Freesurfer

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30084 discussions

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview
by John Plass 01 Mar '16

01 Mar '16

Hi Bruce, Thanks for your help. In freeview, the surface outline overlays on the volume correctly, and both the volume and the surface are oriented correctly in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is oriented correctly, but the surface appears to be oriented with some of the axes swapped. E.g., from the coronal view in tkmedit, I see a coronal slice of the volume, but the outline of an axial slice of the surface, with the anterior part pointing down. John

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ineffective skull strip
by Lars M. Rimol 01 Mar '16

01 Mar '16

Hi, We have run recon-all on 33 healthy subjects in their 20ies with FreeSurfer version 5.3.0, on a Linux CentOS 6.7. The original T1's look good (example image attached). We used the braindeer tool(http://brainder.org/2011/09/10/quickly-inspect-freesurfer-cortical-sur… to check the quality of the cortical reconstruction, and we find that in 10-15 subjects the cortical surface reconstruction was unsuccessful. We think it may have to do with an incomplete skull strip (please see attached images). In order to get rid of residual dura (and some skull) we changed watershed first to 20 then to 5, using these commands: 1) recon-all -skullstrip -wsthresh 20 -clean-bm -subjid <subject name> 2) recon-all -autorecon-pial -subjid <subject name> ( We also tried: recon-all -skullstrip -clean-bm -multistrip -subjid <subject name> ) None of this changed the outcome much. Neither did -gcut ..... An alternative is of course manual editing, but we are wondering whether using BEaST to do the skull strip, and then replacing the brainmask.mgz with the brainmasking resulting from BEaST (and then recon-all -autorecon-pial -subjid <subject name> ), could be a workable solution. Would you recommend to do that/ not to do that? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Regarding: skull strip
by Dr Sampada Sinha 01 Mar '16

01 Mar '16

Dear freesurfer experts, I am trying to do analysis of T1w images. However, with one participant, try as I might I am not able to get rid of a portion of skull. I tried all the three methods explained very well on freesurfer skullstrip wiki page. But, the portion of skull still remains. I also tried to run the recon-all after fsl bet process, but then I am getting a large topological error and the process get stuck there for days on end, until I don't close the terminal. I am attaching all the processed images using ws threshold, multistrip, gc strip and finally of talairach_with_skull_2.lta. I will greatly appreciate if this can be sorted by you all. Also, I would like to bring to your notice of the command error while doing skullstrip with talairach_with_skull_2.lta. The third command IMHO should be (as it works with this one!): cp talairach_with_skull.lta talairach_with_skull_2.lta and not, cp talairach_with_skull_2.lta talairach_with_skull.lta Thanks and regards, Sampada Sinha Pre-doctoral student KGMU, Lucknow India

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Problem with brainstem substructures segmentation
by Riccardo Gubellini 01 Mar '16

01 Mar '16

Dear Freesurfer users, Sorry for reposting this message again, but I really need your help. We have downloaded the Freesurfer 6.0 version since we are really interested in the brainstem segmentation. We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM. We installed freesurfer6.0 on a virtual machine Linux (CentOs 6.7) enabling 4vcpu 11Gb of RAM. Disk space was 50 GB and after installation we have 15 GB free for data. We have launched recon-all –all for some cases and everything went right. Then we have tried to launch recon-all –all –s nameofsunbject –brainstem-structures and the process, after about 6 hours, stacks, during the SegmentSubject process and after having computing hyperparameters for estimation of Gaussian parameters. Do you have any ideas of what is happening? We tried to launch the brainstem segmentation also for the test data ( ftp://surfer.nmr.mgh.harvard.edu/pub/data/hipposubfields-testdata.tgz) but we still have the same problem. Could it be a problem the use of a virtual machine Linux instead of real Linux machine? Thank you for your help. Riccardo Gubellini

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question about white matter segmentation
by Jasmin Alves 29 Feb '16

29 Feb '16

Hello freesurfer support, I have been quality checking after the recon-all command according to the trouble shooting tutorials and have noticed quite a few participants that have white matter segmentation occurring on parts of the skull (see screen shot) but these regions are not outlined as white matter, is it necessary to use the voxel edit to remove where the skull is considered part of the white matter mask? Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Ex-Vivo Surface Misoriented in tkmedit, but not Freeview
by John Plass 29 Feb '16

