Freesurfer

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downsample fsnative
by Ella Hanns 24 Feb '19

24 Feb '19

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Symposium on Parkinson’s disease, early triggers - MRI, PET, inflammation, genetics
by Alexandru Hanganu 22 Feb '19

22 Feb '19

External Email - Use Caution Dear Colleagues, University of Montreal, Department of Neuroscience is organizing a Symposium on Parkinson’s disease May 3, 2019, in Montreal, Canada. Key Speakers: Roger Barker, Francesca Cicchetti, Antonio Strafella, Janelle Drouin-Ouellet, Thomas M. Durcan, Ashley S. Harms, Kenneth Marek, Diana Matheoud, Anurag Tandon, Malu G. Tansey, Michela Deleidi, Louis-Éric Trudeau, Andrew D. Siderowf, Richard Youle. This Symposium aims to outline to current results and research directions in the early triggers and biomarkers of Parkinson’s disease, from an MRI, PET, inflammation, morphopathology and genetics perspectives. Early registration deadline: 1st March 2019. more details at: http://fourwav.es/neurosciences21-22mai2019 On behalf of the organizing committee, Alexandru Hanganu

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aparc+aseg fails to load in freeview
by Taylor, Lisa Marie 22 Feb '19

22 Feb '19

External Email - Use Caution Hi there, I am fairly new at this but have been using freesurfer/freeview for the past two months to edit MRI images. There is a particular file I am trying to open that fails to load the aparc+aseg volume. I've downloaded from the source and tried to run it through freesurfer again with the same error (it took nearly double the time to process than a typical file). I am not exactly sure how to figure out what/where the issue is coming from. Would you be able to help? I am using OSX Yosemite. I have attached the recon-all.log file to this email. Thank you for your understanding and help in this issue. Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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vlrmerge for visualization only?
by Haroon Popal 22 Feb '19

22 Feb '19

External Email - Use Caution Hello FreeSurfer Developers, I have functional contrast maps from the HCP dataset. I converted these to fsaverage space and now have GIFTIs for the surface data and a NIFTI for the subcortical volume data. I would like to combine these into one file for an analysis where I will be predicting the intensity of individual voxels. I thought I would use vlrmerge to do this, but noticed that the documentation notes that vlrmerge should only be used for visualization purposes. I was wondering if you thought that doing my analysis on the vlrmerge output would be a bad idea, even though I am not doing any real computation on the merged volume maps. If this is a bad idea, is there another method that I can use to combine the surface and subcortical volume data? Thank you. -- Haroon S. Popal Ph.D. Student Cognitive Neuroscience Laboratory Department of Psychology | Temple University

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downsampling orig.mgz
by Ey Dude 22 Feb '19

22 Feb '19

2 1

petsurfer Kinetic Modeling (MRTM1, MRTM2)
by john Anderson 22 Feb '19

22 Feb '19

External Email - Use Caution Hi Dr Greve, I would like to use petsurfet to do kinetic modeling (KM), the pipeline is straightforward and easy to use. Thank you so much! I would appreciate any clarifications relevant to my questions bellow: 1) I understand that the flag "--km-ref" define the reference region for normalizing PET signal. in the linear below the reference region is cerebellum cortex. If we need to normalize to occipital just we change the numbers based on labels in aparc+aseg atlas? --km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale 2) --km-hb define the high binding regions. Are these regions represent the regions that are pathologically involved where we expect it to have higher PET signal OR it represent the regions where PET tracer has the maximum binding in general regardless of pathology? I mean every tracer have high level in specific regions in the brain is this what the flag is referring too? Thanks for any clarification, John

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recon-all -hires
by Nasiriavanaki, Zahra 22 Feb '19

22 Feb '19

Dear Freesurfer experts I was running recon-all command with hires flag for our high resolution fMRI data, but it has been in a constant status since yesterday. I copied the last few lines that are currently in my terminal. I had the same issue with another subject before, and I had to terminate the recon-all and run it without -hires. Could you please let me know how I can solve this issue? Thanks Mona #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019 mris_fix_topology -rusage /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019 mris_fix_topology -rusage /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh Waiting for PID 8994 of (8994 8997) to complete...

