Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

Re: [Freesurfer] orig.mgz versus T1.mgz
by C.P.E. Rollins 02 May '18

02 May '18

External Email - Use Caution Just to clarify, by that I mean would the NIFTI converted from orig.mgz (with mri_convert) be different than the NIFTI produced by dcm2niix from the raw DICOMs? Thanks, Colleen -------- Original Message -------- Subject: orig.mgz versus T1.mgz Date: 2018-05-02 10:24 From: "C.P.E. Rollins" <cper2(a)cam.ac.uk> To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Thanks Bruce. Will the orig.mgz file be different from the raw data in any significant way? Thanks again, Colleen -------- Original Message -------- Subject: orig.mgz versus T1.mgz Date: 2018-04-30 11:54 From: "C.P.E. Rollins" <cper2(a)cam.ac.uk> To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Dear Freesurfer developers, A collaborator shared with me Freesurfer outputs, but I would like to some analyses requiring the scans in NIFTI format. I understand mri_convert should do the trick for this, though I was wondering whether I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 NIFTI files. Many thanks, Colleen

2 1

Two year postdoc in Cambridge UK
by Anne-Laura Van Harmelen 02 May '18

02 May '18

External Email - Use Caution Dear Colleagues, I would like to draw your attention to a postdoc vacancy in Cambridge on the MQ funded HOPES<https://www.mqmentalhealth.org/news-blog/post/hopes-help-overcome-and-preve…> project<https://www.mqmentalhealth.org/research/profiles/help-overcome-and-predict-…>. The MQ HOPES role is a two year post available from May 2018. The candidate will be part of a large collaborative effort (The HOPES project) that aims to elucidate neurobiological mechanisms and behavioural phenotypes that underlie risk for STBs during adolescence, a critical period of development when STBs emerge. HOPES is a consortia of researchers across the world including Yale and Orygen (Melbourne), and is led by the University of Cambridge. The candidate will work together with researchers from those institutions to examine the neural underpinnings of adolescent suicide behaviour. The candidate will investigate the neurobiological underpinnings of youth STBs (suicidal thoughts and behaviours). This will include pooling existing large, cross-sectional and longitudinal international neuroimaging datasets of youth with a range of psychiatric disorders to investigate a model that integrates brain structure and functioning as well as cognitive and social environmental factors to predict current and future STBs. The candidate will use multivariate statistics (such as Structural equation modelling) to do so. Candidates should have a PhD or equivalent, in a related subject such as Neuroscience, Psychology, Psychiatry or otherwise relevant subject areas or be very close to completion/award of same prior to their appointment to the post. The funds for this post are available for two years in the first instance. The advert can be found here<http://www.jobs.cam.ac.uk/job/17288/> Very best, Anne-Laura van Harmelen av391(a)cam.ac.uk<mailto:av391@cam.ac.uk> Dr Anne-Laura van Harmelen Royal Society Dorothy Hodgkin Fellow Senior Research Associate Department of Psychiatry University of Cambridge 18b Trumpington road Cambridge, CB2 8AH +44 (0)1223-465245 www.annelauravanharmelen.com<http://www.annelauravanharmelen.com/> @DrAnneLaura

1 0

orig.mgz versus T1.mgz
by C.P.E. Rollins 02 May '18

02 May '18

External Email - Use Caution Thanks Bruce. Will the orig.mgz file be different from the raw data in any significant way? Thanks again, Colleen -------- Original Message -------- Subject: orig.mgz versus T1.mgz Date: 2018-04-30 11:54 From: "C.P.E. Rollins" <cper2(a)cam.ac.uk> To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Dear Freesurfer developers, A collaborator shared with me Freesurfer outputs, but I would like to some analyses requiring the scans in NIFTI format. I understand mri_convert should do the trick for this, though I was wondering whether I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 NIFTI files. Many thanks, Colleen

1 0

Mapping left to right for fsaverage 5 (ico5)
by Davide Tabarelli 02 May '18

02 May '18

External Email - Use Caution Dear all, I have a question about left-right sphere based co-registration. I have a scalar quantity defined on the fsaverage5 ico5 surfaces and I would like to map left to right hemisphere. I’ve computed left_right registered spheres by running following commands in the fsaverage5 folder: mris_curvature -w lh.white mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right mris_curvature -w rh.white mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right As far as I understood, the lh.sphere.left_right contains the lh mesh warped to be consistent with the anatomical landmarks on rh. Thus in mapping or interpolating, I have to use vertices in lh.sphere.left_right and map/interpolate them to rh.sphere. Is that correct? There is a better way to do that? Moreover I cannot find information about the “thresh” and “distances” arguments in mris_left_right_register help. Maybe those options are not fine for the fsaverage ico5 ? Thank you all in advance. D. — Davide Tabarelli, Ph.D. Center for Mind Brain Sciences (CIMeC) University of Trento, Via delle Regole, 101 38123 Mattarello (TN) Italy

