Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

Neighborhood thickness in a 10mm radius
by Dorian P. 31 Jan '17

31 Jan '17

Hi Freesurfers, Thank you for the help you provide through this list. Is there a way to get, for each vertex, the identify (or thickness values) of the surrounding vertices in a 10mm radius? The command mris_convert has the '-v' option, but that produces only 5-6 vertices and there is no option to query a particular radius. I imagine this can be done manually outside Freesurfer by first identifying the neighbors for each vertex based on the coordinates, then getting the respective thickness value, but I wanted to check whether there is any easier way or any advice on how to proceed. Dorian

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Binary images multiplication
by Sahil Bajaj 31 Jan '17

31 Jan '17

Hi, I would like to multiply two binary images (standard brain image with an ROI) using fslmaths (or may be using some other way) command. Although both are in standard space but image dimensions are different. I was wondering if there is any way I can do that without any co-registration step. 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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Postdoctoral Position in Division of Neurotherapeutics at MGH/HMS (Boston, MA)
by Afzal, Afsana 31 Jan '17

31 Jan '17

Hi everyone, The Division of Neurotherapeutics at Massachusetts General Hospital (Boston, MA) has an open postdoctoral position. The posting is below: NEUROIMAGING POSTDOCTORAL POSITION IN DIVISION OF NEUROTHERAPEUTICS AT HARVARD MEDICAL SCHOOL/ MASSACHUSETTS GENERAL HOSPITAL The Division of Neurotherapeutics at the Massachusetts General Hospital is looking for a neuroimaging postdoctoral fellow to join the research group of Drs. Darin Dougherty MD, Thilo Deckersbach PhD and Alik Widge MD PhD. Overview Research projects will focus on developing pipelines for multi-modal MRI analysis with the aim of investigating psychopathology along transdiagnstic domains under the TRANSFORM DBS project, using task-based and resting-state fMRI and structural MRI data. The post-doctoral fellow will have the opportunity to collaborate and work with an interdisciplinary team of clinicians, neuroscientists and engineers and have significant opportunities to advance their career. Your Profile We seek a postdoctoral candidate with a Ph.D. in psychology, neuroscience, or related discipline with an interest translational neuroscience with a strong background in Python, Matlab, or R. The ideal candidate would have extensive knowledge of computational neuroimaging. Expertise in cognitive modeling, graph theory, or machine learning is also highly desirable. Knowledge of common neuroimaging software, especially FreeSurfer and FSL, is also appreciated. Interest in understanding mechanisms underlying major psychiatric disorders and enthusiasm for working with psychiatric populations is necessary. Highly motivated individuals with a record of productive research are encouraged to apply. Benefits Benefits of this postdoctoral position include (1) access to numerous sets of high-quality, multi-modal MRI data; (2) opportunities to analyze and publish on these datasets; (3) mentoring for career development; and (4) access to imaging experts from around the world and to state-of-the-art tools for the development of neuroscientific and clinical research at the Martinos Center. Lab Description The Division of Neurotherapeutics at MGH is a multidisciplinary translational neuroscience group located at the Athinoula A. Martinos Center for Biomedical Imaging in Charlestown, MA. Our focus is on neurotherapeutic interventions for severe, treatment-resistant psychiatric illnesses, particularly for major depressive disorder, obsessive compulsive disorder, anxiety disorders, and eating disorders. Our research spans both mechanistic studies, clinical trials, and device-based interventions employing a variety of techniques, including neuroimaging and electrophysiology. We also provide clinical services and surgical treatments for psychiatric illness. Our work utilizes functional and structural magnetic resonance imaging (fMRI), positron emission tomography (PET), electroencephalography (EEG), magnetoencephalography (MEG) to further understanding of psychiatric illness and treatment. We use transcranial magnetic stimulation (TMS), vagus nerve stimulation (VNS) and deep brain stimulation (DBS) as tools to both treat disease and understand the neural correlates of mental illness. Lab Website: http://www.massgeneral.org/psychiatry/research/researchlab.aspx?id=1659 Contact: Afsana Afzal - aafzal(a)mgh.harvard.edu ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Centre on label double click in freeview
by Chris Adamson 30 Jan '17

30 Jan '17

Thanks for putting in the "centre over label" feature in Freeview. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Re: [Freesurfer] Edits to Aseg in the Longitudinal Stream
by Antonin Skoch 30 Jan '17

