Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

fsaverage for externally preprocessed subjects.
by Alvarado,Luis R 09 Dec '19

09 Dec '19

External Email - Use Caution Hi all, I have a couple of questions regarding fsaverage: 1. Is this file updated every time a new subject is process with recon-all? 2. If I obtain externally preprocessed datasets (e.g., from the 1000 Functional Connectomes Project) should I register those subjects to my local fsaverage? * Ultimately, I would like to conduct an ROI analysis of the differences between normative data from a large online biobank and locally imaged patient population. The workflow for such analysis recommended on (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI) suggests to draw ROI labels directly on fsaverage (a template to which all subjects run with FreeSurfer have been registered to) and then use the mri_label2label command to map the label to individual subjects. Would this work for both locally and externally preprocessed groups? Thank you, Luis R. Alvarado Ph.D. Candidate Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

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Reconstruction on BLADE sequences
by Funk, Quentin 09 Dec '19

09 Dec '19

External Email - Use Caution Freesurfer experts, We're attempting to get some reconstructions on MRI's for very advanced alzheimer's subjects. Many of these subjects have pretty extensive motion artifacts in their acquisitions. There has been some work with the so-called BLADE sequences to eliminate motion. Indeed, some of the blade sequences produce fairly good contrast. But these acquisitions have slices that aren't normalized for brightness and I think this complicates the reconstruction--see ( https://imgur.com/ZWhBlcm ) for an example. It seems like we should be able to perform some kind of slice-wise normalization to fix this, but I can't see a good way to do that with the freesurfer tools. Any advice would be greatly appreciated! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Thalamic nuclei segmentation
by Miguel Ángel Rivas Fernández 08 Dec '19

08 Dec '19

External Email - Use Caution Dear Freesurfer devs, I tried to run the thalamic nuclei segmentation (T1 and T2 as input) using the freesurfer dev version and the terminal gave to me the following error rmnlab1:~ neucoga$ segmentThalamicNuclei.sh 4001 /Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii THALAMUS BBREGISTER_MODE t2 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing domingo, 8 de diciembre de 2019, 20:55:24 CET ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_dev/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib Error using SegmentThalamicNuclei (line 138) Additional volume does not exist 255 Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 Thalamic nuclei exited with ERRORS at domingo, 8 de diciembre de 2019, 20:55:31 CET For more details, see the log file /Applications/freesurfer_dev/freesurfer/subjects/4001/scripts/thalamic-nuclei-BBREGISTER_MODE.log Is the command right? I think that I have followed correctly the instructions of the website. Best regards, -- *Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Hippocampus subfields outputs missing
by Iglesias Gonzalez, Juan E. 06 Dec '19

06 Dec '19

Dear Naveed, You need the development version; these files are not given by FreeSurfer 6.0. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Muhammad Naveed Iqbal Qureshi <mniqureshi(a)hotmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 6 December 2019 at 13:44 To: Freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampus subfields outputs missing External Email - Use Caution Hi I ran the following command not the subject on HPC module load matlab/r2013a module load freesurfer/6.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh fixup_mni_paths recon-all -all -no-isrunning -s /hpf/projects/glongoni/ADHD-200/$file -subjid ADHD-${PBS_ARRAYID} -hippocampal-subfields-T1 -sd /hpf/projects/glongoni/ADHD-200/ -openmp 8 in the output directory I get only following files for both left and right hemisphere lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz lh.hippoSfLabels-T1.v10.mgz lh.hippoSfVolumes-T1.v10.txt How can I get following files? lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.CA.mgz lh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.HBT.FSvoxelSpace.mgz I try to find this command but it is not available in my installation segmentHA_T1.sh Regards, Naveed

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Hippocampus subfields outputs missing
by Muhammad Naveed Iqbal Qureshi 06 Dec '19

06 Dec '19

External Email - Use Caution Hi I ran the following command not the subject on HPC module load matlab/r2013a module load freesurfer/6.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh fixup_mni_paths recon-all -all -no-isrunning -s /hpf/projects/glongoni/ADHD-200/$file -subjid ADHD-${PBS_ARRAYID} -hippocampal-subfields-T1 -sd /hpf/projects/glongoni/ADHD-200/ -openmp 8 in the output directory I get only following files for both left and right hemisphere lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz lh.hippoSfLabels-T1.v10.mgz lh.hippoSfVolumes-T1.v10.txt How can I get following files? lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.CA.mgz lh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.HBT.FSvoxelSpace.mgz I try to find this command but it is not available in my installation segmentHA_T1.sh Regards, Naveed

