Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

Help with mergecontrasts-sess function
by Paula Maldonado 27 Jan '21

27 Jan '21

External Email - Use Caution Dear experts, I am running an fMRI experiment in which I have four conditions: two main conditions (condition A and condition B) and two respective control conditions (condition Acontrol and condition Bcontrol). I would like to create a map showing significantly greater activity for condition A relative to condition B, after subtracting out the activity for the respective control conditions. In other words, I would like to perform the following contrast: (condition A - condition A control) - (condition B - condition B control) Then I would like to have a map that shows the reverse contrast too:(condition B - condition B control) - (condition A - condition A control). How do I do that?To obtain the first map: (condition A - condition A control) - (condition B - condition B control) I have tried with the mergecontrasts-sess function with the -conjunction flag and the OR option as detailed below: mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh where Contrast1= (condition A - condition A control) and Contrast2= (condition B - condition B control) however the map I get is exactly the same as (condition A - condition A control), as if subtracting out Contrast 2 had no impact on the map. Thanks, Paula

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Recon_all: COG calculation error
by Julia Yang 25 Jan '21

25 Jan '21

External Email - Use Caution Hi, While running the recon_all, I bumped into this error message below and failed to create a brainmask. I could not attach the T1.mgz and log file because the file were too big. When I looked through, the white matter intensity were only between 70-90. It is pretty much an entire white matter intensity that I think it may be difficult to manually add control points. What would be your suggestions? I have added screenshots of the freeview. \n mri_watershed -rusage /Users/Shared/PD-MCI/Freesurfer/PDMCI107/touch/rusage.mri_watershed.dat -T1 -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Darwin med-cr-mtm0xv 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64 recon-all -s PDMCI107 exited with ERRORS at Wed Nov [A picture containing calendar Description automatically generated] Kind Regards, Julia Yang

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Re: [Freesurfer] Error in longitudinal pipeline
by vittal korann 20 Jan '21

20 Jan '21

External Email - Use Caution Hi Kersten Thank you for kind response. I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all). I attached longitudinal data in csv format. Besides the covariates that you mention, the matrix needs to contain an intercept, a variable for ?time?, a variable for ?group? (assuming you have a control group also), and a group-by-time interaction term in order to asses differential change over time (again, if you have a control group). I do not have a control group. Right now I have only schizophrenia patients who underwent 2 scans: first is baseline and second one is after 3 months of yoga therapy. Wish to know the how can I proceed with my availabe data. Just to make sure: ?age? should be ?age at baseline? (i.e. constant across time per subject), otherwise it will be confounded with time. Yes, I used same across the study. Could you review (and possibly adapt) your design matrix X with respect to which columns it contains, and write it in the reply? I tried but couldn't get there. Any help would be greatly appreciated! Thanks, Vittal

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Group Analysis Question
by Swanson,Clayton 15 Jan '21

15 Jan '21

External Email - Use Caution Hi Freesurfer Team, I am performing an analysis on 23 HC and 26 people with MS and I would like to perform the stats appropriately. I would like to control for (or regress out) age and sex. Therefore, I created my FSGD file which has 4 classes (HC_Male, HC_Female, MS_Male, MS_Female) with age being the only variable. My contrast for this analysis is: 0.5 -0.5 0.5 -0.5 0 0 0 0. Lastly, I want to run a permutation analysis, so I set it up like this: #!/bin/tcsh setenv study $argv[1] foreach meas (thickness volume) foreach hemi (lh rh) foreach smoothness (10) foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir) mri_glmfit-sim \ --glmdir {$dir} \ --perm 1000 1.3 pos \ --cwp 0.05 \ --2spaces \ --overwrite end end end end After running the permutation, my next steps were to view the results in Freeview with the command [ freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=perm.th13.pos.sig.cluster.mgh ] because it’s my understanding that would overlay the cluster-wise corrected map and the view I get is an entirely yellow hemisphere. However, there are no significant clusters when viewing the perm.th13.pos.sig.cluster.summary, so I am a bit confused. Also, when I look at the uncorrected results with the sig.mgh file there are a number of spots on the hemisphere. Does this result mean that there are no cortical thickness differences between HC and MS when controlling for Age and Sex? Or does this result mean something different? What could be the next analysis steps I could perform? My goals are to assess cortical thickness differences between HC and MS. Thanks for any help you can provide, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Candidate Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu> (He/Him)

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Post-Doctoral position available in human neuroimaging and sensory testing at the University of Minnesota School of Dentistry
by Estephan Moana Filho 13 Jan '21

