Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask
by lindsay hanford 04 Jan '19

04 Jan '19

External Email - Use Caution Hello Freesurfer Community, I am wondering if it is possible to recalculate cortical thickness metrics (perhaps using mri_segstats or aparcstats2table) while including either a SD threshold or an exclusion mask. Using mri_surf2surf to register scans to the same space and then mri_surface_stats to create the std maps I have been comparing the variability of cortical thickness across the cortex for multiple scans across the same subject. From this I can determine a SD threshold point (0.5 say) or create a mask that includes all regions above that threshold. I would like to use this to threshold the regions showing the highest variability out of my calculations for mean hemispheric thickness and also regional thickness. Is there a way to use an SD threshold within mri_segstats or aparcstats2table? Otherwise apply a mask image to exclude specific vertices? Thank you in advance, Lindsay

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gammafit flag in mkanalysis-sess
by Nasiriavanaki, Zahra 04 Jan '19

04 Jan '19

Hi Freesurfers I have a few questions about gammafit flag in mkanalysis-sess command and I appreciate if you could respond whenever you had time. -How should we decide which function is best to apply on hemodynamic response signal? I have used both spmhrf and gammafit and I see slightly different results. -Does Freesurfer has a default function that applies on hemodynamic response signal if I don't use these flags? -Where should I get gfdelta and gftau from? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Freesurfer 5.3 vs 6
by Nasiriavanaki, Zahra 04 Jan '19

04 Jan '19

Dear Freesurfers Hi I have a bunch of data that is preprocessed in Freesurfer version 5.3 (both recon and preprocessing). My question is whether I can do the first level and group analysis on this data using Freesurfer version 6? Or should I do everything in version 6 from the beginning? I need to compare their results with my other data set in FS v 6. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Postdoctoral Fellowship: Neurobiology of Reading {Disarmed}
by Meaghan Perdue 04 Jan '19

04 Jan '19

External Email - Use Caution *Postdoctoral Fellowship: Neurobiology of Reading* The LandiLab (PI: Nicole Landi https://landi.lab.uconn.edu/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__landi.lab.uconn.edu_&d…>) at Haskins Laboratories and the University of Connecticut is seeking to hire a full-time postdoctoral research fellow. Haskins Laboratories *https://haskinslabs.org/ <https://haskinslabs.org/> *is located in New Haven, CT and is closely affiliated with Yale University and the University of Connecticut. This postdoc will join an NIH funded project investigating the neurobiological basis (brain structure, genetics) of reading. The successful applicant will be responsible for conducting and interpreting analyses of neuroimaging data (primarily gray matter structure and diffusion imaging). This position is part of a multi-site project (Haskins Laboratories, Yale University, University of Houston, Baylor College of Medicine, Florida Center for Reading Research) that is analyzing neuroimaging and genotyping data from 9000+ individuals to explore gene-brain-behavior relationships. *Required qualifications:* · PhD or equivalent in Psychology, Neuroscience, Cognitive Science, Computer Science, or related field · Experience analyzing neuroimaging data · Experience with one or more imaging analysis packages (e.g., FSL, SPM, AFNI, FreeSurfer) · Programming skills, including knowledge of at least one language and Unix commands · Proficiency with writing academic manuscripts · Leadership, communication, and organizational skills *Preferred qualifications:* · Experience analyzing diffusion weighted imaging data · Experience with advanced neuroimaging analysis techniques, e.g., independent components analysis, functional and context-dependent connectivity, VBM, machine learning · Demonstrable interest in the neurobiology of language and/or reading · Familiarity with genetic analyses or imaging genetic analyses This postdoctoral scholar will work with an interdisciplinary and highly collaborative team of PIs and affiliated scientists from the *LandiLab <https://urldefense.proofpoint.com/v2/url?u=https-3A__landi.lab.uconn.edu_&d…>* (PI: Nicole Landi, University of Connecticut, Haskins Laboratories, Yale Child Study Center) and the *GENESIS <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uh.edu_class_psycho…>* lab (PI: Elena Grigorenko, University of Houston & Baylor College of Medicine, Houston TX).This position is based at Haskins Laboratories (New Haven, CT), but will coordinate with research partners at multiple locations. Interested candidates should send 1) a CV; 2) the names and contact information of three references; and, 3) a cover letter to Dr. Nicole Landi at *Nicole.Landi(a)UConn.edu <Nicole.landi(a)uconn.edu>* . This position will remain open until filled; desired start date is Spring 2019. Salary will be commensurate with NIH postdoctoral funding levels. Haskins Laboratories is an equal opportunity employer. -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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ROI Analysis
by Larissa Bechtle 04 Jan '19

04 Jan '19

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Job Opportunity
by Smith, Arleen 04 Jan '19

