Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011
by Michael Kranz 26 Aug '13

26 Aug '13

Hi all, I was wondering how I could go about getting anatomical stats for the different regions from the Choi2012 and Buckner 2011 parcellations. The Yeo 2011 cortical parcellation files were available in the fsaverage folders and I could get stats and labels for those, but I couldn't figure out how to get stats on these other two. Thanks, Mike Kranz

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Re: [Freesurfer] Otto: images again (compressed)
by Douglas N Greve 26 Aug '13

26 Aug '13

This problem has been fixed in version 5.3 doug On 08/23/2013 06:48 PM, Otto Muzik wrote: > Hi Doug, > > Here are the images again - this time compressed. > The uncompressed images were rejected due to excessive > size. > > Hope you get these > > Many greetings > > Otto > > > > On Aug 23, 2013, at 11:37 AM, Douglas N Greve wrote: > >> Can you send a *single* dicom file to me? No need to copy the list >> >> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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FW: How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
by Boric, Katica A. 26 Aug '13

26 Aug '13

________________________________________ From: Boric, Katica A. Sent: Monday, August 26, 2013 4:02 PM To: Douglas N Greve Subject: RE: [Freesurfer] How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory? Hi Doug! Thanks for getting back so fast! I did the registration but I only got this email: Here is your FreeSurfer license. Place the three lines between the CUT HERE markers in a file named ".license" in the directory pointed to by the $FREESURFER_HOME environment variable (see the FreeSurfer documentation). #---------------CUT HERE--------------- kboric(a)partners.org 16851 *C9NanJsRCd7o #---------------CUT HERE--------------- and this is where I am stuck.... don't know how to procede! Thanks again, Katica ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Sent: Monday, August 26, 2013 3:59 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory? Hi Katica, on that page there is a link to the registration page. Once you register (free), you will be given a .license file doug On 08/26/2013 03:22 PM, Boric, Katica A. wrote: > Hello! > I am new to free surfer and Linux and I am having installing free > surfer. I am using Fedora on a VMware workstation > I successfully (I think) downloaded it and installed it following the > instructions (https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) > But now I am stuck trying to copy the three lines of the license info > to the file .license. > Any advice? > Thank you very much, any help is appreciated it! > > Katica > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FDR in different hemispheres
by Emily Boeke 26 Aug '13

26 Aug '13

Hi Freesurfers, I have a contrast that produces comparable activation in both hemispheres. But when I set the threshold using FDR in the Configure Overlay Display window, the threshold is set to 5.1 for left hemisphere and 3.3 for the right hemisphere, leaving significant clusters only in the right hemisphere. Does someone know why the FDR threshold would be so different between the two hemispheres? Thanks! Emily

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How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
by Boric, Katica A. 26 Aug '13

26 Aug '13

Hello! I am new to free surfer and Linux and I am having installing free surfer. I am using Fedora on a VMware workstation I successfully (I think) downloaded it and installed it following the instructions (https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) But now I am stuck trying to copy the three lines of the license info to the file .license. Any advice? Thank you very much, any help is appreciated it! Katica

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Freesurfer Editing Strategy
by Khadka, Sankalpa 26 Aug '13

26 Aug '13

Dear freesurfer experts, I have a question about making edits in the freesurfer results. During the workshop which I attended this year, I learned about white matter edits and control points edits when white matter is not segmented accurately. I have used these tools quite successfully in our projects. However, in our research in multiple sclerosis, often times we encounter cases with lesions on grey matter. The lesions in grey matter causes intensity of the voxel over that region to become hypo-intense like CSF. Due to this, the pial surface line is pushed inward into the lesion, missing some grey matter around it. Since, cortical thickness is the most important measure in our research, we could like to be able to solve this issue. We would like to make sure that the pial surface line goes around the lesion without missing grey matter for accurate thickness calculation. In order to solve this issue we have tried to first delelte and fill the lesion in the brainmask.mgz with voxels with grey matter intensity in the region using the voxel editing tools (instead of 255(default) used in white matter edit, we use 70-75 for grey matter). After editing, we run recon-all with autorecon-2 and autorecon-3. Quite surprisingly, this strategy has not resolved our problem. My understanding is that the pial and main surface lines (red and yellow) were draw based on the intensity of voxel. Our question is, why would the lesions which are now filled with grey matter not treated as grey matter? We have tried this strategy, and it has not worked. What would you recommend us for solving such issue? I have attached a screen shot of a slice where you can notice that in the top right corner, the lesion on the grey matter causes the pial surface line to miss grey matter around it. Ideally, we would like the pial surface line to go around the normal grey matter surface. Thank you, Sankalpa Khadka Research Assistant Neurolgy, Yale School of Medicine

