Freesurfer January 2022

freesurfer@nmr.mgh.harvard.edu

69 participants
112 discussions

Ubuntu VM Password reques
by Jihye Noh 06 Jan '22

06 Jan '22

External Email - Use Caution Hello, I am attempting to start Ubuntu, but Ubuntu requests a login password for the Developer account. Can I ask for the password? Thank you

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7T fmri analysis in native space
by Nasiriavanaki, Zahra,M.D. 06 Jan '22

06 Jan '22

Hello freesurfers, I have one quick question and appreciate it very much if you could please respond. I have been running some resting state fmri analysis acquired on 7T scanner. In order to do the analysis on the surface, I’ve been using "-surface self lh” for left hemisphere analysis in mkanalysis-sess. My question is if there is an equivalent command to use for subcortical analysis. I have been using -mni305 1 for subcortical analysis. but I’m not sure if this the right flag to use when doing the analysis on the subject’s own space and not on fsaverage? here are the commnds I’ve been using. running the analysis with mni305 1, gives me maps like the one attached. I can’t see any blob, but I see dots of activation, which makes me think there’s something wrong. mkanalysis-sess -a stat_native.lh -runlistfile goodruns -fsd bold3 -surface self lh -fwhm 0 -event-related -TR 3 -nc 24 -polyfit 2 -nuisreg mcprextreg 6 -tpef TPEF.txt -spmhrf 0 -refeventdur 3 -per-run -nskip 0 -p stat.par -force mkanalysis-sess -a stat_native.mni -runlistfile goodruns -fsd bold3 -mni305 1 -fwhm 0 -event-related -TR 3 -nc 24 -polyfit 2 -nuisreg mcprextreg 6 -tpef TPEF.txt -spmhrf 0 -refeventdur 3 -per-run -nskip 0 -p stat.par -force Thanks, Mona

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slicesdir for FreeSurfer
by Boa Sorte Silva, Narlon 05 Jan '22

05 Jan '22

External Email - Use Caution Hi there, Hope all is well Is there a tool in FreeSurfer similar to FSL's slicesdir? That could output a web report or something similar? Thanks for your help! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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Tracula Processing: MRI_binarize error
by Kaplan, Elizabeth 04 Jan '22

04 Jan '22

External Email - Use Caution Hello, I am working to process DWI images using Tracula, however my processing stops during the mri_binarize command. In my Trac-all.log, it reads "mri_binarize done" Furthermore, when I run the command independently it runs smoothly, without error. My configuration file and trac-all.log are included below. Thank you in advance for any suggestions on how to navigate this issue Elizabeth

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Ventricle segmentation issue - ventricle mislabeled as white matter
by Kang, Jee Won 04 Jan '22

04 Jan '22

External Email - Use Caution Hello all, I found a very common error in our data while I was correcting recons. The lateral ventricles (usually the horns) are being misclassified as white matter in aseg.mgz. This happened in around 1/3 of our 108 subjects. We were able to fix this issue by manually filling in the ventricles in aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg -autorecon3, but this is obviously quite a labor-intensive fix for a substantial portion of our data. This was also the only way to fix the segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix the problem. I'm not sure why Freesurfer is having issues here, as the areas it is mislabeling have very distinct intensity boundaries - the T1 intensity is usually between 20 and 45 in the areas that are being mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who had this ventricle segmentation issue, and you can see that a large portion of the right ventricle has just not been segmented properly; the intensity of the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white matter) in aseg.mgz. Would you be able to provide some insight into why this might have been happening, and what we could do in the future to prevent such extensive manual editing in the future? I can also say that this data was processed with a T2 image as well, and supplying that flag didn't help with the segmentation issue. Thank you, Jee Won

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Stanford Postdoctoral Fellow Position in Neuroimaging based Biomarkers of Chronic Pain
by Christine Sze Wan Law 04 Jan '22