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?h.white does not exist
by Weber, Wade A 22 Feb '19

22 Feb '19

External Email - Use Caution Hi all, I'm trying to run -autorecon2 on 3 subjects (I already ran -autorecon1 on them with no errors.) and I'm getting an error after the -final_surfs part saying that lh.white does not exits (and it doesn't, I checked for it). I have run about 10 other subjects, and they all ran fine and contain ?h.white files. I saw 2 other strings in the archive with this same issue, but there was no resolution to them. This error just started happening, and I didn't change anything. Here's the command I've been using: recon-all -subjid <my subject #> -T2 <name of t2.nii file> -T2pial -autorecon2 Here's the error output: MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/analysis_files/ANG_1034/surf/lh.white): could not open file I'm running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c on a virtual machine running Red Hat Enterprise Linux Workstation 7.6 I've attached the recon-all.log file Thanks! ---- Wade A. Weber, MS Psychiatry Research Program Coordinator Dell Medical School | The University of Texas at Austin o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu

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[All] postdoctoral position in PET imaging available at MGH / Martinos Center
by Bruce Fischl 22 Feb '19

22 Feb '19

Postdoctoral position in integrated PET/MRI at Massachusetts General Hospital / Harvard Medical School The Loggia and Hadjikhani Labs are inviting applications for a Post-Doctoral Research Fellow in the Department of Radiology at Massachusetts General Hospital (A.A. Martinos Center for Biomedical Imaging) and Harvard Medical School. The candidate will use state-of-the-art integrated PET/MRI scanners to image neuroinflammation in the central nervous systems of migraine patients, and the effect of nonpharmacological therapies. The candidate will collaborate with Dr. Julie Price and several other members of the Martinos Center. Requirements include a Ph.D. in Neuroscience, Physics, Chemistry, Engineering, or a related field, as well as good command of written and oral English. Experience with Positron Emission Tomography is preferred. Compensation is competitive and commensurate with experience. If interested, please email Marco Loggia (marco(a)nmr.mgh.harvard.edu) with your CV. _______________________________________________________ Marco L. Loggia, PhD Assistant Professor of Radiology, Harvard Medical School Associate Director, Center for Integrative Pain NeuroImaging (CiPNI) A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 Email: marco.loggia(a)mgh.harvard.edu Web: http://scholar.harvard.edu/loggia _______________________________________________ All mailing list All(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all

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Templates used for eTIV computation in recon-all
by Ami Tsuchida 22 Feb '19

22 Feb '19

External Email - Use Caution Dear experts, We were comparing recon-all output of Freesurfer 5.3 and 6.0 in our database, and found that eTIV values can increase by up to 40% going from 5.3 to 6.0. However, closer inspection revealed that it was not due to the version per se, but how we call recon-all. We had computed one version with recon-all -all, and the other with recon-all -autorecon1, thinking that eTIV output from these two were identical. Some testing in two versions with two flags showed that in both versions, using -all flag automatically add --atlas 3T18yoSchwartzReactN32_as_orig in the talairach_avi command, while -autorecon1 does not. The talairach_avi.log indicates that the former set the target to 3T18yoSchwartzReactN32_as_orig, while the latter use the 711-2C_as_mni_average_305. My first question is, is this some kind of bug or is it intentional? We thought that the difference in the templates caused the change in the estimates, but it looks like that's not the only answer: We still get very different eTIV values from -autorecon1 option in FS5.3 and 6.0, even though the target images are the same. The results from -all option are more comparable. Here is the eTIV from one subject we tested: -FS5, autorecon1: 1318267 -FS6, autorecon1: 1561456 -FS5, -all: 1662005 -FS6, -all:1678336 Here I attached the shortened recon-all log files from two versions of Freesurfer, with with -all or -autorecon1, as well as eTIV output from the four variations we tested in one subject. Could you help us resolve why we get the varying estimates? Thank you!

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