Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Start a nNew thread

mri_glmfit
by John Anderson 18 Mar '16

18 Mar '16

1 0

Per-vertex regression model
by Sophie Maingault 18 Mar '16

18 Mar '16

Hello FS experts, I would like to correlate for each vertex 2 anatomical variables (for example cortical thickness and surface area), i.e. doing a vertex-wise correlation between 2 maps for a cohort of subjects. Maybe it is possible with the command line mri-glmfit and with the argument "--pvr » for per-vertex regressors? Is that possible or not ? If yes could i have some extra information to use properly the command ? Thanks by advance, My best, Sophie Maingault - PhD Student IMN, Institut des Maladies Neurodégénératives, UMR 5293 Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université de Bordeaux Université de Bordeaux 146 rue Léo Saignat - CS 61292 - Case 28 33 076 Bordeaux cedex http://www.imn-bordeaux.org/ <http://www.imn-bordeaux.org/>

1 0

Position Deep Learning of Neuroimaging in AD - Barcelona
by Juan Domingo Gispert López 18 Mar '16

18 Mar '16

The Barcelonaβeta Brain Research Centre (BBRC) welcomes applications for a full-time research position to develop deep learning methods to predict the onset of Alzheimer’s disease and its preclinical stage based on neuroimaging and other wet biomarkers, as part of its clinical research program. Qualifications: - PhD in Neuroscience, Medicine, Computer Science, Bioengineering or related disciplines (It is mandatory for the candidates to hold a PhD) - Proven experience in modelling and/or deep learning is required. - Strong understanding of the biological basis of AD and the course of AD biomarkers is needed. - Experience in neuroimaging and/or genetic data analysis would be positively considered. - Proven record of first authorship and co-authorship on scientific is required. Skills: - Experience working with large and multidisciplinary data sets is required. - Database manipulation skills, with strong attention to detail. - Proven ability to lead and orientate a team of computer scientists - Interest in joining a non-profit organization with a mission of high social impact. - Strong interpersonal skills (empathic and focused team-worker). - Ability to think independently and work collaboratively. Benefits: - Starting date: Second quarter 2016. - The research position is scheduled initially for two years (open to renewal). - Salary will depend on experience. In order to apply: To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: cminguillon(a)fpmaragall.org Deadline for submitting applications: April 29th 2016. -- Aquest missatge i els seus annexos poden contenir informació confidencial i exclusiva per al destinatari. El seu contingut no constitueix un compromís per part de l'emissor. Si rep aquest missatge per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent. Gràcies per la seva col·laboració. *This message and attachments may contain confidential and exclusive information intended only for the individual named. The content of this message does not imply any commitment by the sender. If you have received this e-mail by mistake, please delete it before reading or distributing and notify the sender. Thank you for your cooperation.*

1 0

mri_robust_register question
by Ji Won Bang 17 Mar '16

17 Mar '16

Dear. All. Hi. How are you? It might be a very naive question, but your advice is greatly appreciated! I'm trying to register 2 T1s obtained from 1 subject on different days and then register the functional scans to their corresponding T1s (registering the functional scans to the same day's T1). By doing so, I expect to get everything into the same space. (Each subject was scanned twice on two different days etc., day1 and day2) After running mri_robust_register onto day2's T1 as targetting day1's T1, I get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run preproc-sess(that does registration as well) onto day2's functional scans. Is there a way to make preproc-sess do register functional scans of day2 to v2to1.mgz(of day2 that's created by mri_robust_register), not the original 046.mgz? The commands that I run are: recon-all -s $SUBJECT -all mri_robust_register --mov /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale --satit preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force -fwhm 0 Please feel free to give me any advice! Thank you very much. Best, Ji Won

3 4

HIRING: Research Assistant
by Rockers, Elijah D. 17 Mar '16

17 Mar '16

Hello, The Houston Methodist Research Institute is hiring for a research assistant position. Please see the attached document for details. Please also note that candidates must be able to work in the city of Houston day-to-day. If you are interested in applying, please follow the instructions enclosed. Thank you, Elijah Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

1 0

Post-doctoral position available – Human Neurocognitive Aging
by Arnold Bakker 17 Mar '16