04 Jan '22

External Email - Use Caution DESCRIPTION The Systems Neuroscience & Pain Laboratory at Stanford University (SNAPL) is actively recruiting a postdoctoral fellow who will join our research project on chronic pain. Funded by the National Institute of Health and directed by Professor Sean Mackey, in collaboration with an internationally renowned group of collaborators from the Departments of Computer Sciences, Sleep Medicine, Genetics, Neurosciences and others, our goal is to develop and validate objective diagnostic and prognostic biomarkers of chronic pain. The focus of work for this postdoc will be on the neuroimaging of people with chronic pain using structural and functional MRI techniques. Our plan is to characterize neurobiological, multiomic, sensory testing, sleep/function actigraphy and other mechanisms underlying chronic pain and use this information to develop objective biomarkers of pain, ultimately, to derive new personalized interventions. When you join, you will have opportunity to collaborate with top neuroscientists, psychologists, machine learning experts, sleep medicine researchers, genetics experts and pain specialists at Stanford. Additionally, you will have access to cutting-edge fMRI technology; to invent and develop your own related research. Multidisciplinary aspects of this project will allow you to explore diverse chronic pain topics ranging from biomarker design for degenerative conditions to heart rate variability as a simple biomarker for psychological disorders. We have a strong track record for successfully transitioning postdoctoral fellows to independent grant funding and faculty positions. We can offer NIH T32 training to select candidates. The ideal candidate is a motivated problem solver and innovator who has a neuroscience background, enjoys challenging the paradigms of contemporary research and experimentation, is proficient with computer-aided analysis, and is enthusiastic and passionate about fMRI acquisition. RESEARCH AREA 1. fMRI and behavioral data from Healthy Control and patients with musculoskeletal pain, * Multivariate pattern analysis of spinal cord/brain data for corticospinal biomarker, * Integration of multimodal biomarkers into composite predictive signatures, QUALIFICATION Applicants must have received, as of the beginning date of the appointment, an MD/PhD, MD or PhD or comparable doctoral degree from an accredited domestic or foreign institution. Experience in neuroimaging analysis is a must. Additional experience in any of these is a plus: 1. Cognitive / Affective Neuroscience 2. Computational modeling / Machine Learning / Neural Networks / ICA 3. Chronic pain 4. MATLAB / Python / R / Linux / C 5. SPM / AFNI / FSL / fMRIPrep APPLICATION MATERIALS Submit (1) CV, (2) NIH Biosketch, (3) Letter of Research Intent to our website: https://secure-web.cisco.com/1ABmBj6X2X29g9HrZ1ZLolHPeQzNWnu11Jz0vgtmCS2aVp… Find instructions, blank format pages, and sample biosketches here:<https://secure-web.cisco.com/1csa_0XW8UI_EkNb5mzSQ58y7HwmZG5C0y_8F-qQF25UCc…>biosketch formats<https://secure-web.cisco.com/1csa_0XW8UI_EkNb5mzSQ58y7HwmZG5C0y_8F-qQF25UCc…>. Applicants follow non-fellowship templates. Letter of Intent template is available<http://secure-web.cisco.com/1q5SO_B929vZkGtkCeFY04WCGlo8hbQDMk_6OkrJgCYkp3K…>here<http://secure-web.cisco.com/1q5SO_B929vZkGtkCeFY04WCGlo8hbQDMk_6OkrJgCYkp3K…>. For more information, visit http://secure-web.cisco.com/1aWjdBb4KyyuH7HcXUy0GWZHPMdv1I4URZotOrABhrgX-ll…

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Making a Patch
by Alison McDonnell 04 Jan '22

04 Jan '22

External Email - Use Caution Hi Freesurfer, I am currently trying to make a patch to make a flat map. I make the relaxation cuts and circular cut in midline region but then when I try to remove the circle it removes everything but. I can't work out why this is happening as I was able to do it with the other hemisphere and have tried variations of cuts etc. Any advice would be appreciated. Thanks, Ali

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Re: [Freesurfer] Questions about contrasts
by Laura Willers de Souza 04 Jan '22

04 Jan '22

External Email - Use Caution Got it! Thank you so much, Laura.