1 0

Freeview surface volume misalignment
by Kambiz Tavabi 01 May '18

01 May '18

External Email - Use Caution Hi all, I am not sure why I occasionally hit this issue, but for reasons, I don't know the surfaces and the corresponding volume in Freeview are misaligned. This is not the case in tkmedit. In this particular case the surface(s) were created using: (1) mri_convert input.nii output.mgz (2) fsl_rigid_register -r rawavg.mgz -i output.mgz -o output_reg.mgz (3) mri_make_bem_surfaces [image: alignment.png] Thanks in advance. Kambiz

1 0

question about hippocampal vols
by Anik Dar 01 May '18

01 May '18

External Email - Use Caution Hi All, I have run quantifyHAsubregions.sh hippoSf <T1>-<analysisID> <output_file> <OPTIONAL_SUBJECTS_DIR> and have the volumes for the hippocampal subfields. From which of the following segmentation files are these volumes computed from ? lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.CA.mgz lh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.FS60.mgz lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.HBT.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.HBT.mgz lh.hippoAmygLabels-T1.v21.mgz Please let me know. Thanks Ani

2 3

Call for PRIME-MICCAI 2018 papers **1st International Workshop on PRedictive Intelligence in MEdicine **
by Islem Rekik 01 May '18

01 May '18

External Email - Use Caution Dear all, We present the 1st edition of the *PR*edictive *I*ntelligence in *ME*dicine (*PRIME*) workshop in conjunction with *MICCAI 2018* in Granada, Spain. The main aim of PRIME is to propel the advent of predictive models in a broad sense, with application to medical data. We hope that PRIME workshop becomes a nest for high-precision predictive medicine, one that is set to transform multiple fields of healthcare technologies in unprecedented ways. We welcome contributions fitting the following research topics (*but not limited to*): Modeling and predicting disease development or evolution from a limited number of observations; Computer-aided prognostic methods (e.g., for brain diseases, prostate cancer, dementia, acute diseases, neurodevelopmental disorders); Forecasting disease/cancer progression over time; Predicting low-dimensional data (e.g., behavioral scores, clinical outcome, age, gender); Predicting the evolution or development of high-dimensional data (e.g., shapes, graphs, images, patches, abstract features, learned features); Predicting high-resolution data from low-resolution data; Predicting image modality from a different modality (e.g., data synthesis); Predicting missing data (e.g., data imputation or data completion problems). --------- *** Paper Submission *** Paper submission deadline, June 11 via https://cmt3.research. microsoft.com/PRIME2018 <https://cmt3.research.microsoft.com/PRIME2018> <https://cmt3.research.microsoft.com/PRIME2018> For more information visit http://tiny.cc/prime2018 <http://tiny.cc/prime2018> <http://tiny.cc/prime2018> *Flyer (if not attached, **check)*: http://basira-lab.com/wp- content/uploads/2018/01/PRIME-MICCAI_2018_flyer_final.pdf <http://basira-lab.com/wp-content/uploads/2018/01/PRIME-MICCAI_2018_flyer_fi…> <http://basira-lab.com/wp-content/uploads/2018/01/PRIME-MICCAI_2018_flyer_fi…> --------- *** Important dates *** - Paper submission deadline: June 11, 2018 - Author notification: July 15, 2018 - Camera-ready: July 20, 2018 - Workshop date: September 16, 2018 --------- *** Keynote Speakers *** Prof Dinggang Shen (University of North Carolina) Dr Ender Konukoglu (ETH Zurich) Dr Ipek Oguz (University of Pennsylvania) Dr Kilian M. Pohl (Program Director in the Center of Health Sciences at SRI International) --------- *** Highlights *** - Proceedings will be published in *Springer Lecture Notes in Computer Science (LNCS)* (EI, ISTP indexed). - The PRIME 2018 *Best Paper Award* will be granted to the best overall scientific paper. If you have any questions, please contact me, Islem Rekik at irekik(a)dundee.ac.uk Please feel free to forward this email to those who might be interested. We are looking forward to your PRIME submissions! Sincerely, The PRIME 2018 Chairs ---------- Islem Rekik (University of Dundee, UK), Point of Contact: irekik(a)dundee.ac.uk Gozde Unal (Istanbul Technical University, Turkey) Ehsan Adeli (Stanford University, US) Sang-Hyun Park (Daegu Gyeongbuk Institute of Science and Technology, South Korea)

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer May 2018