Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

Extracting fMRI time course and computing correlations among them
by liang wang 19 Jul '10

19 Jul '10

Hi, Does anyone know one of studies which uses the parcellations (aparc or aparc.a2009s) Freesurfer provides to extract fMRI time course from each subject's fMRI data. Reading the instructions in Freesurfer Wiki, I know how to do that. However, I am not sure whether I should use the parcellations from the average output (obtained from make_average_subject), or the parcellations based on each subject. I would next compute functional connectivity between these regions. I am appreciated for any suggestions. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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Any suggestions for imaging parameters on a GE 3T with 8 channel head coil
by Mira Michelle Raman 19 Jul '10

19 Jul '10

Hi Freesurfers, We would like to optimize the 'Freesurferability' of images for a new project involving fidgety young children. Ideally, the structural scan time will be under 5 minutes. We have a GE Signa 3T MR750, with an 8-channel head coil. Preliminary experiments have found two short structural scan options, but both require some intervention after autorecon2 in the Freesurfer pipeline. Does anyone have a suggestion for a sequence that a) runs in under 5 minutes b) freesurfs with minimal intervention and c) that they would be kind enough to share. Thank you in advance, Mira ____________________________________________________ Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620

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recon-all -make all -s (subject) ERROR
by aekairys＠umich.edu 19 Jul '10

19 Jul '10

Hi freesurfers, I just got this error while continuing processing of a subject: mri_average: MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img) failed Linux titan 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 19 09:52:39 EDT 2010 make: *** [/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/rawavg.mgz] Error 1 Any suggestions would be greatly appreciated thanks best, Anson K. (freesurfer rookie)

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unknown region in aparc+aseg
by Deniz Ozgen 19 Jul '10

19 Jul '10

Hello All, Looking at aparc+aseg of some subjects we see some regions of the cortex labeled as "unknown" especially in the medial region / temporal lobe, close to amygdala. Additionally, around these regions there are some regions of the cortex that are not labeled at all. We see this on images acquired on both 1.5T and 3T magnets, with poor and good SNR. I was wondering what this "unknown" regions refer to, and if there is a way to fix this (using control points, or manual editing etc.) Thanks in advance. Deniz

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Surface and Volume do not align in Slicer3
by Steffen Bollmann 18 Jul '10

18 Jul '10

Dear freesurfer-mailinglist, I'm struggling since a few days with a problem I can't resolve: I ran recon-all without errors on my data and got the surfaces. Now I want to display surf/l(r)h.pial and mri/T1.mgz (or /orig/001.mgz) together to check the result in slicer3 (3.61.0). The problem occurring is, that any surface and the original volumes do not fit together - there is a small shift of the surfaces to the front. I already tried to apply transforms from mri/transform to the T1.mgz but nothing solved that issue. here is a screen shot of my problem: http://dl.dropbox.com/u/1263357/problem.png What am I doing wrong? Thank you for any hint in advance Best Regards Steffen

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OASIS Brains data...
by Gonzalo Rojas Costa 18 Jul '10

18 Jul '10

Hi: I used the command: "recon-all -subject OAS1_0153_MR1 -all -legacy" but I got the error: "ERROR: you have specified -legacy, but this does not look like a legacy analysis." Sincerely, Gonzalo Rojas Costa

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OASIS Brains data...
by Gonzalo Rojas Costa 17 Jul '10

17 Jul '10

Hi: I want to reprocess some OASIS-Brains data with the newest version of freesurfer... Which are the freesurfer command line that I must use (with "legacy" option) ?... And, I must do the complete processing or only some of the stages (autorecon1, autorecon2 autorecon3) ?... Sincerely, Gonzalo Rojas Costa

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mri_watershed error
by Toh Hock Wong 17 Jul '10

17 Jul '10

Dear freesurfer experts, I need your help on recon. I tried to perform recon-all on my anonymized control subjects (chunk of face/eyes removed on T1.mgz) and run autorecon1. It ran smoothly till the end of workflow of autorecon1 and came up with the following: mri_watershed Error: GLOBAL region of the brain empty! It then exited without compiling brainmask.mgz file. What should i try from here! Thanks for your help! Toh Wong Sydney, Australia

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Total Grey Matter Volume Mismatch
by Matthew Ku 16 Jul '10

16 Jul '10

Dear Freesurfer Experts, I have been analyzing the data output from Freesurfer for grey matter volumes and have been manually tabulating the total grey matter from the lh.aparc.stats and rh.aparc.stats files. Upon totaling the grey matter values in these .stats files, I have found that the totals do not match with the total grey matter volume found in the mris_anatmoical_stats file. Does anyone know why the total grey matter from the lh.aparc.stats and rh.aparc.stats files does not match with the total found in the mris_anatomical_stats file? Thanks, Matt _________________________________________ Matthew Ku University of Pennsylvania School of Engineering Class of 2013 (845) 596-3840 mattku(a)seas.upenn.edu

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Questions about mcparams2extreg
by Gabriel A. Tobon 16 Jul '10

16 Jul '10

Hi, I noticed that mc-sess produces a file for external mc regressors that can be used for analysis with "mcparams2extreg". I can see the added regressors in my design matrix if I decide to include them. How are these external regressors actually calculated? Are the same set of motion parameters used at every voxel? The design matrix looks different than the design matrix produced by FSL's FEAT process when motion parameters are added there: http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#stats FSL documentation says that adding these parameters is not really recommended. Is this the case for mcextreg in FsFast analysis? Thank you! Gabe

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Freesurfer July 2010