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Re: [Freesurfer] Questions about contrasts
by Laura Willers de Souza 04 Jan '22

04 Jan '22

External Email - Use Caution Hi Douglas, Actually I have one more question. I went to look at the contrast examples on the wiki and in the example that fits my analysis (Two Groups (One Factor/Two Levels), One Covariate) it says "DODS only", and you mentioned in the previous email that my analysis turned out to be DOSS, because the interaction is non-significant. So my question is why on the wiki (https://secure-web.cisco.com/1lSrkY1qx9oAVl14F4HmZZXqrWillSwx2jFAY6OURvMGOy…) it's like "DODS only"? My fear is that I have not explained my analysis correctly to you. Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil --------------------------------------------------------------------------------------------------- De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: domingo, 02 de janeiro de 2022 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Questions about contrasts Dear Douglas, Again, thanks for the reply. Please check if I understand correctly: * First I do the contrast [0 0 -1 1] to test if there is an interaction between diagnosis and cortisol; if there is, I do DOSS [1 -1 0], if there isnt’t, I continue with DODS. * Having no interaction, I do the contrast [1 -1 0 0] to check if only the diagnosis changes cortical thickness regardless of cortisol. Did I interpret correctly? You have it backwards. If there is no interaction, use DOSS. If there is an interaction, consult a statistician. Fortunately, there is no interaction (whew!) And how do I check if cortisol changes cortical thickness regardless of diagnosis (assuming there is no interaction)? [0 0 1] with DOSS Thanks again! Best, *Laura Willers de Souza* --------------------------------------------------------------------------------------------------- De: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Enviado: quarta-feira, 15 de dezembro de 2021 Para: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: Questions about contrasts Dear Douglas, Again, thanks for the reply. Please check if I understand correctly: * First I do the contrast [0 0 -1 1] to test if there is an interaction between diagnosis and cortisol; if there is, I do DOSS [1 -1 0], if there isnt’t, I continue with DODS. * Having no interaction, I do the contrast [1 -1 0 0] to check if only the diagnosis changes cortical thickness regardless of cortisol. Did I interpret correctly? And how do I check if cortisol changes cortical thickness regardless of diagnosis (assuming there is no interaction)? Thanks again! Best, Laura Willers de Souza --------------------------------------------------------------------------------------------------- De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: terça-feira, 14 de dezembro de 2021 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Questions about contrasts This contrast will do it: [1 -1 0 0] But I would first test [0 0 -1 1] to see if the slopes are different. If not, then use [1 -1 0] with DOSS instead of DODS --------------------------------------------------------------------------------------------------- De: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Enviado: terça-feira, 14 de dezembro de 2021 17:30 Para: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: Questions about contrasts Dear Douglas, Thank you so much for your answer! Sorry, but I don't think I explained myself correctly in the previous email. I want to analyze the difference in cortical thickness between two groups (CU and CI), adjusting for a covariate (cortisol CSF) and the interaction between them. So my model would be: cortical thickness ~ diagnosis + CSF cortisol + diagnosis*CSF cortisol Using the GLM DODS, the contrasts, according to the wiki example (https://secure-web.cisco.com/1lSrkY1qx9oAVl14F4HmZZXqrWillSwx2jFAY6OURvMGOy…<https://secure-web.cisco.com/1qbucUNWhNS-2uW6Lox1w2bMK8EUHU0lm2XC7ywMcgAz1o…>), would be: * To verify if only the diagnosis regression coefficient is significant (diagnosis changes cortical thickness regardless of cortisol): 1 -1 0 0 * To verify if the regression coefficient of the interaction between diagnosis and cortisol is significant (the two change cortical thickness dependently): 0 0 1 -1 * To verify if only the cortisol regression coefficient is significant (cortisol changes cortical thickness regardless of diagnosis): 0 0 0.5 0.5 Are these contrasts corret to represent the model we designed? Thank you so much again! Best regards, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil --------------------------------------------------------------------------------------------------- De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: terça-feira, 12 de dezembro de 2021 18:23 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Questions about contrasts The model is actually, two independent linear models: thicknessCU = CUOffset + CUcortisol*CUslope thicknessCI = CIOffset + CIcortisol*CIslope There will be four regression parameters: [CUOffset CUslope CIOffset CIslope] --------------------------------------------------------------------------------------------------- De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: terça-feira, 12 de dezembro de 2021 10:48 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Questions about contrasts Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups in cortical thickness, having cortisol levels as covariate. This is my model: cortical thickness ~ pathology (CU/CI) + CSF cortisol + pathology*CSF cortisol From the GLM DODS analysis I want to know if: * the regression coefficient is significant only for the difference between groups, this could possibly mean two things: the difference in offset [1 -1 0 0] or the difference in slopes ([0 0 1 -1] * or only for cortisol, [0 0 0.5 0.5] will test whether the cortisol slope is different than 0 * or for both, both what? * or if the coefficient of the intercept between group and cortisol is significant. this does not make sense to me Is my FSGD file (attached) correct? What would the contrasts look like? --------------------------------------------------------------------------------------------------- De: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Enviado: terça-feira, 09 de dezembro de 2021 19:50 Para: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Questions about contrasts Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups in cortical thickness, having cortisol levels as covariate. This is my model: cortical thickness ~ pathology (CU/CI) + CSF cortisol + pathology*CSF cortisol From the GLM DODS analysis I want to know if: * the regression coefficient is significant only for the difference between groups, * or only for cortisol, * or for both, * or if the coefficient of the intercept between group and cortisol is significant. Is my FSGD file (attached) correct? What would the contrasts look like? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Research Fellow Position (7T Methods) in the SPM Team at WCHN, London, UK
by Guillaume Flandin 04 Jan '22

