Freesurfer May 2016

freesurfer@nmr.mgh.harvard.edu

135 participants
197 discussions

visualization tk surfer
by maaike rive 14 May '16

14 May '16

Dear Freesurfer experts, I have a question regarding tk surfer. If I load the cache.h13.abs.sig.cluster.mgh file, I'll only see the clusters surviving the statistical threshold I set, don't I? (e.g. I set the cluster finding threshold at 0.05 (Monte carlo simulation), keeping all clusters with p<0.001, which gives me for example one cluster; it's only this cluster that will be visualized, right?) I ask this because sometimes only a few clusters are kept, but I see a lot of the brain coloured in tk surfer, presumably because the clusters are very large. Thanks, Maaike

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R: Re: mri_surf2vol
by stdp82＠virgilio.it 14 May '16

14 May '16

Thanks. I'm reading the surf2surf help but I do not understand the --trgsurfreg options. I'using mri_surf2surf --hemi rh --srcsubject fsaverage --srcsurfval thickness -- src_type curv --trgsubject Control21 --trgsurfval file?? Which is the file? Thanks Stefano >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 14-mag-2016 0.06 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] mri_surf2vol > >The overlay Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz is >in fsaverage space, so either change the subject to fsaverage, or use >mri_surf2surf to map the overlay into Control21's space, then run >mri_surf2vol > > >On 05/13/2016 06:03 PM, stdp82(a)virgilio.it wrote: >> Hi list, >> >> I'm using FS-FAST for seed based functional connectivity. >> For a subject, I would like to report the sig.nii.gz from the inflate >> to volume space. >> >> I'm using >> >> mri_surf2vol --surfval >> Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz --hemi rh >> --fillribbon --subject Control21 --identity Control21 --template >> Control21/orig.mgz --o ramg2rh_sig_volspace.nii.gz >> >> but this error reported below was obtained. >> >> ERROR: dimension inconsistency in source data >> >> Number of surface vertices = 123044 >> >> Number of value vertices = 163842 >> >> >> Thanks >> >> >> >> Stefano >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > >

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postdoc at UCSF
by Bruce Fischl 13 May '16

13 May '16

The Neuroradiology Section and Memory and Aging Center (MAC) at the University of California, San Francisco (UCSF) are seeking an exceptional postdoctoral candidate in imaging genetics of neurodegenerative disorders. Using a variety of techniques, ranging from human structural and functional MRI to whole genome sequencing, our research involves elucidating the genetic, neuroanatomic, and molecular characteristics of Alzheimer's disease, frontotemporal lobar degeneration, Parkinson's disease and neuroinflammation. We seek a postdoctoral candidate with a strong background in genetics (and preferably, human imaging) and a desire to use a multi-disciplinary approach to pursue neurodegenerative research. The candidate should have considerable experience with Matlab, R, PLINK and potentially, MRI image analysis tools such as Freesurfer, FSL and SPM. Applicants should have a Ph.D. or M.D. degree with less than five years of postdoctoral experience. Highly motivated individuals with a record of productive research are encouraged to apply. The position is available starting July 1, 2016. Salary is commensurate with qualifications and experience. Interested applicants should send curriculum vitae/NIH biosketch, and three references to: Drs. Rahul Desikan (rahuldesikan(a)gmail.com) and Jennifer Yokoyama (jennifer.yokoyama(a)ucsf.edu)

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WmParc
by Caroline Beelen 13 May '16

13 May '16

Dear FS team, We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran the following command: mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz (<subjid> was replaced by our subject) We get the following error: option --ribbon unknown. The ribbon.mgz folders exist and are located in the right directory. We also tried to re-create them and this worked fine, but again after running the command above we got the same error. If we changed the command --ribbon to -- no ribbon, the script ran, but when we looked at the stats-file, only cortical grey matter labels were segmented (no wm). The same applies to other subjects we tried. Could you please help us out? Many thanks. Jolijn & Caroline

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mri_surf2vol
by stdp82＠virgilio.it 13 May '16

13 May '16

Hi list, I'm using FS-FAST for seed based functional connectivity.For a subject, I would like to report the sig.nii.gz from the inflate to volume space. I'm using mri_surf2vol --surfval Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz --hemi rh --fillribbon --subject Control21 --identity Control21 --template Control21/orig.mgz --o ramg2rh_sig_volspace.nii.gz but this error reported below was obtained. ERROR: dimension inconsistency in source data Number of surface vertices = 123044 Number of value vertices = 163842 Thanks Stefano

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Split a lablemap in the .annot format into parts
by Boris Rauchmann 13 May '16

13 May '16

Dear FS Community, is there an easy way to split a lablemap in the .annot format into parts? In detail I would like to split network 6 (frontoparietal) of the yeo atlas (fsaverage/label/rh.Yeo2011_7Networks_N1000.annot) into the frontal, parietal and temporal part on each side. Is there an easy way to do this in FS? Thank you, Boris

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Connectivity from external seeds
by Sahil Bajaj 13 May '16

13 May '16

Hello FS experts, I am sorry for reposting this question in the forum: I calculated subject-wise resting-state FC maps after defining seeds into subject-wise anatomical space as mentioned in the manual. Now, location of seed regions across subjects differ a little. According to manual, FS maps the time-series on fsaverage lh and rh hemisphere. That means connectivity maps for each subject are registered to fsaverage space and it should be fine to calculate 2nd level maps. If that's correct then my questions are: (a). How seeds can be overlaid on 2nd level maps or 1st level maps because seeds are not in fsaverage space but both 1st and 2nd level connectivity maps are. When I see subject-wise FC maps, those are little far from the actual seed locations which I defined in subject-wise anatomical space. (b). How FS deals with seed regions in terms of 2nd level analysis because it calculates FC from seeds which are in subject-wise anatomical space but it reports FC in fsaverage space, so 2nd level results are even more far away from actual seed region locations? I would really appreciate any thoughts/suggestions on this. Thanks, Sahil -- -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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2 unrelated questions regarding structural data
by Josh Gray 13 May '16

