Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

How to remove segments from white and left cerebral white matter and get cerebral white matters without these segments
by Ammar Shujaa 06 Sep '21

06 Sep '21

External Email - Use Caution Hello freesurfer developer, I have extracted the right and left cerebral white matter (label 2, and label 4) I just want to know how I can remove label 4, 43, 28, 60 (brown and purple labels) from the the right and left cerebral matter so that I can get the cerebral white matter without the segments corresponding to the labels 4, 43, 28, and 60. I am looking forward to hearing from you. Best regards,Ammar Shujaa Addin

2 1

Total Brain volume normalization
by Fabiola Macruz 06 Sep '21

06 Sep '21

External Email - Use Caution Hello Free Surfer developers, >From my understanding, the volumes provided in the aseg.stats document is not corrected by the head size. In order to do that, it is recommended to use the ITV and the label ID's: mri_label_volume -eTIV \ $sdir/transforms/talairach.xfm 1948 \ $sdir/aseg.mgz 17 53 However, I need the corrected volume of the Brain Segmentation Volume without Ventricles, the Total gray matter volume, Left hemisphere cerebral white matter volume, and Right hemisphere cerebral white matter volume, none of which have a label ID. Is there any way to obtain these corrected volumes in free surfer itself? Thanks, Dra. Fabíola Macruz MD from Faculdade de Ciências Médicas da Santa Casa de São Paulo PhD from Faculdade de Medicina do Hospital das Clínicas da USP Former Research Fellow from Stanford University Former Clinical Innovation Fellow/ Project Leader from Mass General Brigham Phone: + 1(650)686-0668 / + 55(11)99571-5906

2 1

Mask Correlation Analysis Area by Yeo Network
by Haley Park 06 Sep '21

06 Sep '21

External Email - Use Caution Hello, I would like to run a correlation analysis but limit the analysis area to three of the seven networks of the Yeo 2011 network parcellations. Would this be possible? Would I do it via a --mask option in mri_glmfit? Thank you, Haley

2 1

SAMSEG esitmation error
by achille.teillac＠chu-lyon.fr 06 Sep '21

06 Sep '21

External Email - Use Caution Dear experts, We are working with a large MRI dataset (FLAIR, T1) and we are performing SAMSEG pipeline to estimate lesion volumes. We computed the registration between the two input images and the resampling as advised in the SAMSEG page (mri_coreg and mri_vol2vol) which worked perfectly. However, when we do the visual chek on the segmentation after running SAMSEG, it is completely wrong for some subjects. By looking at corresponding mode01_bias_corrected.mgz and mode02_bias_corrected.mgz images, they are too cropped (centered on the cerebellum) compared to the original ones (3D_T1 .nii.gz and 3D_FLAIR.nii.gz). We also noticed a < RuntimeWarning: invalid value encountered in true_divide > during the burn-in phase (in the GMM.py code). Do you have any clue of what is happening with this cropping (can it be linked to the bias field estimation ?) and how we can correct it ? Thanks for your help and I can provide some screenshots of the cropped images to help visualize the issue. Best, Achille Teillac

2 1

How to cite Freesurfer
by Camargo, Aldo 03 Sep '21

03 Sep '21

External Email - Use Caution Hi Freesurfer group: How should I cite freesurfer in my manuscript ? Thanks a lot and have a nice day, Aldo

2 2

Python Surface API discussion
by Christopher Markiewicz 03 Sep '21

03 Sep '21

External Email - Use Caution Hi FreeSurfers, I wanted to reach out to this group about plans to create a new Python API for working with surface data in Nibabel. As you are all undoubtedly aware, surface meshes are too large and cumbersome to pack with data sampled on the surface, necessitating something like FreeSurfer's directory structure. We're looking to create a common API that would work with FreeSurfer directories, collections of GIFTI files, CIFTI-2 + WBspec, etc., to allow efficient access to the topology, geometry and sampled data as needed. We need input from users and developers of downstream tools who would like to work with these data. Non-Python developers are also welcome to share their experience and advice! I'd like to plan a meeting in the next couple weeks. I'm (slowly) trying to start discussions over at https://secure-web.cisco.com/18kV2cNFE9uq84UPL5TGr7HSq3wVmYRpi0JhnQnLHwSQ5x…. Please reach out over there or email me directly if you're interested in taking part in these discussions. On behalf of the Nibabel developers, -- Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University

1 0

Troubleshooting creating a new atlas
by Gibson,Cierra N 03 Sep '21

03 Sep '21

External Email - Use Caution Hello Freesurfer developers, I am attempting to create a new atlas for the freesurfer software that would allow me to analyze rat brain MRI images. I saw on the SurfaceRegAndTemplates page that I need to register and create an inflated template, but I am having trouble understanding how to do that. Could you possibly help, please? Thank you, Cierra Gibson

1 0

creating a new atlas
by Gibson,Cierra N 03 Sep '21

03 Sep '21

1 0

fs_install permission denied
by Junyeon Won 02 Sep '21

02 Sep '21

External Email - Use Caution Dear Freesurfer experts, I was tiring to install fs_install using the below command. cd $FREESURFER_HOME/bin && curl https://secure-web.cisco.com/186mRL7xDETIpN5cZS-wivuTmyhZn0PmwqT8bMpnWm3D4D… -o fs_install_mcr && chmod +x fs_install_mcr It showed an error message saying permission denied so I added sudo as suggested here. https://secure-web.cisco.com/1d_mS4e4I0j64PnpWDAM0mBO-6wAmGqcg5riZxWWy6VAP8… However, even after adding sudo in front, it shows the same error message. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2010 100 2010 0 0 17104 0 --:--:-- --:--:-- --:--:-- 17179 chmod: Unable to change file mode on fs_install_mcr: Operation not permitted Could you please let me know how to resolve this? Best, JW ᐧ

2 2

recon-all Longitudinal processing (baseline on 1.5T; followup on 3T)
by Jayachandra Raghava 02 Sep '21

02 Sep '21

External Email - Use Caution Hello Experts, I am planning to run the longitudinal processing pipeline (Freesurfer version 7.1.1). But I have a few subjects who were scanned on different scanner field strengths at baseline and followup. For example : Baseline was scanned on a 1.5T Siemens Scanner Followup was scanned on a 3.0T Siemes Trio Scanner I am planning to 1) run the cross-sectional processing for baseline without the 3T flag 2) run the cross-sectional processing for followup with the 3T flag 3) then generate the unbiased template and longitudinally process all the time points without any special flags. Is this the best way to process such data? Please let me know if there are any additional flags in the longitudinal processing pipeline to accommodate Scanner/Field strength changes. Best wishes Jay

3 2

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