Freesurfer December 2019

freesurfer@nmr.mgh.harvard.edu

85 participants
117 discussions

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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Multiple comparison using Monte Carlo
by Ting Li 05 Dec '19

05 Dec '19

External Email - Use Caution Dear Freesurfer Expert: I have used the simulation code as show below: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces My question is how many iterations are done during this simulation? I didn’t specify the iteration number. Why I didn’t have the csd file? Thanks a lot for your response! Best regards, Ting

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negative SUVr using PETsurfer
by miracle ozzoude 05 Dec '19

05 Dec '19

External Email - Use Caution Hello Experts, I ran the PETsurfer pipeline using AV45 pet and performed pvc using pons as reference point. When i looked at the gtm.stats.dat file for one of my subjects, the SUVr for right and left nucleus-accumbens areas were in the negative (left = -0.361; right = -0.046). This is strange because SUVR shouldn't be negative. How do i go about fixing this error? Below, is my pvc command. mri_gtmpvc --i pet.nii --reg register.lta --psf 6 --seg gtmseg.mgz --default--seg-merge --auto-mask PSF .01 --mgx .01 --o subject_gtmpvc --rescale 174 Thanks. Best, Paul

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Freesurfer December 2019