Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

negative ICV volume
by Guang Zeng 17 May '10

17 May '10

Hi, there, Recently, I ran a subject through FreeSurfer 4.5.0. I load the segmentation results using tkmedit, it looks fine to me. But, from both aseg.stats and wmparc.stats, I read a negative ICV volume, # subjectname 01290403_20080924 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2010/05/06 18:15:29 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1284740, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1284740.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 847219.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 897849, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 897849.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, -1057.998574, mm^3 Did anyone meet this kind of problem before? Thanks! Guang _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28…

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Freesurfer Linux Config Error
by Tina Jeon 17 May '10

17 May '10

Good afternoon, Hello Freesurfer gurus, I am running into an error when I use the visualization tools (i.e., tkmedit, tksurfer) in freesurfer and just wondering if you can shed some light on this. I am using Red Hat Linux Version 5.1 on the latest version of freesurfer. When I use the above commands I get the error: GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: :0.0 I am using the NVidia NV44 driver (Quadro NV5 285). Do I need to change the xorg.config file? And/or update the driver? Also when I use tkregister I get the error: Opening window subjid No glx extension! register: ### tkoInitWindow(name) failed The visualization tools previously ran flawlessly until I just revisited freesurfer after a 6 month hiatus. Let me know if you have any answers. Thank you in advance. Tina Jeon

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Fsgd_DODS
by Kelly Silva 17 May '10

17 May '10

Hello, We are using the DODS model and we saw on the Freesurfer`s tutorial that we can create an fsgd with DODS contrast with 4 groups and 1 covariate. We have 3 groups and we want to use 1 or 2 covariates. Is it posible to run this analysis? If so, how can we do that? Thanks in advance and best regards, Kelly

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Re: [Freesurfer] How to measure hippocampal volume
by Bruce Fischl 17 May '10

17 May '10

Hi Leonardo, the aseg.stats file will contain the relevant volumes. cheers Bruce On Mon, 17 May 2010, Leonardo Chesi wrote: > Hi, after your help, now I can segment my MRI images fine with the > nu_correct command. Now I'd like another little help from you. I study AD's > patients and I need to extract the hippocampal, the amygdala and another few > volumes from the segmented images. Can you help me? What kind of command I > can give to FreeSurfer to obtain this?, I have to use qdec? > > Thank a lot > > LEONARDO > >

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How to measure hippocampal volume
by Leonardo Chesi 17 May '10

17 May '10

Hi, after your help, now I can segment my MRI images fine with the nu_correct command. Now I'd like another little help from you. I study AD's patients and I need to extract the hippocampal, the amygdala and another few volumes from the segmented images. Can you help me? What kind of command I can give to FreeSurfer to obtain this?, I have to use qdec? Thank a lot LEONARDO

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Hippocampus
by p.s.bjerkan＠studmed.uio.no 17 May '10

17 May '10

Hi, We have a paper under review where we have analyzed hippocampal volumes obtained by FreeSurfer version 3.0.2. One reviewer asks for the grey matter fraction of the hippocampus. The FreeSurfer aseg output provides only total volume for the various subcortical structures, so we asssume it's not possible to obtain grey or white matter fractions? Thank you! Petr S. Bjerkan

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Importing Freesurfer output into "R" - Data Dictionaries, etc.
by Max Gunther 14 May '10

14 May '10

Dear Freesurfers, I am new to Freesurfer and I am wondering if there is a relatively painless way to import Freesurfer raw output data (e.g. .cvs or .xls files) into R? I mostly wondering if anyone has created data dictionaries to label and create the variables in a way that is formatted for R (or SPSS or SAS or whatnot). I.e., this must have already been done by someone? Any shortcuts? Any suggestions or help would be much appreciated (and would save us a lot of time!) Cheers, Max Max Gunther, PhD Vanderbilt University Medical Center Departments of Psychiatry and Medicine Center for Health Services Research Nashville, TN www.ICUdelirium.org

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Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego
by Don Hagler 14 May '10

14 May '10

Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego The Multimodal Imaging Laboratory (MMIL) at the University of California, San Diego invites applications for a postdoctoral research scholar position under the direction of Drs. Donald Hagler and Anders Dale. The successful candidate will join a multi-disciplinary team of scientists, programmers, and support staff addressing a variety of neuroscience questions using multimodal brain imaging, electrophysiology, behavior, and genetics. An important component of the work done at MMIL, and an integral role of the currently announced position, is the development and improvement of methods for the analysis of neuroimaging data. This will include extending our recent work on a white matter fiber tract atlas (Hagler et al., HBM 2009) to encompass a more diverse population of subjects, additional fiber tracts, and a larger age range, including infants. The postdoctoral researcher will receive training in brain imaging and methods development, and will be encouraged to develop his or her own research projects. Applicants for the position must have completed relevant Ph.D. research activities within the past five years. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Experience or expertise in the following areas is highly desired: 1. computer programming (e.g. MATLAB, C/C++). 2. structural MRI, diffusion MRI 3. neuroimaging analysis software (e.g. FreeSurfer, FSL) 4. scientific writing This posting is for a 2-year appointment beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Review of applications will begin immediately and will continue until the position is filled. To apply, please send your CV, a brief statement of research interests and goals, and any selected reprints to dhaglerjr(a)hotmail.com with the subject line "MMIL postdoctoral position". Letters of reference will be required before final approval of hiring. Informal inquiries for more details are welcome. _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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correlation between thickness and volume
by Rajagopalan, Venkateswaran 14 May '10

14 May '10

Dear All, I ran group comparison between control and patients independently on thickness, area and volume. I found significant difference between the two groups on volume and thickness, now i am wondering it is possible to run a correlation between the volume and thickness results to see how good they are related. How to do this using mri_glm command line version and what should be the contrast for this comparison. Any help would be appreciated. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Question concerning Fractional Anisotropy
by Weisinger, Brian (NIH/OD) [E] 14 May '10

14 May '10

Hello, I am trying to run the dt_recon with the fractional anisotropy to do a project with white matter. I am running into a problem actually getting the command to work. I am trying to follow the example online dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti But I am not sure where/what I am supposed to put after the -i. The other stuff I am pretty sure I know, --s = the subject folder --o = the folder I want the output to go in Can you fill me in on what I'm missing, I looked in the subjects output files and could not find anything that ended with .dcm. Thank you, Brian Weisinger

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