Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Qdec
by free_surfer＠virgilio.it 18 Jun '09

18 Jun '09

Dear Freesurfer users, We are experiencing a problem using Qdec (FS version 4.2.0; Qdec 1.0) for group data analysis. Indeed, the qdec display [after creating the qdec.table.dat and the <factor>.levels files] doesn't visualize properly (as in the tutorial) the Data Table View and other window-options that should allow us to select "Generate Stats Data Table" and proceed with the group analysis. Any suggestion would be greatly appreciated. Many Thanks in advance for your help, Antonio Gallo, MD, PhD Department of Neuroscience Second University of Naples Ph: +39-081-5665090

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talairach_afd error
by Pål Gunnar Larsson 18 Jun '09

18 Jun '09

I have one volume that stops with error in tailarach_adf. The volume was axial rotatet some 20 degrees, but that was manually corrected. Recon-all still stops with the same error. The nu.mgz looks OK. What is the problem? I have attached the last part of the output. I am using Freesurfer Centos 4.3.1 on Ubuntu 8.10 Regards Pål

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Error in Analyze
by Toh Hock Wong 18 Jun '09

18 Jun '09

Hi Douglas, Thank you for your quick reply. I have tried again with two discrete and continuos factors. The same error of mri glmfit --y still appears towards the end. I have attached a more detailed version of the error for your reference. Any suggestion will be much appreciated. Cheers! Toh Wong

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Co-vary
by Jeff Sadino 18 Jun '09

18 Jun '09

Hello Freesurfers, My apologies for this very basic question more about statistics than freesurfer, but I have not found an answer anywhere on the wikis, or the web (maybe it is too basic :-) ) I am interested in age-related effects of hiv and I wanted to covary for age and education in mri_glmfit. For example, if my fsgd file is: class control class hiv variables age ed input subj1 control 40 13 input subj2 hiv 35 12 ... ... and I use dods, is my contrast matrix the place where I would tell it to covary? Something like: 0 0 -1 1 1 1 1 1 (y-int) (age slope) (covary for age) (covary for ed) As always, thank you for your help, Jeff _________________________________________________________________ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori…

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Questions on ROI Comparisons
by nmaleki＠mclean.harvard.edu 18 Jun '09

18 Jun '09

Dear all, 1-Is there a way to use mris_anatomical_stats to calculate mean ROI values on the re-sampled and smoothed individual subject data that is produced in the pre-processing step, rather than mapping the ROI back to each subjects’ space? If so what is the command? 2-If you define a ROI where there is statistically significant difference (between 2 groups) at the group level on your average subject and then map the ROI back to each subject’s space and measure the mean value of say thickness in that ROI, should you expect to find the same significant difference between the groups that you are comparing? What does it mean if you don’t for some ROIs? 3- Is there a way to smooth the vertices in a ROI similar to what is done at the preprocessing level? 4- There is a comment on wiki (qdec, ROI analysis) that indicates the usefulness of mapping the ROI back to each ubject's space to 'check the integirty of your reults'. Could you please elaborate more on this? Thank you, Nasim

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Partial Volume Correction and wmparc.stats
by Nasim Maleki 18 Jun '09

18 Jun '09

Dear Freesurfer developers, I'm wondering whether the wmparc.stats is computed with a partial volume correction at the boundaries of the structures. Thank you, Nasim

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label2vol
by xforever＠ucla.edu 18 Jun '09

18 Jun '09

Dear Freesurfer experts, I'm trying to convert the annotation file into (binary Analyze file), I tried the command mri_label2vol and it seems to worked fine, but I find out that the output file is in 32bit/vox resolution, and the program I want to use to open the file doesn't support that and crashes everytime I try to open it. I was wondering if there's anyway to make the output file 16 bit/vox instead? also the output file is in COR, is there anyway I can make it Axial? Best, Andy

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[FSL] Postdoctoral Positions for EEG/fMRI Research at UC San Diego (fwd)
by Bruce Fischl 17 Jun '09

17 Jun '09

FYI ---------- Forwarded message ---------- Date: Tue, 16 Jun 2009 22:55:11 -0700 From: Tom Liu <ttliu(a)UCSD.EDU> Reply-To: FSL - FMRIB's Software Library <FSL(a)JISCMAIL.AC.UK> To: FSL(a)JISCMAIL.AC.UK Subject: [FSL] Postdoctoral Positions for EEG/fMRI Research at UC San Diego The Center for Functional MRI at the University of California, San Diego (UCSD) invites applications for two postdoctoral positions. The research projects will involve the use of simultaneous EEG and fMRI methods to (a) investigate neurovascular coupling mechanisms in both resting-state and functional paradigms, and (b) characterize the spatiotemporal dynamics of unsupervised learning. The UCSD Center for Functional MRI is equipped with two research-dedicated GE 3T HDX short-bore scanners and a 64-channel Brain Products MRI-compatible EEG system. More information about the Center is available at our website: http://cfmriweb.ucsd.edu. Applicant must have a PhD in Engineering, Computer Science, Physical Science, Neuroscience, or a related field. Candidate must be adept at scientific computing, and experience with MATLAB and C is desirable. Experience in fMRI and EEG is beneficial, but not required. Please send a CV, a statement of research interests, and the names and contact information for 3 references by e-mail to Dr. Thomas Liu (ttliu(a)ucsd.edu) Please use PDF file format. Interested candidates may also arrange to discuss the position at the 2009 HBM meeting in San Francisco.

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New release, v4.4.0
by Nick Schmansky 17 Jun '09

17 Jun '09

A new release of Freesurfer is now available, v4.4.0: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall This release contains an updated longitudinal analysis stream. See the Release Notes page for details on this and prior releases: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

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Installation
by sfcrc＠aol.com 16 Jun '09

16 Jun '09

Hello, I am new to Linux, so bear with me. We downloaded the file: freesurfer-Linux-centos4-stable-pub-v4.3.1-ful.tar.gz When we try to open this file from the desktop, the archive manager opens up and says "An error occured while loading the archive" The command line output reads: tar: skipping to next header gzip: stdin: invalid compressed data--crc error gzip: stdin: invalid compressed data--length error tar: Child returned status 1 tar: Error exit delayed from preious errors We would really like to get this program up and running.? Please let us what we're doing wrong. Thanks for your help, -Daniel

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