Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

averaged subject
by Jose Luis Cantero Lorente 04 Feb '09

04 Feb '09

Dear Freesurfers, I have a couple of question regarding the averaged map and resultant statistics. Starting from a population composed by three groups (controls, patients1, and patients2), and considering that my statistical comparisons will be: Controls-patients1 Controls-patients2 Patients1-patients2 1) Should I build my averaged subject by including all subjects (controls, patients1, and patients2), independently of the pairwise comparison? Or just using the two subgroups of subjects included in each comparison? In the first case, we would use the same averaged map in all comparison. In the latter case, we would obtain 3 different averaged maps (one for each comparison). 2) How would affect the chosen averaged map method to build the resultant statistic? Is just a question of displaying, or it indeef affects to the obtained results? Sorry for these basic questions, but I need to be sure before running my cortical thickness analysis. Thanks in adavance. Best, Jose L. Cantero --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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optseq2 and post hoc sorting
by Aaron Trachtenberg 04 Feb '09

04 Feb '09

Hi, I am trying to design an event-related memory encoding task. Simply put, the subject either sees familiar or novel pictures (the familiar ones having been shown outside of the scanner before hand). After scanning, recognition for the pictures is tested. I am interested in the novel > familiar contrast but also subsequent memory (i.e. which images were remembered). I have two questions: 1) For planning the schedule, I will use optseq2 with an input of 2 evs (novel and familiar). It is my understanding that these will be optimized for maximum efficiency. But if I post-hoc separate the novel events based on if they were subsequently remembered or not, could this not result in a very inefficient design? In other words, is an optimized schedule output from optseq2 remain fairly optimal under a variety of possible post-hoc sortings? Is there anything special I can do, knowing that I plan to use post-hoc sorting? 2) Having worked through the examples on the internet, is my understanding that a stimulus event always occurs at the start of a TR correct? How does this affect sample bias? Is there away to have a stimulus onset at different points in the TR? I may be confused about this point, but it is my understanding that you don't want the stimulus occurring at the same time with respect to every TR or else every slice will always be at a consistently different position in the HRF? Any help on these questions, or general insight into this kind of experiment would be great. Thanks a lot Aaron Trachtenberg DPhil candidate, FMRIB, University of Oxford

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error in map label to subject
by Lucia Garrido 04 Feb '09

04 Feb '09

Dear all, I'm using Qdec and wanted to map an ROI to all participants in the study, but I always get an error. I've used FS 4.0.2 for recon-all for all subects. Now I'm running stats with FS 4.1.0 (I did 'recon-all -qcache -subjid <sub>' for each person using version 4.1.0). I'm using Debian.the qdec I've saved the ROI to the SUBJECTS_DIR folder. The error I get is: mri_label2label --srclabel rh.mtg1 --srcsubject fsaverage --trgsubject C01_CY --trglabel rh.mtg1 --regmethod surface --hemi rh srclabel = rh.mtg1 srcsubject = fsaverage trgsubject = C01_CY trglabel = rh.mtg1 regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 SUBJECTS_DIR is /tmp/qdec_project_archive FREESURFER_HOME is /home/lgarrido/freesurfer_v4.1.0/freesurfer Loading source label. Found 240 points in source label. Starting surface-based mapping Reading source registration /tmp/qdec_project_archive/fsaverage/surf/rh.sphere.reg MRISread(/tmp/qdec_project_archive/fsaverage/surf/rh.sphere.reg): could not open file No such file or directory ERROR: could not read /tmp/qdec_project_archive/fsaverage/surf/rh.sphere.reg command failed: mri_label2label --srclabel rh.mtg1 --srcsubject fsaverage --trgsubject C01_CY --trglabel rh.mtg1 --regmethod surface --hemi rh Many thanks for your help. Regards, Lucia

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Faculty and Research Assistant Positions Available in Boston
by David Salat 04 Feb '09

