Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Freesurfer dev version: Hyppocampus, amygdala and thalamus segementation
by Steve Petersen 26 Nov '19

26 Nov '19

External Email - Use Caution Dear Freesurfer devs, We are considering segmenting with the Freesurfer 6 dev version the hippocampus, the amygdala and the thalamus of several subjects who have already done the recon-all. Since we have a T1 image and T2 image with smaller voxel size, we have thought about using the *mode B: segmetation with an additional scan* as explained in the freesurfer webpage. In addition to voxel size, both images have slight differences in acquisition parameters. Taking into account this situation we have these questions: - Since there are other slightly different parameters between image T1 and T2 in addition to voxel size (e.g. matrix size), it is correct to use B mode with additional scan or we should use multispectral segmentation? - Is it necessary to make some previous modification on some image before running the script segment_HA.sh (e.g. coregister both images)? - Is there a quality control that you can recommend after segmenting these structures? Thanks for your help! Best regards,

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How do I fix this white matter boundary issue?
by Taylor, Lisa Marie 26 Nov '19

26 Nov '19

External Email - Use Caution Hi there, I am working on a participant that has abnormally large ventricles. This has previously posed an issue with freesurfer by failing with errors but I have been successful this cycle without the job failing. However, after my first round of edits and running recon-all there is a major issue with the WM and Pial boundary area. I am unaware of how to address it. I have attached images to highlight where my concern is. Any insight? Thank you so much! Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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V1 length
by Melissa Wright 26 Nov '19

26 Nov '19

External Email - Use Caution Hi everyone, I'm currently using mris_divide_parcellation to create segmentations of V1 by dividing along its long axis. However, I would like to extract the length of this long axis (in mm), in order to compare it with CMF. Would anyone know how best to go about this? Sorry if there's an obvious answer! I have tried looking online and at the function scripts, but no luck. Thank you and best wishes, Melissa E Wright Melissa E Wright, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Maindy Road Cardiff CF24 4HQ UK Tel: +44 (0)29 208 20275 Email: WrightME(a)cardiff.ac.uk<mailto:WrightME@cardiff.ac.uk> Web: Cardiff University webpage<http://www.cardiff.ac.uk/people/research-students/view/482937-> Twitter: @MEW_Neuro Melissa E Wright, MSc Myfyrwraig PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU Ffôn: +44 (0)29 208 20275 E-bost: WrightME(a)caerdydd.ac.uk<mailto:RountreeLC@cardiff.ac.uk>

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freeview parallelized binary
by Clark, Dustin Christopher 26 Nov '19

26 Nov '19

External Email - Use Caution Hello, We recently noticed freeview on the MGH cluster was using multiple cores when loading niftis, however, our local installation only uses one core when loading the same nifiti. Is it possible to get access to this freeview binary or the source code to build it for parallelization on our system? Thank you, Dustin Clark

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linyanyan@outlook.com
by Lin Yanyan 25 Nov '19

25 Nov '19

External Email - Use Caution

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Research Scientist / Engineer 3 position at the University of Washington
by Daniel J Peterson 25 Nov '19

25 Nov '19

External Email - Use Caution The University of Washington Department of Radiology currently has an outstanding opportunity for a RESEARCH SCIENTIST ENGINEER 3. The Research Scientist/Engineer 3 contributes to the growth & success of the Department by executing the mission and vision. The Integrated Brain Imaging Center in the UW Department of Radiology is a research resource center for the interdisciplinary triangle of human MRI based imaging, cognitive neuroscience, and medicine. This is a vibrant multidisciplinary unit working on cutting edge multimodal imaging methods, interoperable software tools, and translation of these approaches to clinical populations. Reporting to the Director of the Integrated Brain Imaging Center (IBIC), this position provides specialized science and research consulting support for the IBIC Research Group within the Department of Radiology. The successful candidate will be one who thrives in a multidisciplinary environment; can maintain a cutting edge conceptual understanding of image processing methods, analysis, and interpretation; views operationalizing methods on science as an exercise in problem solving; and enjoys integrating science and methods, operationally and conceptually. The successful candidate will demonstrate a trajectory of increasing responsibility for facilitating projects requiring divergent intellectual disciplines Please see the full posting for more details: https://uwhires.admin.washington.edu/ENG/Candidates/default.cfm?szCategory=…

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Re: [Freesurfer] Is -skullstrip set by default?
by Bruce Fischl 25 Nov '19

25 Nov '19

Hi Tashrif yes, because then you can just run it by itself (as opposed to part of one of the -autorecon targets) cheers Bruce On Mon, 25 Nov 2019, Billah, Tashrif wrote: > Hi Bruce, > > Thanks for your reply. But then we wouldn't need a -skullstrip option again given it's on my > default, would we? > > Best, > Tashrif > > ------------------------------------------------------------- > > Tashrif Billah, MS > > Research Engineer > > Brigham and Women's Hospital > > Harvard Medical School > > tbillah(a)bwh.harvard.edu > > http://pnl.bwh.harvard.edu/tashrif-billah-m-s/ > > >

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Is -skullstrip set by default?
by Billah, Tashrif 25 Nov '19

25 Nov '19

With recon-all, is [-skullstrip](https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip) option set by default? I am trying to understand why there is a separate -noskullstrip option. Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS<https://www.linkedin.com/in/tashrif-billah/> Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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Recon-all Error
by Meena M. Makary 22 Nov '19

22 Nov '19

External Email - Use Caution Hi, I have been getting this error with one of my subjects Recon-all. I am attaching the recon-all log file. any help would be appreciated! Meena -- — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Radiology, Harvard Medical School <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> Postdoctoral Fellow | Athinoula A. Martinos Center, MGH <https://www.nmr.mgh.harvard.edu/user/4550386> Career Development and Mentoring Manager | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>

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freesurfer linux-ppc build
by Ryan Schneider 22 Nov '19

22 Nov '19

External Email - Use Caution Hello, Is there an available freesurfer linux power pc (Power 9) build? I can not find any information about this online. If not , I have been working on making one and would like to know if anyone else has any progress ... Thanks, Ryan Schneider Boston University

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