Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

Recon-all error- mri_convert.bin: can't determine type of output volume
by Ariana Marie Stickel 27 Apr '17

27 Apr '17

Dear Freesurfer Developers, I am attempting recon-all on one subject. I immediately get the following error: mri_convert.bin: can't determine type of output volume See recon-all.log (attached). Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: CentOS Linux 7 I have successfully completed recon-all on an older virtualbox (Windows host) version of Freesurfer with the same subject, so I do not think there is an issue with the subject data. Any help would be hugely appreciated. Thank you, Ariana Stickel

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TRACULA anterior/posterior
by Funk, Quentin 27 Apr '17

27 Apr '17

Freesurfer experts: I'm interested in comparing anterior and posterior pieces of a tract generated by TRACULA. Ideally, I'd like to take the probabilistic map (i.e. the path.pd.nii.gz from one of the folders in SUBJECT/dpath) and obtain a "posterior part" and an "anterior part" by masking. Then I'd like to extract stats similar to the stats found in pathstats.overall.txt Is this at all possible? I can produce the poster/anterior mask by hand for each individual subject, (although if there were an automated way to do this that I'm unaware of it would be great) but getting the stats out is something I can't quite figure out from the tutorials I've looked through. Thanks for any help! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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using mni152reg for hippocampal subfields
by Annie Duchesne 27 Apr '17

27 Apr '17

Hello All, I have successfully ran the recon-all -all -s subject -hippocampal-subfields-T1 using free surfer v.6 on macOS Sierra. In addition to the structural analysis, I want to run resting state functional connectivity analysis using the whole l/r hippocampus as well as specific subfields as structural seeds. I don<t want to generate an average ROI, but generate subject specific HCSF ROIs. My understanding is to perform such analysis I need to: 1)convert the l/rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to mni space (MNI152_T1_2mm_brain.nii.gz). I ran the mni152reg command, however I doubt that the default settings apply to the hippocampal subfields. Is there options I could use to have the subfields register to MNI 2mm space using mni152reg? 2)Generate .nii rois for the whole and subfield regions of the hippocampus. Using mrs_convert I was able to convert the (l/r)h.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to .nii, getting one global hippocampus per hemisphere. Is there a way to automatically generate subfields ROIs? Thank you, Annie

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Last weeks to register for HCP Course 2017
by Jennifer Elam 27 Apr '17

27 Apr '17

It's not too late to register for the 2017 HCP Course: "Exploring the Human Connectome" <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstore.huma…>, to be held June 19-23 at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada! FreeSurfer is a major part of the HCP structural processing pipeline and has been critical to the processing of the project's over 1100 released high quality imaging datasets. Spaces for the course are limited and registration is on a first come, first served basis. May 17, 2017 is the deadline to reserve discounted UBC accommodations within walking distance to the course venue: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A… The 5-day intensive HCP course is a great opportunity to learn directly from HCP investigators and designed for those interested in: - using data collected and distributed from the HCP young adult study - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - using Connectome Workbench tools and sharing data using the BALSA imaging database - learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data - exploring the HCP MMP 1.0 multimodal parcellation brain map and learning about how it can be used in your analyses - positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from HCP development (healthy subjects ages 5-21) and aging (healthy subjects ages 35-90+) and Connectomes Related to Human Disease projects See https://store.humanconnectome.org/courses/2017/exploring-the-human-connecto… for more info. If you have any questions, please contact us at: hcpcourse(a)humanconnectome.org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff

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Questions on fsdg file using complex study design
by stdp82＠virgilio.it 27 Apr '17

