Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

trilinear interpolation
by 1013364183 25 Feb '19

25 Feb '19

External Email - Use Caution Dear Bruce, Hello, we used mri_convert –vs [] –I [] –o[] –rt interpolate to perform the trilinear interpolation on the image, and also used the trilinear interpolation in the torch to process the image. We found the result obtained by the interpolation method in freesurfer is better than the result obtained by the trilinear interpolation method in the torch. Does the freesurfer perform other operations when performing the trilinear interpolation on the image? What is the principle? Thank you! yours yujunjie

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Control points to include hyperintensity in wm surface
by Rachel Hoel 24 Feb '19

24 Feb '19

External Email - Use Caution Dear Freesurfer Developers, Our study is using the longitudinal processing pipeline with version 6.0. We have one subject (screenshots included) where there is a hyperintenisty in the right temporal lobe, and even after adding several control points and running recon-all, the white matter is still not fully being included in the surface. For this particular subject, we are performing both white and grey matter edits starting at the cross-sectional. The screenshots included are that of the cross-sectional. Are there any other types of edits we can make to try and include this region in the white matter segmentation? All the best, Rachel

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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

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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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Freesurfer February 2019