Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

roisummary-sess from binary mask
by Emily Ward 10 Feb '11

10 Feb '11

Hello, I am trying to get a summary of beta value activation for a hand-drawn binary mask. This mask is a sphere, so it does not correspond to a particular anatomical label or functional contrast. Is there any way to apply roisummary-sess to this type fo binary mask (in nii or mgz format)? If not, can I specify my mask as an roi so that the roisummary-sess function will work? Or is there another command I should be using to get a summary of beta values for a particular mask? Thank you, Emily

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surfaces to voxelspace
by Steffen Bollmann 10 Feb '11

10 Feb '11

Dear freesurfer experts, I would like to display freesurfer surfaces in the voxelspace of the original subject image using matlab. Which coordinate transformation do I have to apply to get the vertex-coordinates to the RAS space and finally to the original voxelspace of the subject? (i guess for RAS2Vox I can use the matrix I can obtain with mri_info ... but I cannot find a way from vertex-coordinates to RAS) Thank you for any hint Best Regards Steffen Bollmann

2 2

RA position available at VA Boston
by Scott Hayes 09 Feb '11

09 Feb '11

Preliminary Announcement for Neuroimaging Research Assistant Position National Center for Posttraumatic Stress Disorder (Boston) The Behavioral Science Division of the National Center for PTSD, located at the VA Boston Healthcare System, anticipates an opening for a research assistant who will work on projects related to neuroimaging of posttraumatic stress disorder and memory disorders. Responsibilities for this position include: Collecting behavioral and neuroimaging data from healthy and clinical subjects, entering data and managing databases, performing statistical analyses, and assisting in the preparation of grants, manuscripts, and professional presentations. Applicants should have a B.A./B.S. (concentration in Cognitive Neuroscience/Psychology is preferred), experience working in an imaging laboratory and running functional magnetic resonance imaging (fMRI) experiments, proficiency with UNIX and MATLAB, FSL, and/or SPM, and the maturity and interpersonal sensitivity necessary for working in a clinical setting. Openings are expected for June 2011. Salary and benefits are highly competitive with similar positions at institutions in the Boston area. A two year commitment typically is required. Official job postings and formal application instructions are expected to appear in early March 2011, but potential candidates are encouraged to submit the following materials prior to formal application: 1) a letter describing their interest in a position and related career goals, 2) a resume, 3) a current transcript, and 4) at least two letters of recommendation. Materials can be sent electronically or by mail to: Andrea Carney National Center for PTSD (116B-2) VA Boston Healthcare System 150 South Huntington Ave. Boston, MA 02130-4817 andrea.carney(a)va.gov Further information can be obtained via e-mail or by phone at (857) 364-4143, or visit the websites: http://www.bu.edu/traumamemorylab/ http://www.bu.edu/brainlab/ -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Boston University School of Medicine

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wm and pial edits
by Larissa Stanberry 09 Feb '11

09 Feb '11

Dear Freesurfers, Can I run recon-all -autorecon2-wm and recon-all -autorecon2-pial on the same subject at the same time? Or can I perhaps do smthg like recon-all -autorecon2-wm -autorecon2-pial? Many thanks Larissa

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testing FreeSurfer
by Carolina Valencia 09 Feb '11

09 Feb '11

Hi FreeSurfer's user, I'm new using this software, I try to install on Ubuntu and to set up following the recommendation of the webpage. Then I tried to test but any commmand seems to be recognized, also when I started a new terminal a warning is shown: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 Thanks in advance for the support, Best regards, cvalencia

1 1

two vol fields for retinotopic analysis?
by Jason Connolly 09 Feb '11

09 Feb '11

Dear freesurfer experts: I noticed that there are two 'vol' fields when I use MRIread. 1) mri.vol 2) mri.analyzehdr.vol My question is: I have two arrays, one with 3D coordinates and a second 1 dimensional array with corresponding phase values. Which 'vol' field do I put the 3D coordinates in and which do I put the phase values in? Many thanks! -jason.

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Abblocked Setup
by Chindhuri Selvadurai 09 Feb '11

09 Feb '11

Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

3 6

Three starting questions
by Tetiana Dadakova 09 Feb '11

09 Feb '11

Dear FreeSurfer community, You were very helpful for my last question, thank you. Now I have three basic questions. 1. I would like to check the segmentation by loading T1.mgz and aseg.mgz as an -aux volume, so that I can switch between them. How can I do this? (<tkmedit subject T1.mgz -aux aseg.mgz> gives some king of black and white segmentation instead of colorful one). 2. When I press View -> View configuration, I have three options there (Single view, Multiple orientations, and Mosaic). How can I view just 3 orientations or 2 (e.g. sagittal and transverse)? 3. Do MacOS users have problems with mouse? When I try to edit segmentation or surfaces with Edit Tools, my mouse doesn't seem to work. I mean, when I click on the pixel with any of three buttons, nothing changes. I saw similar problem on the mailing list, but there was no answer. Thank you for your time, Tanja.

2 1

reg-feat2anat: a problem!
by Agnieszka Burzynska 09 Feb '11

09 Feb '11

Dear all, I am using the command reg-feat2anat to transform functional data pre-processed in FSL to the anatomical image in Freesurfer. As suggested, I check the registration with reg-feat2anat --feat run2.feat manual. I have 3 runs of functional data for each subject. Surprisingly, some runs are registered well but others not (even of the same subject, so using the same reference anatomical images: see the attached image. Upper row: bad registration of one run and lower row: good registration of another run). I have no problem to manually correct the registrations, it works well, but as I have many subjects, I wonder if there may be a way to change some options of reg-feat2anat to make it work better? Can you see from the attached image what is the problem with my images? (I viewed the functional and anatomical data of a few subjects, some woth good and some with bad registration and see no difference or flip) Thanks a lot for your help! Aga

3 6

Re: [Freesurfer] FreeSurfer TrackVis Transforms
by pablo maturana 09 Feb '11

09 Feb '11

Dears expert, I would like to know how can i get the transformation from trackvis to a space Freesurfer?. I have here a link http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms But i don't understand what mean this command, how I could load the file .dtk trk_verts_crs.xyz = trk_verts.xyz / (trkHeader.voxel_size[0], trkHeader.voxel_size[1], trkHeader.voxel_size[2]) and then I have a problem with this command trk_verts_tkreg = CRS2XYZtkreg * trk_verts_crs Could you give an example using a file .dtk? Many thanks Pablo >

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Freesurfer February 2011