27 Apr '17

Dear list, we have several difficulty to understand how I should build fsdg file and we are worried to produce correct results. On FS site, it is not available an example if we would look for differences among 4 different groups (A, B, C, D; 4 Groups - One Factor/Three Levels - No Covariates).The proposed design with 2 levels and 2 factors is no helpful in our case. We have 4 groups (1 factor and 4 levels, no covariates) and we our hypothesis (in term of impaiment) is A<B<C<D. Which should be the group.effect.mtx?How should we look to difference between Group1, Group2, Group3 and Group4? Should we opt for G1+G3 vs G2+G4 or G1+G2 vs G3+G4? Other option? Please may you argue a rationale? e.g. Looking your example on three Groups (One Factor/Three Levels), No Covariates, we wonder why if Normals==MCI AND Normals==AD, then it MUST be the case that MCI==AD? We aim at assess differences by using more complex design (4x2x4), including 4 different structures, looking at right and left structures and having 4 levels (4 different groups). How should we do, please? Thank you very much. Best regards Stefano

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Error when transforming aal.nii to lh.aal.label
by haidong wang 27 Apr '17

27 Apr '17

Hello FS experts, I want to get the thickness of 90 ROIs of AAL using freesurfer. I use the following commands to transform aal.nii to lh.aal.label. 1.bbregister --s sub_con_sub01 --mov ch2.nii --t1 --init-fsl --reg register_vol2surf.dat 2.mri_vol2surf --mov aal.nii --reg register_vol2surf.dat --hemi lh --out_type mgh --o lh.aal.mgh --interp nearest 3.mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf sub_con_sub01 4.mri_label2label --srclabel lh.aal.label --srcsubject fsaverage --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh 5.mris_anatomical_stats -l lh.aal.label -t lh.thickness -b -f sub_con_sub01/stats/lh.aal.stats sub_con_sub01 lh 6.aparcstats2table --hemi lh --subjects sub_con_sub01 --parc aal --meas thickness -t ./aal_thickness.txt The result is that there is no measurement in the produced document named lh.aal.stats. I am also confused about how to set id in mri_cor2label.Could you please give me some suggestions? I am looking forwad for your prompt reply. Yours, Haidong The attachment is the screenshot of my working directory. Here is the error: mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf sub_con_sub01 $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.aal.mgh ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 75659.000; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 6451 label voxels Writing label file ./lh.aal.label LabelWrite: saving to ./lh.aal.label Centroid: -9707.33 -0.50 0.50 mri_cor2label completed SUCCESSFULLY admi@admi:~/Desktop/freesurfer_thickness$ mri_label2label --srclabel lh.aal.label --srcsubject fsaverage --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh srclabel = lh.aal.label srcsubject = fsaverage trgsubject = sub_con_sub01 trglabel = lh.aal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/admi/Desktop/freesurfer_thickness FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6451 points in source label. Starting surface-based mapping Reading source registration /home/admi/Desktop/freesurfer_thickness/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.white Reading target registration /home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. Label point 0: vno = -1, max = 163842

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NEW ANIMAL MODELS TO UNDERSTAND THE BRAIN symposium - 15th May 2017 - Nouzilly, Loire Valley, France
by Frederic Andersson 27 Apr '17

