Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

SIP disabled, fs_update run, still getting "dyld: lazy symbol binding failed" from within MATLAB
by Frederick Barrett 31 May '18

31 May '18

External Email - Use Caution Greetings freesurfer folk, Following previous posts here, as well as the freesurfer v6.0 release notes, I have disabled SIP (I'm in Mac High Sierra 10.13.4), updated my installation ($> sudo -E fs_update), and rebooted my computer, but I still get this problem. I am trying to run mri_vol2surf using the 'unix' command from within MATLAB (2017b), and upon doing so, I receive the dreaded "dyld: lazy symbol binding failed" error. I can run mri_vol2surf just fine on the command line (outside of MATLAB), and I've made sure the unix path accessible within MATLAB matches the unix path on the command line, and that freesurfer environment variables are all accessible within MATLAB. Does anyone have any ideas on how I might fix this problem? Thank you very much for your time. Best, Fred ---------------------------------------------------------- Frederick Barrett, Ph.D Assistant Professor of Psychiatry and Behavioral Sciences Behavioral Pharmacology Research Unit Johns Hopkins School of Medicine 5510 Nathan Shock Dr / Rm 3048 Baltimore, MD 21224 Voice/mail: (410) 550-9777 Email: fbarret2(a)jhmi.edu<mailto:fbarret2@jhmi.edu> | frederick.barrett(a)gmail.com<mailto:frederick.barrett@gmail.com> Google Scholar: http://goo.gl/vjrrsl<http://scholar.google.com/citations?user=KCtXPmAAAAAJ>

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Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease
by Arnaud Boré 31 May '18

31 May '18

External Email - Use Caution *Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease* We are looking to recruit a post-doctoral fellow in Dr. Julien Doyon’s *Motor Learning and Plasticity Laboratory*, at McGill University. The suitable candidate will join a team of post-doctoral fellows and PhD students who are conducting neuroimaging research in motor learning, both fundamental and clinical. For the current job opening, we seek to recruit a post-doctoral fellow who will *conduct neuroimaging and behavioral studies on healthy individuals and Parkinson’s Disease (PD) patients*. These studies are part of a research program aiming to characterize motor learning related plasticity in both brain and spinal cord, as well as to identify neuronal correlates of early stages of PD at both spinal and supra-spinal levels. The position is based at the Montreal Neurological Institute (MNI). The ideal candidate is expected to take the lead in regards to the methodological aspects of the study, addressing specifically the challenges related to the functional neuroimaging of the spinal cord, and to the analysis of complex data sets. The fellow will be involved in all stages of the research projects, from experimental design to data analysis and manuscript writing. The following requirements are mandatory: - PhD degree in neuroscience or a related field; - Experience with functional neuroimaging in human participants and with neuroimaging data analysis techniques and software (i.e. SPM, FSL or similar); - Ability to work independently and to collaborate with other team members; - Excellent organizational and social skills, especially when dealing with patient participants; - Established publication record attesting the above-mentioned requirements; - Good English proficiency (especially scientific writing and oral communication). The following requirements are assets: - Experience with spinal cord imaging; - Experience with multivariate data analysis approaches as implemented in established neuroimaging data analysis software; - Good proficiency with programming (such as Python or Matlab); - French proficiency; - Research experience with PD patients (or other movement-related disorders); - Availability to start as soon as possible. If you are interested in this position, please send your CV, a cover letter and the contact information of two individuals who can provide references at the following e-mail address: *francine.belanger(a)mcgill.ca <francine.belanger(a)criugm.qc.ca>*

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Could not read curvature from curv
by Anneliis Sartin-tarm 31 May '18

