Freesurfer February 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
118 discussions

data sharing of freesurfer processed data
by STACEY M SCHAEFER 04 Feb '21

04 Feb '21

External Email - Use Caution Does the freesurfer group have any recommendations or procedures for public sharing data that has been processed with freesurfer? In particular, procedures to automatically swap out participant IDs to anonymize the data? Stacey M. Schaefer, Ph.D. Center for Healthy Minds University of Wisconsin-Madison 625 W Washington Ave Madison WI 53703

2 1

ERROR:DOF=0
by 吴敬宇 03 Feb '21

03 Feb '21

External Email - Use Caution When we ran this group of analysis programs, this bug appeared. How can I solve it?

1 0

white matter volume
by Sara Lyn 03 Feb '21

03 Feb '21

External Email - Use Caution Hi, Is there a way to get at the white matter volume from a group analysis? Sara

2 5

FIR Analysis and task regressor
by Doll, Laura 03 Feb '21

03 Feb '21

External Email - Use Caution Hi everyone, Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related). This works when I use "-spmhrf" or other HRF options. However, for FIR I cannot get the expected time course in the single subjects data. Tksurfer ends with an error because it cannot find the file h.nii.gz: ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h This file indeed does not exist, there is only one called "h-offset". The commands I used until that point are (here neglecting the original task, but using -event-related etc instead of no task results in the same error): mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1 selxavg3-sess -s S01_3 -analysis PupilFIR.lh tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer Is there any solution for this? Or any reason why it should not be done that way? Best, Laura

2 1

define freeview colormap from command line
by Simone Cauzzo 03 Feb '21

03 Feb '21

External Email - Use Caution Dear all, Using your precious hints in a past thread, I'm now displaying several surface analyses and taking a screenshot for each of them, everything from command line using the command freeview -f ***/mni152.fnirt/surf/lh.inflated:overlay=***mni152.fnirt.lh.nii.gz:overlay_threshold=5,8 -zoom 1.6 -ss ***.tif Now, the colormap I'm using is thus by default "heat" with thresholds 5 and 8. My images are very red. Opening the "configure overlay" menu in the GUI, I noticed that the colormap is almost entirely red, and fades to yellow only in the end. If I select "custom", the colormap appears more graded, as I would like it to be. Is there any way to specify the "custom" option in the "configure overlay" menu from the command line? Thank you Simone

2 1

White matter parcellation
by Graterol Pérez, José Alberto 03 Feb '21

03 Feb '21

External Email - Use Caution Dear FreeSurfer experts, I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins. I am attaching two images to show what I mean. I would really appreciate some clarification. I am using FreeSurfer 7.1.1 Thanks in advance. José -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1UyleYcIW9IpIEav-uaSJpfZckYD_6rdaRbxs9DgAhomEce… Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

2 2

Hypothalamus segmentation - Freesurfer 7.1
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 02 Feb '21

02 Feb '21

External Email - Use Caution Dear Freesurfer experts, I am having some trouble getting the hypothalamus segmentation recognized on the command line for FreeSurfer 7.1.0. Is it even available for this version? If not, will it work on the 6.0 or the 7.1.1 version? Thanks and stay safe! All the best, Alex

3 3

label to surface
by Sam W 02 Feb '21

02 Feb '21

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam

3 9

cortical thickness ROI
by Sara Lyn 02 Feb '21

02 Feb '21

External Email - Use Caution Hi Freesurfer developers, I wanted to know if I could use an ROI obtained from cortical thickness group analysis to obtain FA values from that same ROI for each of the subjects. Appreciate any guidance, thank you. Sincerely, Sara

2 1

White matter Parcellation
by Graterol Pérez, José Alberto 01 Feb '21

01 Feb '21

External Email - Use Caution Dear FreeSurfer experts, I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins, because the structures are not really visible. I could upload two screenshots to show what I mean. I would really appreciate some clarification. I am using FreeSurfer 7.1.1 Thanks in advance. José -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1fL7_mV1HnVXx_pK-xzWgX0hp1IPRmxfnHHvyPV6axEvIN9… Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer February 2021