Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

T1 with contrast
by Carlos Alcocer 11 Apr '23

11 Apr '23

External Email - Use Caution Can you use T1 with contrast in freesurfer or does it have to be non-contrast images? Tks, Carlos

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Subcallosal cingulate cortex segmentation/parcellation
by Carlos Alcocer 11 Apr '23

11 Apr '23

External Email - Use Caution Hi, I am interested in the aparc+aseg stats for the subcallosal cinuglate cortex (SCC). When learning freesurfer, the lectures/tutorials mention not to make manual edits to medial structures which I believe would include the SCC. Will the stat output files still be accurate if I don't make edits to these areas given that the surfaces can look quite messy in those areas at times? Thank you, Carlos

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dcmunpack behavior with scouts
by Proulx, Jean Sebastien 11 Apr '23

11 Apr '23

Dear Freesurfer Team, The help of dcmunpack says it will ignore scout scans. Is there perhaps a hidden flag to avoid that behavior? We are running multiple scouts throughout a session to combat head motion. Getting those images along the rest would allow visualizing that motion offline. Thanks for your attention and Have a very good day! Sébastiem

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Zip File Passcode
by Mike Iatrakis 10 Apr '23

10 Apr '23

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How to create a functional ROI on surface where activation is peak?
by Andy Kim 09 Apr '23

09 Apr '23

External Email - Use Caution Dear FreeSurfer developers, Hi. I've always appreciated your help. I am writing this email to kindly ask you how to create a functional ROI where activation (which is a result of FS-FAST) is peak. In volume-based analysis, people often make a "3mm-sphere" seed around peak activation for connectivity analysis. But since it is surface based, there is no "3mm-sphere". Then what would it be for surface? I tried: mri_surfcluster --in ./masked_sig1.nii.gz --hemi lh --subject fsaverage --thmin 5 --sum ./summary1.txt, but its output is not actually what I want. It tells peak X, Y, Z coordinates, but I want a fixed size of small cluster (like 3mm-sphere in volume) for creating a ROI in different masks (like peak ROI in V1, peak ROI in V2, etc). In addition, minimum threshold may be diffrent depending on masks. By this I mean, if I choose thmin of 5 for both V1 and V2, V1 may have a huge cluster where vertices have values greater than 5, where as V2 may have a small cluster. I just want to get a fixed size of ROI around "peak". How should I make a functional ROI around peak activation on surface? Kind Regards, Andy (Junghyun) Kim

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Pass code for freesurfer virtual images and QDEC question
by mariangela asimina 09 Apr '23

09 Apr '23

External Email - Use Caution Dear freesurfer team, I have been asked to re-run my analysis with QDEC, so I need to install a previous version in another computer(windows) using virtual box. Could you please give me the pass code for the archive? Alternatively, is it possible to run QDEC with the freesurfer 7+ versions? Or is it possible to have two different freesurfer versions on the same computer? Thank you! Mariangela Asimina

2 1

mris_flatten Version 6 vs. 7
by Nasr, Shahin,Ph.D. 08 Apr '23

08 Apr '23

External Email - Use Caution Hi Surfers, This is the second time that I have brought this issue up. When applied to the same 3D patch, the command mris_flatten generates two completely different outcomes when runs under stable 6 vs. 711 (see the attached files). I checked the documentation if there is any flags by which I can control the process. But I couldn't find anything relevant. Any idea what has happened? Regards Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzc…

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Fwd: Research scientist positions at OSUMC!
by Douglas N. Greve 07 Apr '23

07 Apr '23

Forwarding on an interesting job working Jessica Turner! -------- Forwarded Message -------- Subject: Research scientist positions at OSUMC! Date: Fri, 7 Apr 2023 13:42:55 +0000 From: Turner, Jessica <Jessica.Turner(a)osumc.edu> To: Douglas N. Greve <dgreve(a)mgh.harvard.edu> External Email - Use Caution https://osu.wd1.myworkdayjobs.com/OSUCareers/job/Medical-Center-Campus/Seni… <https://secure-web.cisco.com/1AFF-7GXWrl4IqEbcxoT3m-b8RLDQWdZfnUkXytxDqmooH…> _Job Description_ The Senior Researcher designs and conducts independent complex experimental research in a foundational (basic) biological/health science research laboratory with a psychiatric neuroimaging and genetics research program, in the Department of Psychiatry and Behavioral Health. Expected responsibilities include developing and investigating neuroimaging models of symptoms and response to various treatments across diagnostic groups; applying current analysis techniques to the analysis of behavioral, neurophysiological, and genetic data in combinations; interpreting and evaluating research data; working with collaborative multi-site teams in the analysis of large-scale data collections; preparing manuscripts, articles, reports and abstracts for publication in peer-reviewed journals; attending and presenting results at national and international scientific conferences, seminars, and workshops; collaboratively developing and contributing to grant proposals to obtain extramural funding to support research; developing and implementing new research projects; directing and training other research staff, participating in laboratory meetings and project meetings. Some mentoring of other research personnel may be available. _Minimum Education Required _ Doctorate (Academic) in psychology, biology, engineering, computer science, or a relevant field. _Required Qualifications _ The candidate will be analyzing data as part of their research work and must be capable of independently using some neuroimaging analysis pipelines (for example, fmriprep, SPM, FSL), ideally for structural, resting state, task-based analyses (the more imaging modalities the candidate has worked with, the better). The ability to work in a Linux environment is a must. Experience with multivariate analyses of functional MRI data or combined analysis of imaging and other datatypes such as EEG, EMA, PET, genetics is a strength. An interest in the integration of genetic data with neuroimaging and behavioral data within clinical populations is ideal. Clinical experience is not required but would be a strength. The candidate will also be writing in support of the research program, and must be capable of developing first author papers on neuroimaging results (as demonstrated by previous publications). Many thanks! Jess Jessica A. Turner, Ph.D. /Professor, Department of Psychiatry and Behavioral Health/ /Wexner Medical Center/ /The Ohio State University/ /jessica.turner(a)osumc.edu/

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VM Password
by Janssen, J.A.M. (Julia) 07 Apr '23

07 Apr '23

External Email - Use Caution Dear Freesurfer developers, I am attempting to set up virtual box with the Ubuntu image provided in the installation guide. I would like to request the password to unzip 'FS_7_2_0_ubuntu_18_04_06.ova.7z' - I hope this is the right place to ask. If anyone knows it, would they kindly contact me? Thank you in advance!

1 0

FreeSurfer container recipe?
by Bennet Fauber 06 Apr '23

06 Apr '23

External Email - Use Caution In reply to mail from Mitchell Horn, Douglas Greve replied > The math libraries changed between 7 and 8, nothing we can do about it. When I > have to run things on a centos8 machine, I generally run in a centos7 singularity > container (which we might be able to make available, without support:) Would it be possible to get just the Singularity definition file for the CentOS 7 Singularity image that you use posted to the FS wiki? We're happy to do the building, but having a file that lists the needed prerequisites that need to be installed via yum prior to installing FreeSurfer would be very helpful. It would also help to see how you handle the needed FSL components, and I think at least some portion of ANTs is needed for TRACULA, so even just which binaries are needed would be a help, too.. Thanks for considering this request, which I hope is not as burdensome as providing the fully built container.

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