31 May '18

External Email - Use Caution Hello all, I noticed that after I ran recon-all -autorecon2-wm -autorecon3 to incorporate manual edits from a white matter surface inspection, many abnormal hard failures occurred. First, upon checking to see if my subject successfully ran through recon-all via tail scripts/recon-all.log, I received neither "finished without errors" or "finished with errors," but instead, this: SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form I then checked the subject's status via tail scripts/recon-all-status.log and received this: #@# Smooth2 lh Tue May 22 16:41:17 CDT 2018 #@# Smooth2 rh Tue May 22 16:41:24 CDT 2018 #@# Inflation2 lh Tue May 22 16:41:30 CDT 2018 #@# Inflation2 rh Tue May 22 16:42:10 CDT 2018 #@# Curv .H and .K lh Tue May 22 16:42:56 CDT 2018 #@# Curv .H and .K rh Tue May 22 16:44:22 CDT 2018 #@# Curvature Stats lh Tue May 22 16:45:40 CDT 2018 #@# Curvature Stats rh Tue May 22 16:45:43 CDT 2018 #@# Sphere lh Tue May 22 16:45:47 CDT 2018 #@# Sphere rh Tue May 22 17:20:21 CDT 2018 I then attempted to view the subject in Freeview, which only loaded the surface edges and not the inflated 3-D surface, and this message appeared in my terminal -- which is the same message in the subject's error.log folder: MRISreadNewCurvature: incompatible vertex number in file /Volumes/Vol2/cisler/freesurfer/ testing/annewuwu/surf/lh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /Volumes/Vol2/cisler/freesurfer/testing/annewuwu/surf/lh.curv MRISreadNewCurvature: incompatible vertex number in file /Volumes/Vol2/cisler/freesurfer/ testing/annewuwu/surf/lh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /Volumes/Vol2/cisler/freesurfer/testing/annewuwu/surf/lh.curv MRISreadNewCurvature: incompatible vertex number in file /Volumes/Vol2/cisler/freesurfer/ testing/annewuwu/surf/rh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /Volumes/Vol2/cisler/freesurfer/testing/annewuwu/surf/rh.curv MRISreadNewCurvature: incompatible vertex number in file /Volumes/Vol2/cisler/freesurfer/ testing/annewuwu/surf/rh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /Volumes/Vol2/cisler/freesurfer/testing/annewuwu/surf/rh.curv It looks like I most likely have to rerun the subject through recon-all, but does anybody have any tips to prevent this from happening again? Thank you for your time! Anneliis Sartin-Tarm Associate Research Specialist Neurocircuitry of Trauma and PTSD Study UW-Madison Dept. Psychiatry 608-263-5756

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Regional comparisons between cortical thickness and white matter hyperintensity
by Fotiadis, Panagiotis 31 May '18

31 May '18

Hello, I'm interested in looking into the association of cortical thickness and white matter hyperintensity from a regional perspective. Specifically, I would like to create a figure that depicts in which ROIs does cortical thinning correlate significantly with increased white matter hyperintensity volume of the underlying white matter (not just the overall white matter hyperintensity). I have created binary masks of the white matter hyperintensity burden on each patient, and I was planning on projecting them into each respective cortex. However, I didn't know what the next step should be. I was thinking about the group analysis pipeline but didn't know whether it was applicable, as I don't want to just adjust for global white matter hyperintensity volume. Thanks in advance for any help! Best, Panos Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869

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brainmask volume disappearing in certain planes in freeview
by Rachel Smallwood Shoukry 31 May '18

