Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

[freesurfer] version differences for pial matter / skull strip?
by Michelle VanTieghem 02 Jan '18

02 Jan '18

Hello, I have posted several times about problems with skull-stripping with our dataset. We have tried gcut and multiple other options in other packages (AFNI, FSL, ANTS) to remove skull from structural images in our dataset with little success. Recently, a colleague suggested this may be due to versions: that 6.0 deals with skull stripping much better than 5.3. I wanted to ask if indeed this could be the case before I go install 6.0 and re-run everything in my study. Thank you, Michelle -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

3 15

About the contrast matrix in LME toolbox
by Gong, Liang 02 Jan '18

02 Jan '18

Dear LME developer and expert, I am using LME recently, based on longitudinal brain structural data, but I have two confusions in using it. 1) I followed the tutorial at: https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels However, I don't actually understand the Contrast matrix design in this tool. In the example the contrast C matrix is a 3*14, is there any explain about this matrix design? For my study, I want to explore 3 treatment (2 therapy methods and 1 waitlist) effects on the brain structural, If I want to explore the main effect of treatment, how could I write the Contrast matrix, and whether I can explore each treatment effect on the brain structural? And how can explore the time*treatment effect contrast matrix? 2) For the mass-univariate analysis, the example C matrix is 3*17, and it will explore the group differences in the rate of change over time among the four groups, and if I get the four group difference maps, How can I know the difference between each two groups? If I need to do the another qdec file and do the following steps as mris_preproc and mri_surf2surf? Thank you very much! Best, Gallen

2 1

Question about an error during recon-all process
by 박경일 01 Jan '18

01 Jan '18

Dear experts, I am sorry for asking again. I have some problems in running recon-all. Recon-all process was shut down with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string." I guess this is because of low resolution or small size of images. is it right? Thank you so much for you help in advance. FYI, log file is attached. Kyung

2 3

mris_convert error in finding file: fread error
by João V. Dornas 01 Jan '18

01 Jan '18

Dear Friend, I am trying to run this command using the last version of Freesurfer: mris_convert --combinesurfs my-left-surface.mgz my-right-surface.mgz lh.rh.asc But I receive this error: No such file or directory freadFloat: fread failed The input data file are inside the root directory. I tried to put these files in several other folders but still it does not work. Do you have any ideas in how can I combine my left and right surfaces? thank you very much, best regards, João V. Dornas

2 1

Feat
by N Saf 01 Jan '18

01 Jan '18

Dear FreeSurfer experts, I am trying to view the Feat on volume and surface by following commands: tkmedit bert orig.mgz -aux brain.mgz -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 –fmax 4.3 -seg aparc+aseg.mgz and tksurfer bert rh inflated -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 -fmid 3.3 -fslope 1 it works but thats my question: Is it possible to do the same thing with freeview ? I can not convert above commands in a way which be meaningful for freeview. many thanks to any help you can provide me. BRG, Nazanin

2 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 January 2018