Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30087 discussions

Projecting findings using Freesurfer
by Weisinger, Brian (NIH/NIMH) [F] 11 Feb '11

11 Feb '11

Good Morning, I am attempting to project R squared values that were calculated using Freesurfer volumes for the various automated segmented areas that are calculated in Freesurfer. Is there a way I can can compare two groups in say QDEC and visually see the results? Thank you for your help.

2 1

Contrasts for GLM DODS with both discrete as continues covariates
by Habets P (SP) 11 Feb '11

11 Feb '11

I want to run a GLM DODS in Freesurfer to test whether patients differ from controls with regard to cortical thickness, meanwhile I want to control for several variables, both discrete as continues. This is my manually made fsgd file GroupDescriptorFile 1 Title fsgd pat con.txt MeasurementName Cortical Thickness Class controls Class patients Class female Class male Class mdeft Class adni Variables Age Education Handedness input C002 controls female mdeft 27 6 100 input C003 controls male mdeft 46 5 -89.47368622 input C004 controls female mdeft 43 4 100 input P001 patients male mdeft 32 7 -100 input P003 patients male mdeft 26 6 100 input P004 patients female mdeft 19 6 60 The problem I have is how to specify contrasts, on the Freesurfer website I found that : For DODS, the number of regressors is Nc*(Nv+1) In my case that would be 6* (3+1) = 24 Would the contrast than be: 1 -1 and 22 zero's Does Freesurfer automatically create the correct design matrix using the fsgd file? Because it is not clear to me how I should create the design matrix with some discrete variables as confounders. Bw Petra Habets

2 1

license error
by Pom Sailasuta 10 Feb '11

10 Feb '11

Hello, I just installed freesurfer on my new Fedora 14 desktop following the instruction from the website. Howver when testing for installation, there are errors as follows: [root@pom-PC stable5]# tkmedit bert orig.mgz -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/stable5/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- Cheking .license file , there ia no blank lines at the beginning or end of file [root@pom-PC stable5]# more .license #---------------CUT HERE--------------- pom4pom(a)gmail.com 10301 *CckOVij887CA #---------------CUT HERE--------------- [root@pom-PC stable5]# pwd Also similar error for tksurfer as well but qdec started o.k. Also, according to the instruction freesurfer should be installed in /usr/local/freesurefer directory but SetUpFreeSurfer.csh call for freesurfer/stable5 directory. So I created stable5 dir and move every file up from /usr/loca/freesurfer to /usr/loca/freesufer/stable5. thanks for the help -- Pom

2 1

Questionable T1 sequence
by Scott Sorg 10 Feb '11

10 Feb '11

Hi All, Is the following T1 sequence suitable for surface generation? "T1-weighted 3D SPGR (echo time 5 minimum; repetition time = 24 msec; flip angle = 30; field of view = 24 centimeters; slice thickness = 3 millimeters) collected in the axial plane." It's that 3 mm slice thickness that most concerns me. The sequence was not initially intended for surface reconstruction, but I've run a few volumes through recon-all and they've turned out better than I had expected. We're primarily using the output for automated ROI generation, but I'm wondering if the cortical thickness and volume estimations from such an acquisition are suitable for further analysis (i.e., group comparisons, correlations). -SS

2 1

phase data overlay using fsaverage
by Jason Connolly 10 Feb '11

10 Feb '11

Dear freesurfer experts, I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). I then brought these data into freesurfer using the following: bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header -t2 mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh However, I do not see anything on the sphere (or fsaverage for that matter) ... Can you provide any hints? The phase values are normalized and range from 4 - 5 and I have converted to RAS space properly (I hope) ... Any tips would be a big help! Best wishes, Jason.

3 4

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

2 4

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

1 0

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

4 3

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

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