04 Jan '22

External Email - Use Caution Dear All, *------------------------------------------------------------------------------* *UCL Queen Square Institute of Neurology* *Wellcome Centre for Human Neuroimaging* *(Senior) Research Fellow: Methods developer* *------------------------------------------------------------------------------* We are looking for a post-doctoral researcher to join our Centre's Methods group. They will work on methodological research to *define, implement and deploy strategies for analysing high-resolution functional neuroimaging data* from ultra-high magnetic field MRI (7T or more). Since 2019, in-house facilities of the WCHN include a 7T Siemens Terra MRI scanner with parallel transmission capability, providing access to functional and anatomical information about the human brain in vivo with very high precision, spatial specificity and interpretability. The Centre has pioneered many neuroimaging methodologies, including Statistical Parametric Mapping (SPM) and Dynamic Causal Modelling (DCM). The Methods Group specialises in the development of a broad range of image processing methods based on principled generative models of image data and statistical analyses aimed at interpreting neural signals, see: https://secure-web.cisco.com/1RvqauirtAxJCcs-7Od6J2PA2LtHdLol_vCiMkU73-5eXw… The appointee will engage in their own research projects with flexibility to shape their research directions, in line with the overall goals of the Centre. The developed methods will be made available to Centre researchers, as well as others in the international research community, through the widely used SPM software, which is developed in the Centre. Examples of possible projects include: * Development and optimisation of analysis techniques exploiting 7T fMRI data to probe discrete units of neuronal computation such as layers, columns, stripes and small sub-nuclei; * Development of generative models of anatomically-informed fMRI analyses, for layer-specific, surface-based investigation of cortical processing at 7T; * Devising correction schemes to mitigate imaging artefacts caused by magnetic field inhomogeneities, motion and physiology; * Development of a statistical framework for the multiple testing problem in the context of laminar-specific fMRI analyses. The appointee will liaise closely with the Centre’s Methods, Physics and Computational Anatomy teams to provide solutions to challenges posed by ultra-high field imaging that integrate both acquisition and modelling strategies. Collaboration with neuroscientists from other disciplines working at the Centre is another important aspect of the role, including the provision of advice and guidance on best practice neuroimaging strategies. The post is available immediately and is funded by a grant from the Wellcome Trust until 30 November 2023 in the first instance. *For more details and to apply* see: https://secure-web.cisco.com/1t2MaOYrgLkW_hShDcCggJqa9Ch_Nws2t1cqNmaBmwOn2L… or search via UCL's online recruitment – _http://http://secure-web.cisco.com/1F2ZXVBlu8D8p3-Z2vJB5Jec86RkYm18T5oqSve… you can download a job description and person specification using ref: 1880942. For queries regarding the application process, please contact Oksana Shapoval, HR Officer, UCL Queen Square Institute of Neurology (email: _ion.hradmin(a)ucl.ac.uk <mailto:ion.hradmin@ucl.ac.uk>_). Informal enquiries to Dr Guillaume Flandin (email: g.flandin(a)ucl.ac.uk <mailto:g.flandin@ucl.ac.uk>)*.* This is an ongoing recruitment campaign and we will draw down applications once per month to assess and interview. If you are interested in the role, *we encourage you to apply early*, when post has been filled, we will close the advertisement. We will draw down applications in: early January, February and March. *Closing Date: 28 Feb 2022* -- Guillaume Flandin, PhD Wellcome Centre for Human Neuroimaging UCL Queen Square Institute of Neurology London WC1N 3BG

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Freesurfer January 2022