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4-year PhD studentship ENIGMA Antisocial Behavior
by Stephane De Brito 06 Dec '19

06 Dec '19

External Email - Use Caution Dear all, We have a 4-year fully funded PhD studentship available to work on our ENIGMA working group focusing on different antisocial phenotypes. https://www.findaphd.com/phds/project/enhancing-neuroimaging-genetics-throu… More information about ENIGMA available here http://enigma.ini.usc.edu/ongoing/enigma-antisocial-behavior/ and about the ENIGMA Antisocial Behavior working group here http://enigma.ini.usc.edu/ongoing/enigma-antisocial-behavior/ Best wishes, Stephane --------------------------------------------------- Stephane De Brito, PhD Senior Lecturer Centre for Human Brain Health School of Psychology University of Birmingham, B15 2TT, UK Tel: +44(0)121 414 2641 (internal: 42641) Robert Aitken Building, Room 337a Web: Dr Stephane De Brito - School of Psychology - University of Birmingham<http://www.birmingham.ac.uk/staff/profiles/psychology/de-brito-stephane.aspx> Current projects: http://www.femnat-cd.eu/ and ENIGMA Antisocial Behavior<http://enigma.ini.usc.edu/ongoing/enigma-antisocial-behavior/> Twitter: @SCAN_Lab<https://twitter.com/scan_lab>

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Postdoctoral Researcher in Neuroimaging at Karolinska Institute
by Joana Braga Pereira 06 Dec '19

06 Dec '19

External Email - Use Caution Dear all, We are looking for a Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms, biofluid assays and genetics to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Assistant Professor Joana B. Pereira and it will involve analyzing cross-sectional and longitudinal imaging data, combining clinical measures and cerebrospinal fluid biomarkers, as well as writing manuscripts and presenting results in international conferences. The fellow is expected to be independent, develop his or her own projects, supervise students and show an interest in approaches based on graph theory. In addition, he/she will have the opportunity to develop new skills, analyze large datasets, apply for grants and develop a wide network of collaborations. The ideal candidate should have the following qualities: - A PhD in neuroimaging, computational science, neuropsychology, physics, statistics or a related field; - Experience in statistical techniques, programming, or scripting; - Experience with structural MRI, DTI, fMRI or PET imaging analyses; - Clinical or research experience with aging and/or neurodegenerative disorders. - Excellent record of scientific publications. The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. There are also possibilities for a longer appointment after this 2-year period. To apply please go to: https://ki.varbi.com/what:job/jobID:305265/ For further information or general inquires, please contact Joana B. Pereira (joana.pereira(a)ki.se) Best wishes, Joana

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topological defect error
by Laurel Quinlan 05 Dec '19

05 Dec '19

External Email - Use Caution Hi Freesurfer Support, One of my colleagues receives the following error after running a recon: exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation" I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view. How would I go about fixing the error? Thank you! Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Reporting Results in a three group analysis
by cody samth 05 Dec '19

05 Dec '19

External Email - Use Caution Hi, I have a statistical question about how to approach reporting results from FreeSurfer analyses containing three groups. I ran a group effect (F-test) and then post-hoc tests looking at pair-wise comparisons between the three groups. My question is why is that we run separate vertex-wise analyses for the post-hocs rather than extracting the values from significant clusters and running post-hocs in a statistical software for just the regions where a significance difference was found (ie the clusters)? As a post-hoc vertex wide analysis can lead to different results. For example in my group effect contrasts I found a cluster in the parietal lobe. Whereas in my post hoc-vertex wide analyses one of them found two clusters 1) within the parietal 2) within the frontal lobe. If I choose to run these post-hoc analyses via freesurfer (ie vertex-wise) rather than extracting the results to analyze in a statistical program, is it standard to report the second cluster? Even though it didn't come up in the group model? If so is there a paper that people reference that uses this approach? Thanks, Cody

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surfaceholes in aseg.stats
by Laurel Quinlan 05 Dec '19

05 Dec '19

External Email - Use Caution Hi Freesurfer Support, I'm wondering how ?h.surfaceholes prior to fixing and "Total number of defect holes in surfaces prior to fixing" are calculated in the aseg.stats file for each brain. I compared aseg.stats files for the same brain edited by two different people, and I noticed that there were different numbers of holes listed for each person, despite the brain being the same. For example: lhSurfaceHoles 130 vs 61 rhSurfaceHoles 102 vs 80 Total number of defect holes 232 vs 141 Why would those numbers be so different? Thanks, Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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