30 Jan '17

Dear Tamara, I presume that you edited your reconstruction in "Long" (=3rd) stage of longitudinal stream (recon-all -long )?. If this is the case, I think that you can use recon-all -long tpN1 templateID -autorecon2-wm -autorecon3 or recon-all -long tpN1 templateID -autorecon2-noaseg -autorecon3 (effectively both commands are equivalent, they run the same steps). where tpN1 is name of your directory defining cross-sectional recon (1st stage) and templateID is name of directory of your base (created in stage 2). See https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#RerunningEditsC… Regards, Antonin Skoch Hello, After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes:recon-long -autorecon2-noaseg -subjid <Subj_ID> I assume the -subjid is the name of the edited time point and <Subj_ID> is the name of the recreated volumes? Thank you, Tamara

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Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3
by Antonin Skoch 30 Jan '17

30 Jan '17

Dear Matthieu, your issue is discussed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html and indirectly also here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51111.html I think that with V6.0 you maybe could get slightly better results (some bugs have been fixed and some tools improved), but definitelly it would require to re-inspect your data after reprocessing. Antonin Skoch Dear experts, Does anybody could answer my last request ?Best, Matthieu 2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte <matthieuvanhou...(a)gmail.com>: > Dear FS's experts, > > I have run all my cross with v5.3 and hesitate to run all longitudinal > process with v6. Does that make sense and will improve the process or would > it be risky to do this ? > > Many thanks for your lights ! > > Best regards, > Matthieu

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Fw: Issue with creating inflated surface - poor surface registration?
by Saltzman, David 30 Jan '17

30 Jan '17

Hello FreeSurfer Developers, We have attempted to run the standard recon-all pipeline on multiple MRI datasets, and seem to be encountering the same error. While the recon-all log does not indicate there are any errors (so far as we can tell as novices), when we look at the inflated surfaces, there is clearly some problem creating the inflated surface, in that the hemispheres appeared to be mirrored. For the purpose of simplicity, we will include the log and scan information for the most recent anatomical scan we have to run the recon-all pipeline on. I believe the attached screenshot (anterior coronal view) will make the issue more apparent. 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OS 10.12 3) recon-all.log: see attached 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2 -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner) 5) Scan information: Data Axes Tilt: Oblique (15.784 deg. from plumb) Data Axes Approximate Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Right-to-Left [-orient ASR] R-to-L extent: -80.718 [R] -to- 94.282 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -188.767 [A] -to- 58.233 [P] -step- 1.000 mm [248 voxels] I-to-S extent: -186.650 [I] -to- 68.350 [S] -step- 1.000 mm [256 voxels] Any help would be tremendously appreciated! Thanks, David Saltzman Lab Manager Language and Brain Laboratory Department of Speech, Language, & Hearing Sciences University of Connecticut

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problem with qdec
by Eva Wiedemann 30 Jan '17

30 Jan '17

Dear freesurfer-users, I want to run a qdec analysis, comparing cortical thickness between two groups and using age and gender as nuisance factors. those factors are included in my data.table but when i want to chose the design i can only select gender as a discrete factor and not as a nuisance factor (see images attached). The second problem I have is, when displaying the results, I can't change the threshold. I can mark them but not change them. All the other buttons in the window work though. Thanks for your help in advance! Yours sincerely, Eva Wiedemann PS: I'm using freesurfer v.5.3.0 on Ubuntu 15.10.

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Edits to White Matter
by Gundel, Tristan J 30 Jan '17

30 Jan '17

Hello, I work in a lab that is currently using the Freesurfer algorithm to collect data from MRI images of individuals with Multiple Sclerosis. In order to increase the precision of our white matter masks we have combined your algorithm with ANTS, hoping to achieve more accurate surface volumes and aparc+aseg masks. Unfortunately we have had some issues when we edit our ANTS white matter mask (using value of 255) and then put it through freesurfer again, re-running recon-all (recon-all -autorecon2 -wm -autorecon3 -w <subID>). Our wm_surface and aparc+aseg mask do not change based on the edits we have made, and do not follow the white matter volume surface volume. How can we be sure that our white matter mask, and the edits we make to it, are considered in the creation of wm_surface and aparc+aseg mask? Please let me know if any of this is unclear and I will explain it in more detail. Thank you, Tristan

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Time Series Revision in FS-Fast
by pfannmoelj＠uni-greifswald.de 30 Jan '17

30 Jan '17

Dear Experts, I have a question concerning the evaluation of the time series in the FS-Fast stream. There is one time series for each vertex of a brain. Can single time points or series of time points be excluded from the analysis in the following way: Remove time point 10 from the time series of vertex 220 and time point 550 from vertex 42. This means a time point exclude file can not be used in my case. Can I achieve this removal by setting the value of the time points to not-a-number or something similar? Yours pfannmoe

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Freesurfer January 2017