04 Feb '09

PLEASE POST FOR ALL INTERESTED PARTIES NEUROIMAGING RESEARCH POSITION AT THE VA BOSTON HEALTH CARE SYSTEM IN BOSTON MASSACHUSETTS A research position is available in advanced neuroimaging at the VA Boston Health Care System (VABHCS) in the Jamaica Plain area of Boston. This position is in the new Neuroimaging Research Center at the VA. The candidate will have responsibilities related to development of the imaging center as well as in independent and collaborative research. The applicant should have advanced skills in functional magnetic resonance imaging (fMRI) including utilization of sophisticated experimental design and functional paradigms, knowledge of software packages such as FSL and Freesurfer, and be knowledgeable about advanced analysis procedures such as functional connectivity (fcMRI) and independent component analysis (ICA) of functional imaging data. Experience with advanced data acquisition procedures is desirable. Some knowledge of Unix/Linux and MATLAB is required. Multimodal integration with dynamic (e.g. EEG/MEG/PET/ASL), structural (e.g. morphometry/DTI), or other imaging procedures (MRS/TMS) would be a plus. The candidate should be interested in applying advanced functional imaging to the study of conditions relevant to the VA mission, including traumatic brain injury (TBI), post traumatic stress disorder (PTSD), cognitive neuroscience of learning and memory, cerebrovascular disease, genetic factors of disease, and age associated decline in cognitive function. The VA is equipped with a 3T Siemens TIM Trio imager and a variety of hardware for stimulus presentation, eye tracking, and physiological monitoring. The VA is an affiliate of Boston University School of Medicine and Harvard Medical School as well as several other academic and health care education institutions, and is a site of The National Center for Post Traumatic Stress Disorder (NCPTSD). Interested parties should send a CV and contact information for three references or questions to the Neuroimaging Search Committee at vaimaging(a)gmail.com. NEUROIMAGING RESEARCH ASSISTANT POSITION AT THE VA BOSTON HEALTH CARE SYSTEM IN BOSTON MASSACHUSETTS A research assistant position is available in advanced neuroimaging at the VA Boston Health Care System (VABHCS) in the Jamaica Plain area of Boston. This position is in the new Neuroimaging Research Center at the VA. The candidate will have responsibilities related to patient scanning and data analysis, as well as administrative aspects of the imaging center and ongoing research. The applicant should have some experience in magnetic resonance imaging (MRI) research including some knowledge of one or more common software packages utilized in MRI data analysis (FSL/Freesurfer/SPM). Some knowledge of Unix/Linux and MATLAB is required. The candidate should be interested in working on studies focused on conditions relevant to the VA mission, including traumatic brain injury (TBI), post traumatic stress disorder (PTSD), cognitive neuroscience of memory, cerebrovascular disease, genetic factors of disease, and age associated decline in cognitive function. The applicant should be willing to make a two-year commitment. The VA is equipped with a 3T Siemens TIM Trio imager and a variety of hardware for stimulus presentation, eye tracking, and physiological monitoring. The VA is an affiliate of Boston University School of Medicine and Harvard Medical School as well as several other academic and health care education institutions and is a site of The National Center for Post Traumatic Stress Disorder (NCPTSD). Interested parties should send a CV and contact information for two references or questions to the Neuroimaging Search Committee at vaimaging(a)gmail.com. --

1 0

more info about bbregister
by Wang, Xin 04 Feb '09

04 Feb '09

Hello, Dr. Greve, I am using bbregister to register the BOLD to T1. The --help does not provide any imformation about how it works. What are the difference from bbregister to flirt (fslregister)? more information about --intvol also needed. For example, the format of intvol.reg (.mat or .bat?) Can I reference to the help of same flag in the tkregister2? Thank you,

2 1

mri_convert 001.mgz looks bad
by Angela Wang 04 Feb '09

04 Feb '09

I am using mri_convert to convert some MR images in dicom format to 001.mgz. When I view 001.mgz, using tkmedit, each transaxial slice looks like it is pieced together from the wrong slice of the original transaxials. As I progress from one slice to the next, this band moves across the image. It shouldn't look like this, should it?. Is there something I can do to prevent this when converting to mgz format? Angela

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Research Assistant Positions in Structural and Functional Neuroimaging (Boston)
by Stephanie Lee 04 Feb '09

04 Feb '09

Posted on behalf of Dr. H. Diana Rosas: Research Assistant Positions Available in structural and functional neuroimaging. Massachusetts General Hospital-Athinoula A. Martinos Center for Biomedical Imaging, Charlestown MA PLEASE POST FOR ALL INTERESTED PARTIES. START DATE: Immediately Full-time research assistant positions are available in structural and functional magnetic resonance imaging at the Athinoula A. Martinos Center for Biomedical Imaging in the Department of Radiology at Massachusetts General Hospital. The research assistant position will focus on the application of structural and functional image analysis procedures in the study of brain aging and neurological diseases including Alzheimer's and Huntington's disease. Other tasks include participant scanning, data organization, statistical analysis, and additional lab duties. This individual will be working with patients, so excellent interpersonal, organizational and communication skills are required. This position requires a Bachelor of Arts or Bachelor of Science degree, and some prior research experience is preferred. Familiarity with Linux/Unix and Matlab would be extremely useful. A two year commitment is required. This is an excellent position for a recent college graduate who wants to spend two or more years in a research setting before going on to graduate or medical school. Please send a resume and cover letter or questions to: Dr. H. Diana Rosas, MD rosas AT HELIX.MGH.HARVARD.EDU

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questions
by Silvia biopanda 04 Feb '09

04 Feb '09

1) I need to do the manual segmentation of the hippocampus with freesurfer. How can I do that? 2) How can I export the segmentated image to the binary format? Thanks, Silvia

2 1

Qdec version and covariates
by Vina Goghari 03 Feb '09

03 Feb '09

Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates. Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it? Thanks, Vina

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Talairach X axis seems to be inverted between tkmedit and tksurfer
by Thomas Wallis 03 Feb '09

03 Feb '09

Hello, I have recently started using freesurfer for reconstruction. If I note the Talairach coordinate of a vertex in the left hemisphere in tksurfer, then enter this coordinate into tkmedit, the point appears on the right of the image (i.e. in the "right" hemisphere). Is this as it should be, or have I made a mistake somewhere? I couldn't seem to find anything documenting this in the wiki. Regards Tom Wallis

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Freesurfer February 2009