Freesurfer June 2009

freesurfer@nmr.mgh.harvard.edu

94 participants
140 discussions

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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FW: qdec- aparc.a2005s.thickness
by Sharmili 57 16 Jun '09

16 Jun '09

hey, Loading aparc.a2005s.thickness i get the attached error message. Does anybody know how to solve this problem? Posteingang immer voll? Der erste Speicher, der mitwächst: Unbegrenzter Speicher bei Windows Live Hotmail! _________________________________________________________________ http://redirect.gimas.net/?n=M0906xFTP_SpringCampaign2 --> Für Fotos hier abdrücken <-

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images with poor resolution
by Dana W. Moore 15 Jun '09

15 Jun '09

Hi all, I have a couple images that have poor gray-white boundaries, and the cortical parcellation did not come out well. Is there any way to manipulate thresholds to try to enhance the gray-white segmentation? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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remove random factor
by Dana W. Moore 15 Jun '09

15 Jun '09

Hi all, I have run the same image twice with recon-all and gotten different results for the cortical parcellation, with regions of the cortex differing an average of 2% in volume and the biggest difference being 11% (left bankssts). This is on a healthy, elderly brain. I'd like to try running images removing the random factor that apparently causes these differences. I found instructions on the internet to create an expert-options file to remove this random factor. I was wondering where this file should be saved. My problem is I am actually working remotely with parallel processing nodes, and I don't have permission to write to the freesurfer home directory. I was wondering, if I could use the whole path when I enter this command into recon-all, and then save it anywhere I like. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

2 1

manual talairach details
by Deane Aikins 15 Jun '09

15 Jun '09

Hello, I had a Talairach QA check failure, with the error log indicating a Z = -8 which was below the criterion of z =-6. I then used tkregister2 to attempt a manual alignment (no surf orig was available). After visual inspection, the subject and Talairach volumes looked really closely aligned already. I did some very conservative rotation and movement in the sagital plane, checked other planes, hit "SAVE REG" and then executed recon-all -all -subjid MYFILENAMEHERE in the subj directory. I then get the same error, with the same z score. I've tried several alignments (very little adjustment each time) with the same results. I notice that when I hit SAVE REG there is a new 4 x 4 numerical matrix written to my xterm screen. The values look very very similar to those prior. Is there a way to interpret these values to assist me in my manual alignment? Should I just bag it and use -notal-check? The majority of my patient set ran without errors. Thank you! Deane Aikins, PhD Director, Cognitive Neuroscience Laboratory National Center for PTSD Clinical Neuroscience Division Assistant Professor, Department of Psychiatry Yale School of Medicine

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Freesurfer June 2009