Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Structural resolution and longitudinal processing
by Angstadt, Mike 04 Apr '16

04 Apr '16

We have a large number of scans that have been processed through the standard cross-sectional stream. Subjects have a number of repeated scans, so we now want to take advantage of the longitudinal stream. When first beginning to run subjects through longitudinal template creation, we noticed a warning message in some cases in the log: ******************************************************************************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ******************************************************************************* Looking into it, there does indeed appear to have been a change in the reconstruction stream that led to images at different times during the study to have slightly different voxel dimensions, changing from 1x1x1.2 to 1.01x1.01x1.2mm voxels. Our question is if there is some way to fix this prior to starting the longitudinal stream but without having to redo the original cross-sectional processing and editing that has been completed? -- Mike Angstadt Research Computer Specialist / PANLab Lab Manager Department of Psychiatry / University of Michigan (734) 936-8229 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

2 3

white matter parcellation
by Holleran, Laurena 04 Apr '16

04 Apr '16

2 3

PostDoc Position - Deep Learning in Neuroimaging of AD - Barcelona
by Juan Domingo Gispert López 04 Apr '16

04 Apr '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. The full job description can be found here: https://fpmaragall.org/en/wp-content/uploads/sites/3/2014/07/BBRC_Researche… 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: 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

Freesurfer dev error
by Nathan Malitz 01 Apr '16

01 Apr '16

recently download and trying the dev version of freesurfer 6. it exited with this error #@# Cortical Parc 2 lh Fri Apr 1 13:41:04 AEDT 2016 /usr/local/freesurfer6/subjects/test/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 testphp lh ../surf/lh.sphere.reg /usr/local/freesurfer6/average */lh.CDatlas.2016-03-20* ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ GCSAread(/usr/local/freesurfer6/average/lh.CDatlas.2016-03-20): could not open file reading atlas from /usr/local/freesurfer6/average/lh.CDatlas.2016-03-20... No such file or directory mris_ca_label: could not read classifier from /usr/local/freesurfer6/average/lh.CDatlas.2016-03-20 No such file or directory recon-all -s test exited with ERRORS at Fri Apr 1 13:41:08 AEDT 2016 This file doesn't exist in the directory, neither does the rh one, is it called something else or missing from the build? I'd prefer not to download 9GB again, is it available by itself? any ideas? -- *Nathan Malitz* <http://www.miconsult.com.au/>

2 1

Labeled Nifti atlases
by Gregory Book 01 Apr '16

01 Apr '16

Are there any labeled nifti atlases that correspond to the freesurfer parcellation atlases output from recon-all? I'm basically interested in visualization of group results. -Greg

2 1

Mismatch in dimensions using mri_label2vol
by Afzal, Afsana 01 Apr '16

01 Apr '16

Hi, I'm using mri_label2vol with the parameters below but the output .nii volume has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension mismatch is causing issues in our gPPI pipeline. How can I generate a .nii output file with the 27307x1x6 dimension? mri_label2vol --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from preproc step) --label label_name.label --o label_name.nii --identity Thanks, Afsana ______________________________ 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

3 6

Longitudinal TRACULA - Error in path reconstruction
by Emad Ahmadi 01 Apr '16

01 Apr '16

Hi Anastasia, I hope you’re enjoying your evening! I’m doing longitudinal TRACULA analysis on two subjects, each having two time points. I have already taken the steps of longitudinal recon-all and trac-all -prep & -bedp. Now I’m trying to do trac-all -path, but it gives me an error that I cannot recognize. I would greatly appreciate your help. I’ve attached the log files and the config file. Thank you so much, Emad Emad Ahmadi, MD ----------------------------------------------- Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

2 3

Longitudinal recon-all fail
by Sneha Pandya 01 Apr '16

01 Apr '16

Dear experts, We are running longitudinal pipeline for bunch of our MS subjects. Longitudinal recon-all failed to create volumes and surfaces for few of our subjects. We ran cross-sectional and did all the edits on them and after that ran base script without any issues or errors. When we run longitudinal on them it runs recon-all fine without exiting with errors. However it did not create important surfaces and volumes. Please find attached log file for one of the longitudinal timepoints for details. Not sure why did they fail only for few of them as we have ran 100s of them with no issue earlier. Any advice will be of great help! Thanks, Sneha

2 3

I: FS-FAST bandpass filtering
by stdp82＠virgilio.it 01 Apr '16

01 Apr '16

2 1

tksurfer scale bar
by Michael Asghar 01 Apr '16

01 Apr '16

Hi Freesurfer I'm struggling with trying to edit the scale bar in tksurfer. Commands like 'set scalebar_bright 240' work, but draw_scalebar gives an invalid command error. I've tried redrawing, but it doesn't help. Basically, I want the black background to become white (can do it via convert -fill white -opaque black input.tiff output.tiff), but the numbers on the scalebar are invisible now - I need the scale bar text to be black. Also, I get two bits to my scalebar, e.g. negative values at the bottom from -5 to -3, then a grey gap and then positive 3 to 5 in hot colours. How do I get just the positive T values in a suitable distance (they are currently squeezed up at either side). Thanks! Michael This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

3 8

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