Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Segmentation of hippocampal subfields on FS v6 stable data?
by ts+ml＠rcmd.org 30 Nov '18

30 Nov '18

External Email - Use Caution Dear FreeSurfer experts, we would like to use the 'Segmentation of hippocampal subfields and nuclei of the amygdala' feature [1] that is available in the development version of FreeSurfer. However, we already pre-processed all subjects from the study using recon-all from FreeSurfer v6.0 stable. Can we apply the hippocampal subfields methods to the data pre-processed with the stable version, or should we run recon-all again using the dev version before we proceed? Thanks, Tim [1] https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Using the SUIT atlas
by Nillo, Ryan Michael R 30 Nov '18

30 Nov '18

External Email - Use Caution Hi FreeSurfer users, I am using the SUIT atlas (http://www.diedrichsenlab.org/imaging/suit.htm) to parcellate the cerebellum.To ensure there are no problems with registration, the SUIT pipeline requires that the origin of the input images are centered at the anterior commissure. Does FreeSurfer have any tools to set this origin from the command line? Thank you for your help, Ryan Nillo Research Associate I UCSF Department of Radiology and Biomedical Imaging

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Two problematic participants -- unable to run recon-all
by Rosalia Dacosta Aguayo 30 Nov '18

30 Nov '18

External Email - Use Caution Dear Free Surfer experts, I have run recon-all for all my participants and I am editing the brainmask and making control points. I have seen that for two participants, Free Surfer were not run. I run those two participant again and I saw that they were stuck in the vertex correction, more than 30.000. I do not know how to cope with this problem and I would greatly appreciate any help with this. Would it be possible to upload these two subjects so you can inspect them and tell me what is happening with them? Best wishes, Rosalia

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Correspondence between regions of Harvard-Oxford & DKT atlases
by Tudor Popescu 30 Nov '18

30 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I have a network of interest described in terms of regions from the Harvard-Oxford atlas. I would next need to describe this network in terms of regions from the DKT (Desikan–Killiany–Tourville) atlas. I have not found hints of any correspondence table or script among the files in the dataverse.harvard.edu repository, nor in the Klein&Tourville 2012 paper. How is this sort of correspondence best established, in a way that also quantifies the transformation's accuracy (amount of overlap) for each parcelated region? Many thanks! Best wishes, Tudor

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Re: [Freesurfer] hippocampal subfield question
by Iglesias Gonzalez, Eugenio 29 Nov '18

29 Nov '18

External Email - Use Caution Dear Arkadiy, Technically you should do it after, but the changes will be tiny, so it’s probably fine to do it before (as long as you’re consistent across subjects). Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Maksimovskiy, Arkadiy" <AMAKSIMOVSKIY(a)mclean.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 29 November 2018 at 17:13 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal subfield question Dear Experts, I was wondering if it is important to wait for the manual edits to be done on a dataset before running hippocampal subfield analyses. I believe that recon-all processing is sufficient, and edits can be done in parallel. But wanted to make sure that they will not affect the nuclei/subfield segmentation. Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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hippocampal subfield question
by Maksimovskiy, Arkadiy 29 Nov '18

29 Nov '18

Dear Experts, I was wondering if it is important to wait for the manual edits to be done on a dataset before running hippocampal subfield analyses. I believe that recon-all processing is sufficient, and edits can be done in parallel. But wanted to make sure that they will not affect the nuclei/subfield segmentation. Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Pial surface error
by Miguel Ángel Rivas Fernández 29 Nov '18

29 Nov '18

External Email - Use Caution Hi Freesurfer devs, I´m doing a visual quality control of my pial and white matter segmentation using freeview and I noticed that several subjects could present an error in pial surface segmentation. I have attached two images. Is this an pial surface error? in that case, How can I fix it? maybe adding control points in order to extend the pial surface limit? Thanks Cheers, -- *Miguel Ángel Rivas Fernández*

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Neuroimaging staff scientist position
by bryon mueller 29 Nov '18

29 Nov '18

External Email - Use Caution The Department of Psychiatry at the University of Minnesota is seeking an experienced MR Neuroimaging Analyst to join our Discovery Program initiative. The successful candidate will join a team that will use MR brain imaging and other methods to advance the understanding of and improve treatment in mental health conditions such as psychosis, depression, and addiction. The Neuroimaging Analyst will be involved in all aspects of neuroimage, including collection of MRI data, assembly of comparison MRI data, development of computer modeling, creation of processing workflows and development of statistical analysis and report generation that produces quantitative metrics from computational models of the brain. Required Qualifications Include: • BA/BS plus at least 4 years of experience or advanced degree plus 2 years of experience. Will also accept a combination of related education and work experience to equal 8 years. • Demonstrated/documented excellent analytical and statistical skills • Ability and willingness to work safely within the MR environment • Experience with scientific neuroimaging data processing using standard packages (HCP, FSL, AFNI, etc) • Proficiency in at least one programming language (Python, MATLAB, Java, C++, etc) • Proficiency with the Linux operating system See https://hr.myu.umn.edu/jobs/ext/327198 for additional details on the position.

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lack of convergence when analyzing tbss-data with FreeSurfer's lme code
by Knut J Bjuland 29 Nov '18

29 Nov '18

External Email - Use Caution Dear Freesurfer Experts I used the FreeSurfer univariate lme_fit_FS.m on longitudinal DTI data (FA) from tbss, converted from the skeleton to a matlab matrix so as to be able to use the FreeSurfer lme code. However, the model fit converges in only 20 % of the cases, which is too low for me to be able to use these data. I would appreciate any suggestion as to how I can rectify this situation. How do I troubleshoot this in order to increase the convergence? Can I adjust the convergence epsilon (gradient's norm) in order to increase the number of iterations, is that possible and would that help? Best regards Knut J Bjuland PhD

1 1

Volume, area and thickness external analysis
by Miguel Ángel Rivas Fernández 28 Nov '18

28 Nov '18

External Email - Use Caution Hi FreeSurfer devs, Is there any difference bet I ran the recon-all several participants (using the command recon-all -subjid -all) and I want to out an external analysis using the volume, area and thickness measures of the Destrieux and Desikan-Killiany atlas. *Do these measures suffer any change if I add the qcache flag to the command* (i.e recon-all -subjid -all -qcache) or by contrary this flag is only necessary when the analysis is made using QDEC? I have this doubt because I saw that when I used the -qcache flag, Freesurfer make a smoothing of the images using a FWHM filter of 5,10,12. Thanks in advance, Cheers, -- *Miguel Ángel Rivas Fernández*

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Freesurfer November 2018