17 Mar '16

Post-doctoral position – Human Neurocognitive Aging The Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Division of Psychiatric Neuroimaging (PI: Arnold Bakker, Ph.D.) has a vacancy for 1-2 postdoctoral scholars to perform federally-funded research in the areas of learning and memory, aging, dementia and depression using human functional neuroimaging methods. As part of the research team, the candidate will be responsible for the design and implementation of behavioral and imaging experiments aimed at assessing learning and memory performance, or the effects of depression on learning and memory and cognition, broadly in both young and older adults and in individuals with memory complaints or mild cognitive impairment. Our studies focus primarily on the role of the medial temporal lobe and particularly the hippocampus in memory function, age- and disease-related memory impairment and neuropsychiatric conditions. We are also interested in neural network approaches to learning and memory, cognitive aging and intervention using studies of resting state activity and functional connectivity. The Division of Psychiatric Neuroimaging is affiliated with the Johns Hopkins Alzheimer’s Disease Research Center (JHADRC), the Division of Geriatric Psychiatry and Neuropsychiatry, the Kirby Center for Brain Imaging, the Center for Imaging Science (CIS) and the HOPE4MCI study. These affiliations and the Johns Hopkins community in general provide a rich and unique environment for collaboration and education for candidates interested in learning and memory in aging and disease, and neuropsychiatry. The successful candidate will have a strong background in cognitive neuroscience and will have significant experience with functional MRI, as well as a background in learning and memory. A Ph.D. in Neuroscience, Cognitive Science or Psychology is required. The successful candidate should also have excellent writing and communication skills and be willing to learn new MRI analysis methods. Salary will be dependent on the experience of the individual candidate. To be considered, please send a letter of interest including a brief description of research interests, a curriculum vitae including a record of research accomplishments, and the names of three professional references to Dr. Arnold Bakker (abakker(a)jhu.edu<mailto:abakker@jhu.edu>). -- Arnold Bakker, Ph.D. Division of Psychiatric NeuroImaging Department of Psychiatry and Behavioral Sciences The Johns Hopkins University School of Medicine 600 N. Wolfe Street / Phipps 300 Baltimore, MD 21287 Phone: 410-502-6944 | Fax: 410-614-3676

1 0

ID not identified on surface file
by João V. Dornas 17 Mar '16

17 Mar '16

Dear Friends, I need to 3D render the AAL parcellation volume, with labels (in annotation file) for each ROI. My AAL volume is on MNI152 standard space, with 2mm 91x109x91, as well my results volumes. I used the following command to generate my surface files from my AAL volume. mri_vol2surf --mov aal2std.nii.gz --reg cvs_avg35_inMNI152/mri/transforms/reg.mni152.2mm.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.aal2std-1mm_surf.mgz —reshape mri_vol2surf --mov aal2std.nii.gz --reg cvs_avg35_inMNI152/mri/transforms/reg.mni152.2mm.dat --projdist-max 0 1 0.1 --interp nearest --hemi rh --out rh.aal2std-1mm_surf.mgz --reshape Then I tried to create my labels using the following command: mri_cor2label --i lh.aal2std-1mm_surf.mgz --surf cvs_avg35_inMNI152 lh --id 75 --l lh.Pallidum_L I run this command for each one of the 90 ROIs on AAL volume. My problem is that when I execute the last command specifically for Pallidum, both Left and Right (IDs 75 and 76), I found this error: $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.aal2std-1mm_surf.mgz Loading cvs_avg35_inMNI152/surf/lh.white Scanning the volume Found 0 label voxels ERROR: found no voxels matching id 75 It seems that I loose some voxels when I convert from volume voxels to surface vertexes. Do you know what could be happening? I appreciate any help you could give to us. Thanks very much, best regards, -- João V. Dornas Phd student in Neuroscience Cognitive Biology Group, Institute of Biology Otto von Guericke University, Magdeburg Germany

1 0

FreeSurfer 6.0
by Elisabeth Paul 17 Mar '16

17 Mar '16

Dear ladies and gentlemen, for a research project I need to measure the volume of the different hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if so, when will it be released? If it is already released, could you tell me where to find it? Thank you very much in advance. Kind regards, Elisabeth Paul

5 9

gnumeric file
by Caroline Beelen 17 Mar '16

17 Mar '16

Hi FS team, Sorry for these rather basic questions... I'm not sure whether the gnumeric file is an ascii file (see mails below). Attached you'll find the file. It seems the case when you open it in the terminal screen that the nr's look fine (with command cat). However as soon as you type the command gnumeric and so on, it creates a wrong table from the start (see file attached). Can I somehow change this? I have an additional question: I was looking at the Qdec info (tutorial) and I am not totally sure how to create the table.dat file... Where to get the volume measures from, if you'd like to include those? The statistical folder (where the tables are from)? Thank you for responding in advance. Kind regards, Caroline -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Douglas N Greve Verzonden: dinsdag 8 maart 2016 0:24 Aan: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Onderwerp: Re: [Freesurfer] mean thickness the table file lh.aparc.thickness.table should be an ascii file. when you look at it with cat/more/less, what do you see? Can you send that table file? On 03/07/2016 04:33 AM, Caroline Beelen wrote: > Hi Bruce, > > I'm a beginner in FS, so I just followed tutorial instructions for generating the files carefully... > I generated it by typing in for instance (after recon-all process was > done): aparcstats2table --hemi lh --meas thickness --subjects A01_T1 > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table followed by > the command: gnumeric lh.aparc.thickness.table > > It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770 > CPU @ 3.4GHz x 8) > > Attached the log file (A09). > > Thank you very much! > > Greetings, Caroline

3 7

Re: [Freesurfer] Reading values from overlays with PETcoreg
by Elijah Mak 17 Mar '16

17 Mar '16

Dear Doug, Is it possible to use BP SUVR PET that have been registered to T1 for this gtmseg workflow? You mentioned that the mean TAC should be used as the input. 2 quick questions: What's mean TAC and why? Thanks. Best Wishes, Elijah

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