13 May '16

Hello, 1) I am working with the recent release of human connectome data and am trying to run group analysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) I want to correlate brain volume with an behavioral variable. It is difficult to tell which files I need in order for the pipeline to run properly. Since I did not run recon-all locally, their file arrangement is unique, many files are zipped, etc. Therefore the scripts (e.g., mris_preproc) do not know where to look, as they do with the typical file structure. Can you tell me what specific files this pipeline needs to generate the GLM? Alternatively, if you have performed this process with the human connectome data you can tell me which directories/files need to be unzipped and placed in SUBJECTS_DIR. Just need to know what specific files the scripts in the group analysis pipeline are searching for when I run them. 2) I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website). Is there a quick way to do this? Thank you for your help! Josh -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia

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Postdoc Position in Computational Neuroscience, Max Planck Institute, Leipzig, Germany
by Katharina von Kriegstein 13 May '16

13 May '16

Applications are welcomed for a postdoctoral research position at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, Germany in collaboration with the Technical University Dresden, Germany. The objective of the postdoctoral research project is to use computational modelling and neuroimaging to work towards a novel model for cortico-subcortical interactions for human communication signals. The project is funded by the ERC-consolidator grant SENSOCOM (http://cordis.europa.eu/project/rcn/199655_en.html) The position will be jointly supervised by Katharina von Kriegstein at the MPI-CBS and Stefan Kiebel at the TU Dresden. The MPI-CBS offers a unique research environment with a 7.0 T MRI scanner, several 3.0 T MRI scanners, a 306 channels MEG system, TMS/tDCS laboratories, several EEG suites, and eye-tracking labs. All facilities and data analyses are supported by experienced IT specialists and physicists. The TU Dresden is one out of eleven German Universities of Excellence. It houses a state-of-the art neuroimaging centre with a strong focus on computational modelling and access to the TU Dresden high-performance computing clusters. Besides an excellent infrastructure, both centres offer an international and friendly environment with researchers from diverse backgrounds. The position is ideal for candidates interested in research at the interface between computational modelling and experimental neuroimaging. The candidates must have a PhD (or equivalent) in computational neuroscience, experimental psychology, or a related field, and should be able to demonstrate a consistently outstanding academic record, including publications. The ideal candidate will have expertise in computational neuroscience, physics, mathematics, or similar with a strong interest in implementing computational models (e.g., Bayesian filtering, hierarchical dynamic models, predictive coding) and testing these with neuroimaging experiments. The starting date for the position is flexible. Initially for two years, the position offers the possibility of extension for up to four years. Salary depends on experience and is based on regulations of the Max Planck Society. To apply, please include all documents in one PDF-file in the following order: CV, contact information of two referees, a brief statement describing your personal qualifications and future research interests, copies of up to three of your publications. Applications with the subject heading "CM 16 PD" should be sent via email to: personal(a)cbs.mpg.de. Closing date for applications is the 12th June 2016. Informal enquiries regarding the post should be directed to: Prof. Dr. Katharina von Kriegstein (kriegstein(a)cbs.mpg.de) For more information about the groups see: Prof. Katharina von Kriegstein: http://www.cbs.mpg.de/independent-research-groups/human-communication Prof. Stefan Kiebel: https://tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_mathematik_und_n… A link to the position description is available here: http://www.cbs.mpg.de/454795/job_full_offer_10498685?c=7390 The MPI-CBS is an equal opportunities employer, committed to the advancement of individuals without regard to ethnicity, religion, gender, or disability. --- Katharina von Kriegstein Max Planck Research Group Leader Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1A, 04103 Leipzig, Germany Professor of Cognitive and Clinical Neuroscience Humboldt University of Berlin Rudower Chaussee 18, 12489 Berlin, Germany Phone +49 (0) 341-9940-2476 Fax +49 (0) 341-9940-2448 http://www.cbs.mpg.de/independent-research-groups/human-communication

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Re: [Freesurfer] Manual correction for brainstem module
by Jacky Lee 13 May '16

13 May '16

Hi Eugenio, Yes please give me some advice on the matlab commands for this since I am not very familiar with matlab... Cheers, Jacky Hi Jacky, this is a good question, and unfortunately there isn't a great answer to it. The volume is computed upong a probabilitic segmentation of the voxels that is not written to disk (this is very similar to what happens with aseg.mgz and aseg.stats). In order to properly update the volume estimates, you would have to know the probability that the inpainted voxels belong to the brainstem as estimated by the algorithm, which we don't currently write to disk. Another option would be to toss the volumes given by the algorithm, and compute new volumes for all cases and brainstem structures using the hard segmentations. You would simply have to count the number of voxels labeled as midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. with Matlab (let me know if you need help with this). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee" <cyle...(a)gmail.com> To: "Freesurfer support list" <Freesurfer(a)nmr.mgh.harvard.edu> Sent: Monday, May 9, 2016 2:01:53 AM Subject: [Freesurfer] Manual correction for brainstem module Hi freesurfer experts, I have successfully run the brainstem module for some subjects. On visual checking, I can see there are voxels with T1 hypointense lesions mislabelled as non-brainstem tissue. I manually corrected them on the brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected volume of the brainstem substructures? Thanks. Regards, Jacky

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Freesurfer May 2016