13 Jan '21

External Email - Use Caution *POSITION OVERVIEW* The Division of TMD & Orofacial Pain (OFP) at the University of Minnesota School of Dentistry (UMN SOD) is seeking a highly motivated Post-Doctoral Associate in the field of human neuroimaging and sensory testing for an NIH/NIDCR funded project studying brain-related mechanisms in painful temporomandibular disorders (TMD). The focus of this position will be on acquisition and analysis of neuroimaging data, as well as performing quantitative sensory (QST) and endogenous pain modulation (EPM) testing. This project is led by Dr. Estephan J. Moana-Filho, a dentist-scientist within the TMD & OFP division, who provides clinical care to OFP patients and is interested in expanding the knowledge about brain mechanisms in OFP conditions with a focus on painful TMD. The methods to be used include multimodal magnetic resonance imaging (MRI) based on the Human Connectome Project (HCP) sequences (structural, resting and stimulus-evoked BOLD fMRI, diffusion) combined with sensory testing and psychosocial/behavioral measures (QST, EPM, questionnaires, clinical measures, etc.). Our goal is to further our understanding of brain structural and functional networks involved in sensory processing, and potentially underlying central sensitization features present in painful TMD. *Duties and Responsibilities*: The Post-Doctoral Associate’s responsibilities will include, but are not limited to: 1. Implement multimodal MRI data analysis pipelines (structural and functional connectivity, stimulus-evoked fMRI, diffusion-based tractography and volumetry/cortical thickness measures) based on the HCP pre-processing pipelines (Glasser et al., 2013). 2. Perform sensory/EPM testing in human participants following standardized protocol (Rolke et al., 2006) 3. Acquire neuroimaging data following the HCP neuroimaging approach (Glasser et al., 2016), including stimulus-evoked fMRI. 4. Model and analyze complex datasets including neuroimaging, sensory and clinical data. *Required qualifications*: 1. PhD in neuroscience, biomedical engineering, oral biology, psychology, cognitive science, or a related field. 2. Strong proficiencies with one or more major neuroimaging software suites (e.g., FSL, Freesurfer, Connectome workbench, AFNI, SPM, etc.) and Unix/Linux environment. Familiarity with R, Python, and/or Matlab programming languages is a plus*.* 3. Quantitative and statistical skills, including strong programming skills and comfort with diverse computing environments such as high-performance computing systems. 4. Comfortable with interacting with human participants. 5. Demonstrated ability to complete projects as evidenced by first-author publication(s). 6. Proficient writing skills, motivated and driven to publish in peer-reviewed journals. In addition to these requirements, the ideal candidate should have a passion for self-learning, be inquisitive, critical problem-solving skills and initiative to seek out the resources necessary to achieve the project’s goals. The Moana-Filho lab is part of a vibrant pain research community at the UMN, with access to several resources including: · The Center of Magnetic Resonance Research (CMRR), a world class MRI research center with several research dedicated MRI scanners including three 3T Prisma, 7T and 10.5T human scanners. · The UMN Minnesota Supercomputing Institute (MSI), an interdisciplinary research resource supporting high-performance computing services. The latest MSI’s system is among the top 10 university-owned supercomputers in the nation, with a peak performance of over 670 Tflops and an additional 105 Tflops from a dedicated GPU subsystem. Its main cluster is also equipped with 40 high memory nodes to accommodate large memory requirements. These memory nodes feature 1 TB of memory and large solid state drives for ultra-high performance input/output. All systems are connected to high-performance parallel storage systems, with a current capacity of approximately 3 PBytes. MSI staff manage and operate these resources, offering full support to users in developing and optimizing workflows. Applications will be reviewed on an ongoing basis. Funding is available as a one-year appointment with the possibility of extension. Salary will be competitive and commensurate with experience. In case of any questions, please feel free to contact Dr. Moana-Filho (moana004 at umn dot edu <moana004(a)umn.edu>). To apply, click on “External Applicants” under the banner “Apply now!” and search for Job Opening 337497: https://humanresources.umn.edu/content/find-job

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Non-uniform voxel size
by Julie Ottoy 13 Jan '21

13 Jan '21

External Email - Use Caution Dear freesurfer team, I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a uniform voxelsize prior to these steps or does freesurfer take care of this issue internally? Thank you for the information. Best regards Julie

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Editing Recon-all on Different Computers
by Boa Sorte Silva, Narlon 13 Jan '21

13 Jan '21

External Email - Use Caution Hi FreeSurfer community, Are there any reservations for editing recon-all outputs (cross, base, or long) on a different computer from which the images were originally processed? Both computers are Mac and have the same FreeSurfer version (7.1.1). I intend to use the same computer when re-running the edited images in in recon-all pipeline, but wanted to know whether editing on a different computer would be an issue. Thank you, Best regards Nárlon Cássio Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon

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starting longitudinal pipeline after mri_robust_template
by Marisa Johanna Nordt 13 Jan '21

13 Jan '21

External Email - Use Caution Hello, I have a question regarding the longitudinal pipeline: Is it possible to start the longitudinal pipeline after a template (using mri_robust_template) has already been created in a separate step? Thank you so much, Marisa

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eTIV=0.0 on volumes where control points have been added manually
by Julia Lam 13 Jan '21

13 Jan '21

External Email - Use Caution Dear all, I received values of 0.0 on variables BrainSegVolNotVent and eTIV when running aparcstats2table on volumes where I've added control points. However, when aseg2stats was used, the variable EstimatedTotalIntraCranialVol was different from 0 on all, including the edited ones. Why is that? I've attached the logfile from one of the subjects where I used control points. I really appreciate any help you can provide. Yours sincerely Julia Lam

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Anterior insula thickness
by Hanne Van Der Heijden 12 Jan '21

12 Jan '21

External Email - Use Caution Dear freesurfer experts, I have a question regarding analysis of cortical thickness. In the stats folder of each subject, the {hemi}.aparc.stats file gives the thickness of several areas, one of them being the insula. Is it possible to get only the anterior insula thickness? Thank you in advance, and I hope to hear from you soon. Best, Hanne van der Heijden

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Freesurfer December 2020