31 May '18

External Email - Use Caution Hello FreeSurfer developers, I'm having an odd problem using freeview. When I open a set of volumes (wm and brainmask) and surfaces (both pial and white), everything seems to work fine. However, when I turn off the volumes to look at the 3D view and then turn them back on when switching back to 2D, the situation in Screenshot1 happens. The brainmask volume disappears in the coronal and axial planes but is still there in the sagittal. Also, it looks like a coordinate appears in large text written backwards superimposed over the surface outlines (mirrored, not just in reverse order), but it's not the coordinate from the current slice. For instance, this coronal slice says R 97.66 and the axial slice says R 147.65. If I zoom in or out, the numbers get larger and smaller. The white matter volume is not affected. Everything works normally if I keep the volumes for viewing 3D rendering. I have a similar thing happen when adding control points (it first happened when creating a new set, but if I load an existing set it happens also). The image is fine until I get to a specific coronal slice (usually just a few slices away from where I put the first control point), then the brainmask volume disappears in the coronal view but is still there in sagittal and axial. This time the displayed number is A 58.73 (mirrored), which is actually the label on the exact slice where brainmask disappears for this subject, but this number does change sometimes when scrolling through slices, but not on most slices and it doesn't change to match the current label. If I close and re-open freeview with the same set of volumes and surfaces, they come up the way they should and remain as they should unless I turn off the volumes while looking at the 3D rendering or open the control point file again. This has happened for multiple subjects/sets of files, and no messages appear in the terminal when this happens. I'm using a Linux with CentOS 6.9. Any idea what could be causing this and/or how to fix it? Thanks! Rachel

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Re: [Freesurfer] multi-band slice timing correction
by Douglas Greve 31 May '18

31 May '18

if you are using version 6, then you can just specify the number of slice groups (-ngroups) when running preproc-sess. doug ps. Please post to the FS list. On 5/31/18 1:33 AM, Xu, Yaoda wrote: > Dear Dr. Greve, > > I am trying to do slice timing correction for multi-band data. Is there a way for me to use preproc-sess and include a slice timing file there somewhere? I guess I could do everything using separate commands, e.g., use "stc-sess" for slice timing correction with the slice timing file by including "-sdf slicedelayfile", then do "mc-sess”. > > Any advice you have would be greatly appreciated. Thanks a lot! > > Best, > - Yaoda Xu

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FW: Number of iterations with --cache flag
by Backhausen, Lea 31 May '18