29 Feb '16

Hello Freesurfer Experts, I wrote in recently about my parcellation troubles with an ex-vivo scan ( link <http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg45181.html>). Digging further, I've found that the surfaces I've produced following the Ex-Vivo recon instructions <https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon> are oriented properly when viewed in freeview (freeview -v mri/orig.mgz -f surf/rh.white:edgecolor=blue surf/rh.pial:edgecolor=red), but are misoriented in tkmedit (tkmedit $SUBID orig.mgz rh.white). I suspect that something related this might be the source of the parcellation problems. Any idea why this might be and how I can fix it? Relevant background information: *volumes were reoriented before FS processing using the command "mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz mprage.mgz" *running freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04 As always, I'm very grateful for any help you can provide. John

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Using N3 MNI and N3 FS corrections
by Adam Martersteck 29 Feb '16

29 Feb '16

Hi Freesurfer users, I have a question about using the N3 algorithm twice for processing ADNI data: Is it okay for data to have undergone the ADNI N3 correction (Boyes et al. 2008 http://www.ncbi.nlm.nih.gov/pubmed/18063391) AND then pushed through the Freesurfer pipeline and undergo FS N3 correction (Zheng, Chee, and Zagorodnov 2009 http://www.ncbi.nlm.nih.gov/pubmed/19559796)? The problem stems from the fact that recent ADNI data has either undergone gradient warping correction (http://www.ncbi.nlm.nih.gov/pubmed/16300968) AND N3 correction or no corrections at all. The optimal solution would to have just been able to download the grad warp’d data and push that through. Thanks for any thoughts! Adam

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Neurohackweek: a summer school for neuroimaging and data science, September 5th-9th 2016
by Ariel Rokem 29 Feb '16

29 Feb '16

We are happy to announce a call for applications to participate in the first installment of the Neurohackweek summer school for neuroimaging and data science. This 5 day hands-on workshop, held at the University of Washington eScience Institute in Seattle, will focus on technologies used to analyze human neuroimaging data, on methods used to extract information from large datasets of publicly available data (such as the Human Connectome Project, Open fMRI, etc.), and on tools for making neuroimaging research open and reproducible. Morning sessions will be devoted to lectures and tutorials, and afternoon sessions will be devoted to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. For more details, see: http://neurohackweek.github.io/ We are now accepting applications from researchers in different stages of their career (graduate students, postdocs, faculty, and research scientists) to participate at: http://escience.washington.edu/neurohackweek2016-application Accepted applicants will be asked to pay a fee of $200 upon final registration. This fee will include participation in the course, accommodation in the UW dorms, and two meals a day (breakfast and lunch), for the duration of the course. A limited number of fee waivers and travel grants will be available. We encourage students with financial need and students from groups that are underrepresented in neuroimaging and data science to apply for these grants (email applications to: arokem(a)uw.edu) Important dates: April 18th: Deadline for applications to participate May 6th: Notification of acceptance June 1st: Final registration deadline On behalf of the instructors, Ariel Rokem, UW eScience Tal Yarkoni, UT Austin

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number of vertices
by Yang, Daniel 29 Feb '16

29 Feb '16

Dear FreeSurfer experts, Can you please indicate the number of vertices FreeSurfer use in each hemisphere to reconstruct the brain (e.g., cortical thickness)? Is there a fixed number or an approx. number? Many thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

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Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points
by Ed Gronenschild 29 Feb '16

29 Feb '16

Hi Bruce, I'm confused about this. The manual-intervention workflow directives listed in recon-all (6 beta) tell that the series of commands should be: -autorecon2 -autorecon2-cp -autorecon3 -autorecon2 processes stages 6-23 and -autorecon2-cp process stages 12-23 So it seems to be a waste of time to process stages 12-23 twice. My question is: how to run stages 6-23 with control points? Cheers, Ed On 26 Feb 2016, at 14:13, <freesurfer-request(a)nmr.mgh.harvard.edu> <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Hi Ed > > if you run the skull stripping the autorecon2 and autorecon3 it should > detect and preserve your manual interventions > > cheers > Bruce > > > On Thu, 25 Feb 2016, Gronenschild Ed (NP) wrote: > >> Hi, >> >> I have made some manual skullstrip adjustments and added a >> number of control points in the white matter. >> How should I proceed with recon-all to incorporate both adjustments? >> >> Cheers, >> Ed >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>

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