01 Feb '11

01 Feb '11

Hi, I'm new to Freesurfer and am trying to process some data for the first time. I have two questions: 1. I have done some manual editing of the brainmask for skullstripping, saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing? 2. For then initial analysis of my data, I would like to create a table of intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line: mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm However, this fails with the error: unknown option --surf-ctxgmwm. What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table. Thank you for any assistance or suggestions. Kind regards, Cheryl

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How to cite DOSS / DODS?
by Christian Scheel 01 Feb '11

01 Feb '11

Dear all, does anyone know one or two good method papers to cite when describing the difference of DOSS and DODS? I have already screened Pubmed and Co. but did not really find anything convincing. Any help greatly appreciated! Best wishes, Christian Scheel

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mri_convert problem
by Gabriel Go.Es. 01 Feb '11

01 Feb '11

Dear FS users I'm using FS v5 to convert some dicom images to mgz running the comand: mri_convert -it dicom -ot mgz 000001.DCM 001.mgz And get the error: ERROR: /root/trabajo/freesurfer/subjects/sujeto1/mri/orig/MPRAGE1/000001.DCM is not a dicom file But when I try to open the file in MRIcro it is a dicom (philips) file (see attached file), can any one help me with this? Regards, Gabriel

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Freesurfer February 2011