31 May '18

External Email - Use Caution Hey Doug, thanks for the suggestions! I have some follow-up questions, also regarding your recently published paper about false positive rates (https://www.sciencedirect.com/science/article/pii/S1053811917310960) 1) What will the difference be between 1000 and 10,000 iterations? I read in the tutorial that >5000 iterations are recommended? 2) In your paper you write that permutation requires that data is exchangeable across subjects and that age effects may be a problem. In our study we want to compare adolescent patients with ADHD and conduct disorder with typically developing adolescents. In this context, data would not be exchangeable across subjects, right? Could we still use permutation? 3) When using the CFT thresholds with Monte Carlo simulation you recommend in your paper, do you still only report clusters with CWP<.05 or is the CWP less important when using stricter thresholds? 4) Which surface area do you use in your paper? White or pial? Is one "better" to use than the other? Thank you so much for your input! Best, Lea Backhausen ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Wednesday, May 30, 2018 5:40 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 171, Issue 43 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is mo https://www.sciencedirect.com/science/article/pii/S1053811917310960 re specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: FW: Number of iterations with --cache flag (Douglas Greve) 2. Re: mri_label2label: Empty label file (Douglas Greve) 3. Re: FS-FAST error: (Douglas Greve) 4. Re: Contrast interpretation - between-groups mean (Douglas Greve) 5. QDEC, order of groups for interpretation of results (Avi Gharehgazlou) 6. Re: QDEC, order interpretationof Gracias @batmarandua for aqaa (Markus Gschwind) 7. Re: fthresh function in tksurfer (srishti goel) 8. Postdoctoral Scholar positions in neuroimaging (Roeland Hancock) 9. Installing different versions of FreeSurfer on Same computer (error) (miracle ozzoude) 10. Re: Installing different versions of FreeSurfer on Same computer (error) (Dicamillo, Robert) 11. Subfields Development Version MATLAB:scriptNotAFunction (Lachlan Strike) 12. Re: Subfields Development Version MATLAB:scriptNotAFunction (Iglesias Gonzalez, Eugenio) 13. Re: LME model and contrast for longitudinal covariate and different scanners (Diers, Kersten /DZNE) 14. white matter and grey matter (Ritesh Mahajan) 15. Re: white matter and grey matter (Bruce Fischl) 16. Open Position in Neuroimaging: Barcelona?eta Brain Research Centre ? Pasqual Maragall Foundation, Barcelona, Spain (Juan Domingo Gispert L?pez) 17. Missing register.dof6.lta.file after FAST Preprocessing (Wang, Zhuonan) 18. Re: QDEC, order of groups for interpretation of results (Douglas Greve) 19. hippocampal subfield segmentation error (fsv6.0) (miracle ozzoude) 20. manual edits (John Anderson) 21. Re: manual edits (Bruce Fischl) 22. Re: hippocampal subfield segmentation error (fsv6.0) (Iglesias Gonzalez, Eugenio) 23. Re: manual edits (John Anderson) ---------------------------------------------------------------------- Message: 1 Date: Tue, 29 May 2018 12:06:01 -0400 From: Douglas Greve <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FW: Number of iterations with --cache flag To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <72d462b2-5f9d-f2a7-e3fd-0c60e24f96de(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Actually, I think 1000 is probably fine. Also, you may wan to use permutation since the monte carlo correciton tends to be too liberal. here are instructions http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0… On 5/29/18 11:37 AM, Backhausen, Lea wrote: > > > Sorry, found it! It?s 10000 as indicated in the sig.cluster.summary file. > > Best, > > Lea Backhausen > > ------------------------------ > > Lea Backhausen > > Research Assistant > > Department of Child and Adolescent Psychiatry, Faculty of Medicine of > the TU Dresden, Germany > http://www.uniklinikum-dresden.de <http://www.uniklinikum-dresden.de/> > > *From:*Backhausen, Lea > *Sent:* Tuesday, May 29, 2018 4:53 PM > *To:* 'freesurfer(a)nmr.mgh.harvard.edu' > *Subject:* Number of iterations with --cache flag > > Dear FreeSurfer Experts, > > I am wondering how many iterations are run in the precomputed Z Monte > Carlo simulation when using the --cache flag with mri_glmfit ?sim. > > Sorry if this has been documented somewhere, I cannot find it ? can > anyone direct me to the right page? > > Thank you for your help! > > Best > > Lea Backhausen > > ------------------------------ > > Lea Backhausen > > Research Assistant > > Department of Child and Adolescent Psychiatry, Faculty of Medicine of > the TU Dresden, Germany > http://www.uniklinikum-dresden.de <http://www.uniklinikum-dresden.de/> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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GradUnwarp
by Maryam Abaei 31 May '18

31 May '18

External Email - Use Caution Dear Team, I have some data that I wan to use gradUnwarp to correct them but I can't find the function to download: https://surfer.nmr.mgh.harvard.edu/fswiki/GradUnwarp . Is this function in the Freesurfer package? Many thanks, Maryam

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midbrain mask in standard-space?
by djpeters＠u.washington.edu 30 May '18

30 May '18

External Email - Use Caution Hi Freesurfer email list, I'm trying to get the midbrain mask from the brainstem segmentation pipeline into standard space, for use in analyzing some data in other modalities. I have labeled T1s in individual-space (it's a longitudinal pipeline). Does the brainstem atlas already exist somewhere in MNI-space as a mask? If so, where could I find it? I've found the ROI mesh data, but I don't know how to convert that into a voxel mask. Thanks so much, -Dan Peterson

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Missing register.dof6.lta.file after FAST Preprocessing
by Wang, Zhuonan 30 May '18

30 May '18

Hi Team, I am using FsFastTutorialV6.0<http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0> to run FAST Preprocessing. The Functional-Anatomical Cross-modal Registration should have 6 files but I lost the register.dof6.lta. I try to run the command register-sess -s $subj -per-run -fsd bold but there was still missing register.dof6.lta. file. How can I do for the next step? Thanks you! Zhuonan

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Freesurfer May 2018