Freesurfer February 2016

freesurfer@nmr.mgh.harvard.edu

123 participants
179 discussions

Corrupted head surface with mkheadsurf?
by Maheen Siddiqui 01 Mar '16

01 Mar '16

Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised. Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview. Does anybody have any advice? Thanks, Maheen

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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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QDEC_ information extraction
by nellie 28 Feb '16

28 Feb '16

Dear Freesurfer Experts, Sorry to bother the mailing list again, but I really confused with the information extraction of significant clusters from QDEC. Basically, there were two main questions: (1)I have knew that the stimulation output summary was named “mc-z.abs.th20.sig.cluster.summary” and could be shown in the running terminal, but its detail was not consist with the display of inflated map. Just like the regions of postcentral and temporalpole did not show significantly on this map. How to explain this situation? Is it proper to use this summary as my research result? # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 4.165 90787 2844.40 -38.8 -50.9 -14.4 0.00010 0.00000 0.00020 4259 fusiform 2 -4.112 133001 925.06 -53.9 -15.8 44.4 0.02870 0.02660 0.03080 2169 postcentral 3 3.481 115941 1058.24 -26.0 5.6 -31.7 0.01410 0.01260 0.01560 2505 temporalpole 4 2.745 26991 1295.59 -6.0 37.6 -2.6 0.00350 0.00280 0.00430 2395 rostralanteriorcingulate (The command scrip was shown as:mri_surfcluster --in /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm28/abs/th20/mc-z.csd --mask /usr/local/freesurfer/subjects/qdec/Untitled/mask.mgh --cwsig /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.cluster.mgh --vwsig /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.vertex.mgh --sum /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.cluster.summary --ocn /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.ocn.mgh --oannot /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.ocn.annot --csdpdf /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.pdf.dat --annot aparc --cwpvalthresh 0.05 --surf white) (2)In the inflated map, tow significant clusters involved the regions of superiorfrontal (belong to Cluster 1),medialorbitofrontal(Cluster 1), caudalanteriorcingualte(Cluster 1), rostralanteriorcingualte(Cluster 1), and lingual(belong to Cluster 2), lateraloccipital(Cluster 2), fusiform(Cluster 2),inferiortemporal(Cluster 2).Is there any auto way to extract information (including the Talairach coordinates, cluster size and CWP) of these cortical areas, not just that of the two clusters? Looking for your reply. Many thanks! Cheers, Nellie

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Recon-all problem
by Mohamed Ali Bahri 28 Feb '16

28 Feb '16

Dear Experts, I have the following error with recon-all (freesurfer v 5.3). Anybody have an idea about this problem? Many thanks in advance, Mohamed --------------------------------------------------------orig_nu.log file-------------------------------------- Iteration 1 Fri Feb 26 14:13:20 CET 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.20504/nu0.mnc ./tmp.mri_nu_correct.mni.20504/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20504/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /usr/local/freesurfer/mni/share/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. ERROR: nu_correct -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)ulg.ac.be

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cortex mask
by Ali Radaideh 27 Feb '16

27 Feb '16

Dear FreeSurfer Experts, We have two high resolution datasets (T1 and T2* images). T2* is co-registered to the T1 volume. The T1 volume was processed in freesurfer using the recon-all and we want to use the segmented cortex (by freesurfer) as a mask to extract the cortex from the T2* volume. Would it be possible, please, to let us know which command to use to transfer the segmented cortex to the native space of T1 and T2*?. Many thanks in advance, Ali -- *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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Announcing the Copenhagen FreeSurfer Course 2016
by Melanie Ganz 27 Feb '16

27 Feb '16

We are pleased to announce a European FreeSurfer Course that will be held from August 10th to 12th, 2016 in Copenhagen, Denmark. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital in cooperation with the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. Registration will open on March 15th, however, you can put your name on our list of students now by emailing the course organizers at fs-cph(a)nru.dk! You will still have to do a formal registration later when they are ready to accept payments on March 15th, however, you can reserve your spot in the course before then by emailing them. For upcoming news and further information, please visit: http://fscph2016.nru.dk/ or contact us under fs-cph(a)nru.dk. -------------------------------------------------- Organizing Team FreeSurfer Course Copenhagen 2016 http://fscph2016.nru.dk/ fs-cph(a)nru.dk

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Freesurfer February 2016