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regarding adding and deleting voxels in wm.mgz and brainmask.mgz
by Mehul Sampat 26 Aug '13

26 Aug '13

Hi Folks, I see on the tutorial websites that when voxels are added to wm.mgz or brainmask.mgz, the new voxels are given a value of 255; while when voxels are deleted, these locations are set to 1. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits Can the deleted voxels can be set to 0 or they have to be set to 1; Or is 0 used to differentiate the background voxels from brain voxels ? Thanks Mehul

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Postdoctoral Fellow (neuroimaging) in Aging
by Ayaz, Muhammad 26 Aug '13

26 Aug '13

Postdoctoral Fellow in Neuroimaging (MRI)/Cognitive Aging Area Cerebrovascular Laboratory Department Institute for Exercise and Environmental Medicine Institution The University of Texas Southwestern Medical Center of Dallas Job Description The applicant should have a Ph.D. and/or M.D. degree. Experience and previous training in MRI and image data analysis are required. Previous experience with Freesurfer, FSL, AFNI, MATLAB, SPM is desired. UTSW has an advanced imaging research center equipped with state-of-the-art MRI systems dedicated to research (Two 3 T and one 7T whole-body human MRI unit). The applicant will have an opportunity to work in a highly collaborative research environment with exposure to the cutting-edge research in neuroimaging (MRI/PET), cognitive neuroscience and human physiology. The ideal candidate should have a strong publication record and excellent communication and laboratory skills. She/he will work on a NIH funded project to study the impact of aerobic exercise training on arterial aging, brain perfusion, structure and cognitive function in human subjects. Salary is commensurate with experience according to NIH stipend levels. The fellow will be an employee of both UT Southwestern Medical Center and Texas Health Presbyterian Hospital and will receive comprehensive fringe benefits. If interested please send your CV to, - - - - - - - - - - M. Ayaz Khan, PhD Research Fellow Institute for Exercise and Environmental Medicine Texas Health Presbyterian Hospital Dallas Department of Internal Medicine and Cardiology University of Texas Southwestern Medical Center 7232 Greenville Avenue, Suite 435, Dallas, TX 75231 phone: 214.345.4639 | fax: 214.345.4618 MuhammadAyaz(a)texashealth.org> MuhammadA.Khan(a)utsouthwestern.edu The information contained in this message and any attachments is intended only for the use of 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 you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Final call for special issue: 'Functional brain mapping of epilepsy networks: methods and applications'
by David Abbott 26 Aug '13

26 Aug '13

Hello, Please be advised that a call for papers is closing in one week (Monday September 2, 2013, with a final paper submission deadline of 1st February 2014) for the Frontiers in Neuroscience and Frontiers in Neurology Research Topic: 'Functional brain mapping of epilepsy networks: methods and applications'. This is a parallel topic across two journals: Frontiers in Neuroscience (section: Frontiers in Brain Imaging Methods<http://www.frontiersin.org/Brain_Imaging_Methods/researchtopics/Functional_…>) for papers with a methodological focus, and Frontiers in Neurology (section: Frontiers in Epilepsy)<http://www.frontiersin.org/Epilepsy/researchtopics/Functional_brain_mapping…>for papers with an application or clinical focus. You may click on the links above for further information. Frontiers journals are open access. Publication fees are substantially reduced for papers included in a Research Topic. Researchers from most leading epilepsy imaging labs have already confirmed their participation in this topic. Proposals (in the form of a max. 1 page abstract or outline) should be submitted by 2nd September 2013. If the abstract is accepted, then the associated paper can be submitted at any time up until 1st February 2014. Thus some papers in the topic may be published before the final submission deadline. Regards, David. --- David Abbott, PhD Senior Research Fellow (Physics & Neuroinformatics), Brain Research Institute, The Florey Institute of Neuroscience and Mental Health Honorary Senior Fellow, Department of Medicine, The University of Melbourne. Address: Melbourne Brain Centre - Austin Campus, 245 Burgundy Street Heidelberg, Victoria, 3084, Australia.

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mri_convert command
by 沈庄明 25 Aug '13

25 Aug '13

Hi everyone, I'm new to FreeSurfer. I'm so confused with the difference between mri_convert --in_orientation and mri_convert --out_orientation. Do they all reslice the volume? How do they modify the header files of the volume? I wish someone could explain the difference between them in detail. Thanks! Zhuangming Shen

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Freesurfer August 2013