04 Jan '19

External Email - Use Caution Good Day I would like to extend a job opportunity at the University of Texas at Dallas. Please forward to members of the listserv. The School of Behavioral and Brain Sciences at The University of Texas at Dallas is accepting applications at the Assistant Professor level to join the area of Cognition and Neuroscience. The University of Texas at Dallas (UTD) is a Carnegie R1 classification institution and was recently ranked #1 in the US among universities founded less than 50 years ago by Times Higher Education. Faculty in the area of Cognition and Neuroscience are based both on the main campus and at three research centers located in central Dallas near The University of Texas Southwestern Medical Center (UTSW), with which there are strong collaborative relationships. UTSW houses the Advanced Imaging Research Center, an inter-institutional facility that provides neuroimaging resources supporting the research of UTD faculty. Additional neuroimaging resources are under development under the auspices of UTD. Applicants must hold a PhD degree in psychology, neuroscience, or a related field, and will be expected to build and maintain a scientifically rigorous, extramurally funded research program. The research area of interest should broadly be in the study of human reinforcement learning and decision making relevant to the emerging field of computational psychiatry, applying functional and structural neuroimaging methods. We invite applicants with a strong empirical program in one or more of these areas, and who, in addition, have strengths in applying novel methodological or analytical approaches to cognitive neuroscience. The successful candidate will be expected to actively engage in the research and training activities of the Cognition and Neuroscience area in the School of Behavioral and Brain Sciences, including advising doctoral students, mentoring postdoctoral trainees, and developing collaborative research programs. Applicants should upload (1) a cover letter; (2) a curriculum vitae; (3) a statement of research plans (approximately 2-3 pages); and (4) the names and full contact information for three references via the online application at http://jobs.utdallas.edu/postings/11357. Review of applicants will begin immediately. Administrative questions may be addressed to the Program Office at 972-883-7260. The University of Texas at Dallas is an Equal Opportunity/Equal Access/Affirmative Action Employer committed to achieving a diverse and inclusive community. Thank You Arleen smith The University of Texas at Dallas School of Behavioral & Brain Sciences, GR41 800 West Campbell Road Richardson TX 75080-3021 Office: GR4.506 PH. 972-883-2357 Fax 972-883-2491 [Description: Description: UTD Signature] Life's most urgent question is: What are you doing for others - Martin Luther King Jr.

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post-doc opportunity: structural/functional brain connectivity and networks
by Barbara Kreilkamp 04 Jan '19

04 Jan '19

External Email - Use Caution Dear all, As a current post-doc in this lab, I am happy to announce this three-year post-doc opportunity availabile in Dr Simon Keller's lab at the University of Liverpool, United Kingdom. The successful applicant will be specialising in structural and functional brain connectivity and networks in human epilepsy. Please find more information here https://www.jobs.ac.uk/job/BPF608/postdoctoral-research-fellow-neuroimaging… and in the attachment. Please read this job description (link and attachment) and direct your informal inquiries to Dr Simon Keller (simon.keller(a)liverpool.ac.uk) Kind regards and a happy new year! Barbara

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-qcache error
by 塩浜直 03 Jan '19

03 Jan '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do group analysis for cortical thickness map using Qdec GUI. We've already have recon-all files that were made by “recon-all –s subjid –i subjid.nii –all” on other Linux OS (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Firstly, I try to run command “recon-all –s subject –qcache” for each subject floders. However, the program stopped with error 1 minutes after starting. Last line of recon-all.log showed as follows. #@# Qdec Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 I've searched the list but I can find no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: Free Surfer 6.0 2) Platform: macOS Mojave (64b Intel) 3) recon-all.log: see attached Tadashi Shiohama

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Re: [Freesurfer] map parcellations into DWI space?
by Greve, Douglas N.,Ph.D. 03 Jan '19

03 Jan '19

you might try this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 On 12/30/18 1:45 AM, Yerong Li wrote: > External Email - Use Caution > Dear FreeSurfer experts: > I am trying to map ./mri/aparc.a2009s+aseg.mgz and > ./mri/aparc+aseg.mgz into DTI file. > Let's say, we have a DTI file with its b-vectors: > ./bvals > ./bvecs > ./data.nii.gz > > I am trying to use the command from this webpage: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > > So I used the command : > mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz --o > dk-in-rawavg.mgz --regheader aparc+aseg.mgz > > The output file seems not very reasonable. Could you help me with this? > > Yerong > ================================== > Can you be more specific about which files you want to map into your DWI > space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You > will need a registration file which you can obtain with bbregister > > > On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: >> >> External Email - Use Caution >> >> Dear FreeSurfer experts, >> I have a parcellation and a whole brain white matter files which are >> the outputs of FreeSurfer. >> I want to register them to my DWI. I mean I want my parcellation and >> white matter to be in the physical space of my DWI. >> Can FreeSurfer do it for me? >> If not , can you suggest me a toolbox that can do it fast? >> I would be grateful if u could help me. >> Cheers, >> Maedeh, >> >> >

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Diagnosing a recon error
by Maksimovskiy, Arkadiy 03 Jan '19

03 Jan '19

Dear Experts, I was wondering if someone might be able to help diagnose a recon error. I used the following command to initiate recon: recon-all -subject RMD002 -i /ncf/anl/anl01/MultiMode/Data/structural/T1_MEMPRAGE_5_RMD002_e1.nii -T2 /ncf/anl/anl01/MultiMode/Data/structural/T2_SPACE_6_RMD002.nii -T2pial -3T -all The recon log indicates an error: recon-all -s RMD002 exited with ERRORS Attached is the log file. I used grep to search through it for “failed” or “error”, but am unable to see any indices of errors, other than this message at the bottom of the log. I would love to hear any info for what might have gone wrong. Thank you for all your help, Arkadiy

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Freesurfer January 2019