Freesurfer August 2022

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120 discussions

Van Essen/Glasser Lab Connectome Post-Doc Opportunity
by Glasser, Matt 29 Aug '22

29 Aug '22

External Email - Use Caution Hi FreeSurfer Users, We have a Connectome-related Post-Doc position available immediately in the Van Essen/Glasser lab. Please see the below posting. Feel free to forward to anyone you know who might be interested. Thanks, Matt. Postdoctoral Research Associate (CIRC, Van Essen/Glasser Lab) Position Summary The Adult Aging Brain Connectome (AABC) project has a fully funded and immediately available opening for a Postdoctoral Research Associate within the Informatics, Data Analysis, and Statistics Core (IDASC). This position is based in the Van Essen/Glasser Lab<https://secure-web.cisco.com/1WZvYXfgvuq53cGKgRSB25U5IkW7IQITwIczQxqUnhtsuz…> within the Computational Imaging Research Center (CIRC)<https://secure-web.cisco.com/1uaguVfyCEHq6WsESzrPjgSjZD2SaiuQ4MEvw4TyDAbAUm…> of Mallinckrodt Institute of Radiology (MIR), at Washington University School of Medicine in St. Louis. The AABC is a longitudinal extension of the Human Connectome Project in Aging that seeks to determine the structural and functional brain connectivity trajectories associated with vulnerability and resilience to developing late life dementia. Among the IDASC’s primary aims is to continue the Human Connectome Project (HCP)’s<https://secure-web.cisco.com/1TJ34rCWxWlzejI-JhfFwndMEDUQ2t4IHs7v-4AbXCZ2U3…> innovative neuroimaging methods development, with a particular focus on HCP-Style data analysis optimized for generating multi-modal imaging data phenotypes from longitudinally acquired scans. The selected candidate will have access to the HCP’s large consortium of world experts in multiple neuroimaging domains and ample opportunities to publish research methods and scientific findings in high impact academic journals and at premier scientific conferences. The Van Essen/Glasser lab’s senior staff are highly experienced, having developed much of the HCP’s software themselves, and are excellent at training new users of HCP-Style brain imaging methods. The CIRC hosts a vibrant community of postdoctoral and graduate student trainees together with multiple additional faculty and state of the art computational resources. The position is renewable annually based on performance, and funding is available for up to 4 years. Information on being a postdoc at Washington University in St. Louis can be found at postdoc.wustl.edu/prospective-postdocs<https://secure-web.cisco.com/1Gg_mxIwFSYfuZnIdHM-VK6rM2TfCf8l5Su1ssLBefTvaR…>. Primary Duties & Responsibilities * Develop and aid in the design of longitudinally optimized HCP Pipelines for multi-modal neuroimaging data analysis, including structural, functional, diffusion, and Arterial Spin Labeling (ASL) modalities. * Develop and aid in the design of HCP Pipelines for deriving multi-modal Imaging Data Phenotypes (IDPs) at the neuranatomical levels of brain areas, functional networks, and white matter tracts. * Use the longitudinally optimized multi-modal IDPs to carry out statistical analyses relating these IDPs to behavioral and biological measures relevant for cognitive and dementia outcomes. * Serve as first author for scientific publications and presentations with primary responsibility for preparing, submitting, revising, and presenting such work. * Be a good citizen in the lab/center and follow all applicable institutional policies. Required Qualifications Ph.D. in the field of biomedical engineering, imaging science, neuroscience, or a related field. Preferred Qualifications * Record of accomplishments in at least one of the following fields: neuroimaging, medical image analysis, or a related field. * Proficiency in quantitative analytical methods and computer programming in a Unix/Linux environment (e.g., shell scripting, Matlab, Python). * Prior experience with HCP-Style methods, HCP data, and/or the HCP Pipelines. * Prior experience with the commandline implementations of FSL, FreeSurfer, and Connectome Workbench softwares. * Excellent interpersonal and communication skills, both verbal and written. * Ability to work effectively both independently and within a multidisciplinary team. Salary Range Base pay is commensurate with experience. Applicant Special Instructions To apply, please contact Dr. Matthew Glasser with the following: * Cover letter describing your research interests. * Current curriculum vitae. * Name and contact information for three references who are familiar with your work. * Two or three representative publications. Matthew F. Glasser, M.D., Ph.D. Instructor Washington University School of Medicine Mallinckrodt Institute of Radiology E-mail: glasserm(a)wustl.edu<mailto:glasserm@wustl.edu> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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samseg inputs
by Dilek Özkan 29 Aug '22

29 Aug '22

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have read the paper, accordingly I want to try the t1-flair combination in terms of the accuracy. Do you have any experience with T1 images with contrast agent? I couldn't find anything related to those in the paper. Can I use t1 with contrast in a few patients if the patient doesn't have t1 image without contrast agent? i will declare this situation in the results. Best, Dilek

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Request for the password to expand the ova.7z for FS on VirtualBox
by 김한기 29 Aug '22

29 Aug '22

External Email - Use Caution Hello, I am a post-graduate student at Ajou University, School of Medicine, Department of Brain Science in South Korea. I am planning to use Freesurfer on VirtualBox! I would be grateful if you could tell me the password to expand the .7z file. Thank you so much

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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
by Trolle, Carl 28 Aug '22

