Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Changelog between stable and dev versions?
by Dorian P. 02 Jan '20

02 Jan '20

External Email - Use Caution Hello everyone, and happy new year. I know it's never a good idea to mix versions within a study, but that's what has happened in a large study here, so I am trying to get a sense of what changes there have been. I was wondering if there is a way to see if there are major changes between a stable version and certain dev versions, specifically I am interested in finding out about these versions of freesurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a freesurfer-Linux-centos7_x86_64-dev-20180227-5e5b9aa freesurfer-linux-centos7_x86_64-dev-20190805-8b45905 Thanks!

2 1

mkanalysis-sess.new not found
by Marco Ninghetto 02 Jan '20

02 Jan '20

External Email - Use Caution Dear experts, my name is Marco and I'm using freesurfer to perform retinotopy analysis and I am having a problem with command: `mkanalysis-sess.new` after calling that command I get the following bash error: `bash: mkanalysis-sess.new: command not found` All the previous steps worked well. Why is this command unrecognized? Thank you all, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

2 2

Unable to run recon all
by Sahil Bajaj 02 Jan '20

02 Jan '20

External Email - Use Caution Hello FS experts, I am trying to run recon all on about 100 subjects. But one out of 100 subjects finishes recon all with error, and doesn't complete the process. Here I am attaching recon all log for your reference. Also, before installing freesurfer on MAC Catalina, I ran sudo spctl - -master -disable I would really appreciate any help in resolving this. Thanks, Sahil 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) Platform: MACOS Catalina 3) recon-all.log: see attached

2 1

Fill holes in BOLD surface
by Marina Fernández 02 Jan '20

02 Jan '20

External Email - Use Caution Hi Freesurfer experts, I have projected 4D-preprocessed BOLD data to Freesurfer cortical surfaces. Resulting individual surfaces have many holes (see attached image) that I would like to fill with nearest neighbors values around each hole (avoiding the medial wall). Could you indicate me how to do this? Thank you in advance. Marina

2 1

mapping the reliability of separating GM/WM
by Liu Y 02 Jan '20

02 Jan '20

External Email - Use Caution Hi Freesurfers, The contrast between GM/WM may vary regions by regions. Some regions have high contrast, some regions have low contrast, is there a method can map the reliability of separating gray and subcortical white matter? Thanks in advance, Yawu

3 4

No Colortable Found
by Baptista, Paulo 02 Jan '20

02 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I'm helping researchers test Freesurfer 4.5 and Freesurfer 6. Running same code on Freesurfer4.5 environment produces no image with tksurfer. It says "No colortable found." See attached. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 2) Platform: CentOS release 5.11 (Final) We're are running this in a Singularity container. It's getting close to working properly. It would be nice to have a way to run old code on newer Linux systems. Thanks, Paulo

2 2

Obtaining pre&post values from longitudinal dataset without cross-base-long
by Tudor Popescu 02 Jan '20

02 Jan '20

External Email - Use Caution Dear FS experts, From a pre-&post-intervention data set, is it possible to extract thickness values at those two time points just by using recon-all, that is, without running the full longitudinal processing stream (the Cross, Base and Long steps)? I aim not so much to compute the percentage change measure ( pc1 = (post-pre)/pre ), but simply to use the raw pre&post values for other analyses. Many thanks, and happy holidays to all! Tudor

2 1

FSFAST registration
by Star Xi 02 Jan '20

02 Jan '20

2 1

vol2subfield
by stdp82＠virgilio.it 02 Jan '20

02 Jan '20

External Email - Use Caution Hi list, where/how should I add the file listed below? https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/vol2subf… Thanks

2 1

Problem for mri_glmfit
by Gwang-Won Kim 02 Jan '20

02 Jan '20

2 1

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