Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

hemisphere analysis
by lanbo Wang 15 Dec '17

15 Dec '17

Dear experts, I have two questions about hemisphere analysis: 1) When I run left-right hemisphere paired t-test, can I add age as covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table? 2) I want to reorganize the hemisphere from left-right to symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it? Thanks for your patient and help. All best, Lanbo Wang

5 17

A note about the Freesurfer license file
by Z K 14 Dec '17

14 Dec '17

Hello All, Users on newer linux distributions who upgrade from Freesurfer version 5.3 to version 6.0 may get the following error message: -------------------------------------------------------------------------- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- This is a known issue, and as the message says, it is resolved by downloading a newly formatted license file from our registration page: http://surfer.nmr.mgh.harvard.edu/registration.html Simply overwrite the old license file with the newly formatted one. Sorry for any inconvenience this may have caused. -The Freesurfer team

3 3

Creating functional ROI
by Ashley Cole 13 Dec '17

13 Dec '17

Dear Doug/Bruce, I appreciate any insights on this. Thank you, Ashely ------------------------------------ I am new to FreeSurfer and I apologize in advance if my questions are too naiive. My main goal is to keep everything in the native space. Also, I am looking for percent signal change in selected ROIs. First, I ran recon-all command. Then, I preprocessed the functional data in native space. The command that I ran was: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force Then, I configured my analyses and contrasts in each hemisphere, as well as the volume. Finally, I ran the analyses for each hemispheres and the volume. I ran this command: selxavg3-sess -s sess01 -analysis ffa.native.rh Lastly, I visualized the results by running these commands: tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh -c faces-vs-bodies -self tkmedit-sess -s sess01 -analysis ffa.native.mni -c faces-vs-bodies -self So far, I think I have done everything correctly. I am seeing the activation ROIs where I am supposed to. Now, I would like to be able to select these ROIs/clusters, take their voxel coordinates/numbers and create a mask. (These are my localizer nii files.) Then, use this mask on the main experiment (non localizer) nii files and get the percent signal change in those selected voxels. Is this possible? I have found this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/ CreatingROIs but unfortunately I am not following it. I don't see these options in tksurfer. Also is it possible to create an ROI on the surface? I appreciate any help. Thank you so much Ashley Cole

2 7

Overlaying multiple results onto one surface
by Nguyen, Tin 04 Dec '17

04 Dec '17

Hello, I have been running different analyses through QDEC GUI for different covariates that describe a similar construct, for instance: * Model A: (cortical thickness) ~ (covariate 1) + (nuisance factors) * Model B: (cortical thickness) ~ (covariate 2) + (nuisance factors) * Model C: (cortical thickness) ~ (covariate 3) + (nuisance factors) * Model D: (cortical thickness) ~ (covariate 4) + (nuisance factors) * Model E: (cortical thickness) ~ (covariate 5) + (nuisance factors) As a result, I have 5 different brain images to illustrate each of the 5 models for their corresponding covariates. Is there way to overlay all 5 of the images onto a common space to have 1 representative brain image? This is to show overlapping effects, or the lack thereof, of the covariates. Thank you. -Tin

2 1

Combining parcellated regions within an atlas?
by Michiko H. 04 Dec '17

04 Dec '17

Hi Freesurfer Experts, I was wondering what the best way of combining regions within a parcellation? For example, in the Schaefer 2017 functional atlas, there are regions such as: 7Networks_LH_DorsAttn_FEF_1 0 118 22 0 7Networks_LH_DorsAttn_FEF_2 0 119 17 0 7Networks_LH_DorsAttn_FEF_3 0 119 18 0 7Networks_LH_DorsAttn_FEF_4 0 119 19 0 7Networks_LH_DorsAttn_PrCv_1 0 119 20 0 7Networks_LH_DorsAttn_PrCv_2 0 119 21 0 If I would like to combine all the DorsAttn_FEF areas into 1 node and DorsAttn_PRCv areas into another, what is the best way to do this? I currently have an image that has been parcellated using this atlas that was brought into volumetric space. I would need to have a transformed re-parcellated file and a corresponding color LUT file. Would appreciate any help, thank you! Best, Michiko

2 1

QDEC and comparing two conditions
by Rizvi, Batool 04 Dec '17

04 Dec '17

Hi FreeSurfer experts, We calculated the correlation between thickness two different behavioral conditions using QDEC. We now want to compare the spatial overlap and difference in thickness-correlation between the two behavioral conditions. We would like to do this both visually as well as statistically. Is there an option to do this either in QDEC or in the command line? Thanks for your time! Batool

3 3

Concatenating .mgh surface space functional MRI runs
by Abisan - 04 Dec '17

04 Dec '17

Hi Freesurfer experts, I want to concatenate multiple preprocessed fMRI runs in the form of .mgh freesurfer surface space files (2-D matrices vertexes * time_frames). Is there a tool that can do this easily, or do you have other recommendations how to do this? Thank you!

2 1

FA to MNI
by John Anderson 01 Dec '17

01 Dec '17

Dear Freesurfer experts, I want to register FA map in subject space to MNI. How can I do it using freesurfer tools? Any advice is highly appreciated! J

3 3

Intracranial Volume
by Tamara Tavares 01 Dec '17

01 Dec '17

Hello, Just a quick question regarding the computed intracranial volume. I have ran Freesurfer version 5.1 and I have been using the intracranial volume from the aseg.stats file to correct for head size. I just want to ensure this is where I get the intracranial volume from. Thank you in advance for your help. Best, Tamara

3 2

hippocampus subfields
by 郑凤莲 01 Dec '17

01 Dec '17

Hi professor, I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the result that there was an obvious difference in left hippocampus, but no difference in right hippocampus. Then, I run segmentation of hippocampus subfields. The result showed there is no difference in total left or right hippocampus, and only in two right hippocampus subfields has significant difference. Why is there inconsistent result in two means? Thank you very much. Sincerely, Zheng

3 19

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 November 2017