Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30078 discussions

freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)
by 许霄 16 Nov '21

16 Nov '21

External Email - Use Caution Hello FreeSurfer Developers, I can't access the website of archives, so I have to ask questions in this way. I installed freesurfer7-dev in Ubuntu18 in wsl according to the tutorials FS7_wsl - Free Surfer Wiki (harvard.edu) and FS7_wsl_ubuntu - Free Surfer Wiki (harvard.edu) After adding the license, when I tried to run the 'freeview' command to test if everything works well, an error popped out: Segmentation fault(core dumped). more information about my freesurfer environment is shown as attached. Could anyone help me figure it out? Thanks in advance.

1 0

SUBJECT_DIR using bbregister
by m-maiworm＠web.de 15 Nov '21

15 Nov '21

3 3

Freesurfer: Re-run recon-all in older versions
by Steve Petersen 12 Nov '21

12 Nov '21

External Email - Use Caution Dear all, We conducted the recon-all and applied a quality control protocol in several subjects using the FSurfer 6 version. Now, we would like to run the recon-all again on an older version of FSurfer (5.3 v) but considering the edits we made on those previous recon-all. Is this possible?, and if so, what would be the command? Thank you very much in advance. Best regards, Steve.

3 4

Transform matrix
by Alberto Del Cerro Leon 12 Nov '21

12 Nov '21

External Email - Use Caution Hello Freesurfer team, I did a white matter atlas from surface annot with mri_aparc2aseg. However, when I use this atlas in comparison with the original T1 I have observed that both images don't share the transformation matrix. Do you know how I could I fix this issue?

3 2

FsFastFunctionalConnectivityWalkthrough
by Alice Giubergia 12 Nov '21

12 Nov '21

External Email - Use Caution Thanks for your replies Doug! I copied the previous messages below, since I did not menage to retrieve the original email. 1) Thanks. 2) Regarding question number 2, yes that was what I meant. 3) I ran the task analysis and extracted time series from unwhitened residuals by mri_segstats, upon a specific segmentation. I was thinking now of a correlation matrix by Pearson's coeff. Any further suggestions? Also, I've got a pheraps silly question: - When running a task analysis, I could specify -taskreg and -nuisreg separetly. My assumption is that only -nuisreg are regressed out from the data and that the residuals saved got task-related bold signal. Is it correct? - If so, could I use task regressors as -nuisreg to get a "pseudo" resting state? Hoping all question are clear, Thanks for your patience, Alice Dear FreeSurfer experts, I'm interested in performing a functional analysis on task-based data. I was taking as an example the "FsFastFunctionalConnectivityWalkthrough" tutorial but, if I got it correctly, is specific for resting state data. So I've got some doubts and questions: 1) Given the steps described in the above mentioned tutorial, the file "pcc.mgz" generated in the session folder gives me the correlation strength between the time series of each voxel and the seed (L_Posteriorcingulate in the tutorial)? Yes, correct 2) If I want to make a functional analysis on task data, similar to the one described in that tutorial, could I just add the -event-related option instead of -notask option? (mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5* -notask* -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR <TR>) Do you mean you want to do a simultaneous analysis of the task and the connectivity? I just tried what you suggested and it looked like it worked. 3) Otherwise, does it make sense to you If I run a simple task analysis to regress nuisances out (without seed region), extract time series and get the pair-wise correlation with Pearson coefficient? This is possible, and makes sense. It is a little difficult to do, but not terrible. If you want to go this route, you would need to first analyze your task data as task without FC, specifying -svres-unwhitened to save the residuals. Let me know when you get to that point and I can push you further. Hoping my questions are clear, Thanks a lot for your patience and help, Alice

2 1

lh.thickness can not found
by a Chinese reader 11 Nov '21

11 Nov '21

External Email - Use Caution Hello FreeSurfer Developers,I'm attempting to compute the thickness of the grey matter ,but for some of my subjects I get the following error when I run the recon-all -s <> -all command:Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.I've searched the list and no similar errors have been reported. Did this warning have any effect for my outcome?And why my lh.thickness cannot generated? Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. Best regards, Zhang Xia

2 1

T1 aparc.stats vs T1 with T2 aparc.stats
by Castro Leal, Gonzalo 11 Nov '21

11 Nov '21

External Email - Use Caution Hello, I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1) Many thanks, Gonzalo.

2 11

question regarding FSGD file for coding discrete regressors
by Zeng, Qi 11 Nov '21

11 Nov '21

External Email - Use Caution Hi Freesurfer experts, Here, I want to design a simple group comparison (two levels: Case vs. Control) and also count for 4 covariates (two continuous and two categoricals). However, the GLM model cannot recognize my discrete variables. What do you suggest to change? >> FSDG file: GroupDescriptorFile 1 Title MyStudy Class Control Class Case Variables age gender race eTIV Input sub001_base Control 85 Female White 1350519 Contrast: >> Design matrix for Case-Control and regress out the effect of age, gender, race, and eTIV. -1 1 0 0 0 0 0 0 0 0 Best, Zeng

2 11

turning a surface label into 3d object
by Trisanna Sprung-Much 11 Nov '21

11 Nov '21

External Email - Use Caution Hi there I realize this may be a bit of a stretch, but I wonder if there is any way to turn a surface label into its own 3D object that can then be examined on its own (to observe morphology) in Freeview? Similar to, for example, the sulcal skeletons that can be extracted in BrainVisa? Many thanks~ Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

2 2

[Re]:FsFastFunctionalConnectivityWalkthrough
by Alice Giubergia 11 Nov '21

11 Nov '21

External Email - Use Caution Thanks for your replies Doug! 1) Thanks. 2) Regarding question number 2, yes that was what I meant. 3) I ran the task analysis and extracted time series from unwhitened residuals by mri_segstats, upon a specific segmentation. I was thinking now of a correlation matrix by Pearson's coeff. Any further suggestions? Also, I've got a pheraps silly question: - When running a task analysis, I could specify -taskreg and -nuisreg separetly. My assumption is that only -nuisreg are regressed out from the data and that the residuals saved got task-related bold signal. Is it correct? - If so, could I use task regressors as -nuisreg to get a "pseudo" resting state? Hoping all question are clear, Thanks for your patience, Alice

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