27 Apr '17

We are pleased to announce the 2nd edition of the NAMUB workshop (NEW ANIMAL MODELS TO UNDERSTAND THE BRAIN) in Nouzilly, Loire Valley, France, 2017 15th may. This symposium will present new insights on neurophysiology and in vivo neuroimaging in sheep and pigs. These animals present serious advantages compared to rodents, because in addition to their larger size, their brain is gyrencephalic. Therefore, sheep and pigs are interesting alternative to non-human primates, even more with in vivo imaging tools that are now available to investigate such large animals. By this way, it is possible to perform longitudinal studies to investigate the impact of environment on brain development, these animal models offering new ways for preclinical and therapeutic investigations. The aim of this symposium is to demonstrate how these animals are suitable experimental models to perform preclinical studies in alternative to non-human primates. Parkinson disease, stroke and brain development will be illustrated. Organization Committee Elodie Chaillou (Physiologie de la Reproduction et des Comportements, UMR Inra-CNRS-Université François-Rabelais Tours), Frédéric Andersson (Imagerie et Cerveau, UMR Inserm U930 - Université François-Rabelais Tours), Martine Migaud (Physiologie de la Reproduction et des Comportements, UMR Inra-CNRS-Université François-Rabelais Tours), Yves Tillet (Physiologie de la Reproduction et des Comportements, UMR Inra-CNRS-Université François-Rabelais Tours). Contact and information : elodie.chaillou(a)inra.fr Download the poster [PDF - 594 Ko] <http://sfrneuroimagerie.univ-tours.fr/medias/fichier/affiche-15mai-2017_149…> http://sfrneuroimagerie.univ-tours.fr/fonctionnement/new-animal-models-to-u… <http://sfrneuroimagerie.univ-tours.fr/fonctionnement/new-animal-models-to-u…> PRELIMINARY PROGRAMME: 8:45 - Coffee 9:15 - Introduction of the meeting. E. Chaillou (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly) Session 1 – Diffusion MRI. F. Andersson (INSERM Imagerie et Cerveau, Tours) 9:35 - Diffusion MRI. T. Dyrby (DIG, Copenhagen - Denmark) 10:10 - Impact of early rearing experience on brain development in sheep infant. E. Chaillou (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) 10:45 - Sheep brain connectivity. C. Poupon (NeuroSpin, CEA Saclay, France) 11:15 - Coffee Session 2 – Technical developments H. Adriaensen (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) 11:40 - Use of MPIOs as a contrast agent in sheep. L. Butruille (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) 12:05 - Adenoassociated virus vector for brain manipulations. D. Zelena (Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary) 12:30 - Segmentation of sheep brain images using local probabilistic atlases coupled with topological information G. Galisot (Laboratoire d’Informatique, Université François Rabelais de Tours) 12:55 - Virtual slides for big brain : Services and system. B. Damart (Excilone® Elancourt France) 13:05 - Stereotactic neurosurgery based on 3D imagery (m2e, Inomed, Inra, Inserm). C. Destrieux (INSERM, Imagerie et Cerveau, Tours, France) 13:15 - Lunch Session 3 – Model of neurological troubles 14:35 - Sheep, a model for Batten disease; J. Morton (Department of Physiology, Development and Neuroscience, Cambridge, United Kingdom) 15:10 - Sheep, a model for neurovascular pathology; B. Nitzsche (Fraunhofer Institute, Leipzig Germany). Session 4 – Brain anatomy Y .Tillet (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) 15:45 - The Göttingen minipig telencephalon. C. Bjarkam (Department of neurobiology, University of Aarhus, Denmark) 16:20 - Atlas of the sheep cortex. S. Love (INSERM, Imagerie et Cerveau, Tours, France) Conclusion 16:45 - M. Migaud (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) Regards,

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Interaction effects in QDEC
by Heidi Foo 26 Apr '17

26 Apr '17

Hi all, I was wondering how I could test for interaction effects between a categorical variable and a continuous variable using QDEC. Is there a way to do so? Thank you. Best Regards, Heidi Foo

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Extract time courses corresponding to a brain structure from an stc file
by Maria Hakonen 26 Apr '17

26 Apr '17

Dear Freesurfer experts, I would like to extract time courses of certain brain structures from the stc file in Matlab. Could someone please let me know how I can determine the lables of 10242 verices of my stc file? Or is there some matlab function that gives the time course of a barin structure. Best, Maria

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fs6.0 mri_surf2surf failure
by Dongnandi 26 Apr '17

26 Apr '17

Dear FS experts, I'm trying to transform some files from fsaverage space to fsaverage5 space using mri_surf2surf(fs version: 6.0), however, it is weird that the results turn out to be all zeros on the fsaverage5 surface, the command line I used if : mri_surf2surf -srcsubject fsaverage -sval ${hemi}.fsaverage.nii.gz -hemi ${hemi} --cortex -trgsubject fsaverage5 -tval ${hemi}.fsaverage5.nii.gz -surfreg sphere.reg. There is no error reported. The strange thing is that it works well using FS5.3, it failed after I update to FS 6.0. Any suggestion of solving this? Many thanks! Best! Dong

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Freesurfer April 2017