28 Aug '22

Hi! Thank you, yes, using the Freesurfer dev-version available through the Martinos cluster produced the desired result with the Destrieux-atlas. I’ve been using the 711-version throughout, I hope that I specified the version in my first email. Is it possible to use these commands (mris_register and mris_ca_label) as expert option files during recon-all to correct the incorrect parcellation of the annot.aparc-file? If so, would that also require a later Freesurfer vesion than what we’ve been using? Kind regards, Carl

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Re: [Freesurfer] Freeview quitted unexpectedly
by fsbuild 28 Aug '22

28 Aug '22

External Email - Use Caution Hello Danesh, Try putting your license.txt file into your home directory and setting the environment variable FS_LICENSE to point to it. $ export FS_LICENSE=$HOME/license.txt$ cd $HOME$ cat $FS_LICENSE… you should see your email address used to register for the license plus other license code … Then try source’ing the Freesurfer script to setup the environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.3.2-20220804-6354275 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.3.2 FSFAST_HOME       /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjects MNI_DIR           /Applications/freesurfer/7.3.2/mni Then try running freeview with no arguments and it should bring up an empty window,$ which freeview/Applications/freesurfer/7.3.2/bin/freeview$ freeview - R. On Aug 23, 2022, at 10:36, Danesh kajbaf <daneshkajbaf(a)gmail.com> wrote:        External Email - Use Caution        Dear support team,After installing Freeview, I tried to load a volume, while checking how it works with samples, from the subject folder in the Freesurfer folder. Unfortunately after choosing the file, Freeview crashed out and popped up an error message “Freeview quitted unexpectedly!”. I tried with other files and the same happened again, while all these files could be loaded by FSLeyes, so the problem was not with data. I run Apple Diagnostics to find if the problem was with the hardware or OS and there was no issue.Attached is the text file of the error as I copied and pasted it so it might help to tackle the problem.Freeview 2.0 is installed ,via the Freesurfer 7.3.2 package installer, on macOS Catalina 10.15.7, and my MacBook Pro’s part number is A1706.Regards,Danesh<Error txt.rtf>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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Problem with longitudinal processing
by Wittayer, Matthias 28 Aug '22

28 Aug '22

External Email - Use Caution Dear community, I tried to process MS- patient's MRIs (mostly same scanner, same settings) Longitudinally over a long period of time. I first processed all timeponits crosssectionally and then initialised the base image by recon- all - base TP1 TP2 TP3 etc. Now I am trying to run label based morphometry and it seems some areas are growing rather than shrinking. Which is highly unlikely. I tried to exclude timepoint of a relapse to rule out perifocal edema interfering with measures but the problem remains. Did anybody have the same problem? Is it a potential bug or just a garbage in garbage out problem (though I don't know what would be wrong with our scans)? Does it make sense to make an intermediate template for two timeponits only? I.e. recon- all -base TP1 TP2; recon -all -base TP2 TP3 ... and use them for longitudinal runs? Thanks for your opinions. Best Matthias

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T1 gadolinium
by Gonzalo Rojas Costa 28 Aug '22

28 Aug '22

External Email - Use Caution Hi: SynthSeg is useful for T1-GD volumetric images? Another algorithm, software? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1I2XJrWdFnZxY-dYDbiZg0PV2H4bghSVXCQk63X1VSya6a… https://secure-web.cisco.com/13zfZJFRpU2hG9Abh2YAV0LPmd1V6ff2BdGkKw7NLlRJY9… https://secure-web.cisco.com/1p2HQdyHZcPFsEa80XIMcd_JLnEOosZMvxjlvKnim0-NVW… http://secure-web.cisco.com/1t-sL6HvQklTyxVFyP8KzIDoaaMPtJscszD92RHMNQuJE8k… https://secure-web.cisco.com/1DKuT3Zodsn-rxAY5cLCK0zkUQtPg9820KtzYLjm_ymXLa…

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Inflating norm.mgz
by Elizabeth Haris 28 Aug '22

28 Aug '22

External Email - Use Caution Hi developers! I am running connectivity analyses for amygdala subregions using images from a 7T scanner. I am wanting to transform the amygdala segmentations into fMRI space (1.6 iso voxel) for individual analyses and am looking for the best way to do this. Would it make sense to: 1. Inflate the norm.mgz brain, then run the segmentHA_T1.sh script, and then extract the individual segments. 2. Run the segmentHA_T1.sh script as usual, but inflate the rawavg brain. Then, warp the full segmentation to fit the rawavg space (using mri_convert -input <original_amygdala_segment> -at -rt nearest -reference <inflated_rawavg_brain> -output <inflated_amygdala_segment>), and then extract the individual segments. Does it matter which way I do it? Is there another way to do it that would be better? Many thanks, Elizabeth

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Shift in cortical parcellation, issues with previously suggested solution
by Trolle, Carl 28 Aug '22

28 Aug '22

Ok. I'm trying to attach a copy of the output I get in the terminal-window. The commands I've been running for the mris_register and mris_ca_label are "mris_register -L subject/label/?h.central_sulcus.label FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sphere FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif subject/surf/?h.sphere.reg" and "mris_ca_label subject ?h subject/surf/?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs subject/label/?h.aparc.a2009s.annot". I hope I'm sending what you asked for, otherwise I'll be happy to correct this. Kind regards, Carl

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Freesurfer August 2022