Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

regarding contrast vector in qdec analysis
by Santosh Yadav 19 May '14

19 May '14

Dear FreeSurfer Experts, I am running an analysis in Qedc that include 2 groups (Control and Heart Failure). I want to see the cortical thickness difference between these 2 groups, with age and gender as a co-variate, not interested in any correlation analysis. In Qdec, Model factors have three options that include the fixed factor, continuous factor (Co-variate) and Nuisance. So groups (control and heart failure) belongs to fixed factor while age and gender belongs to both continuous factor and Nuisance. When I am running this analysis in Qdec by selecting the model that include only group in the model the contrast vector in the Qdec terminal is 1, -1, and its fine. But when I am selecting the model that includes age and gender as a nuisance, the contrast vector showing 1, -1, 0, 0, 0, 0. So my question is why we have two extra 0, 0 in contrast vector, it should be 1 -1 0 0. Another question: When I finished the analysis in Qdec and got the state data tables, that have 18 files, with volume, area, curv and thickness from both sides. I am interested in thickness and its have four files with left and right. lh.aparc.a2009s and lh.aparc, I am not sure what file should i used for the analysis. I believe for left side qdec is using lh.aparc, Is I am right? With Regards, Santosh K. Yadav -- With Best Regards, Post Doctoral Fellow, Department of Anesthesiology University of California, Los Angeles, CA 90034 Phone No. 808-5896940

2 1

Small volume correction in qdec
by Narly Golestani 19 May '14

19 May '14

Dear all, I would like to follow up on several posts that have already been made regarding how to restrict the search volume (i.e. do a small volume correction) to a particular region (e.g. to a freesurfer label) within qdec. As far as I can see this query was not answered on the list: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13770.html How exactly can this be implemented in qdec please? Thanks in advance and best wishes, Narly.

2 1

Re: [Freesurfer] Registration and Surface flatten
by Caka 19 May '14

19 May '14

Hi Doug, Thanks for your suggestion on tksurfer, it works. I would like to map all the subjects into a flat map because I am curious about the 2-D thickness patterns between different groups. I think there will be some distinctions. But if I flatten fsaverage, how can I map everyone’s 3D surface onto the fsaverage’s 2D map? Is there a command? Best, Qiongmin On 05/13/2014 11:19 PM, Caka wrote: > Dear Doug and all, I have already done two things: (1) 'recon-all? to > the segmentation for 140 subjects; (2) surface registration to > fsaverage template for 1 subject using: mri_surf2surf --hemi lh > --srcsubject sub001 --srcsurfval thickness --src_type curv > --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz Now I > have got the 'sub001-thickness-lh.mgz' file. I have two questions: (1) > Is this 'sub001-thickness-lh.mgz? a surface file or a volume file? How > can I read it? I used ?freeview sub001-thickness-lh.mgz? to read it, > but a dark scene was shown, nothing can be found. I also used > ?mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz > $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc?, an error occurred > like ?ERROR: number of vertices in > /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match > surface (163842, 132230)?. Try tksurfer fsaverage lh inflated -aparc -overlay sub001-thickness-lh.mgz -fminmax .01 4 > (2) After the registration, I want to flatten the surface of curvature > or thickness into a full plane. The wiki says we should first specify > 5 vertices and cut the whole area without the midline region, then > ?kris_flatten? can be used. Indeed, this procedure requires quite a > lot manually operation. I am wondering if there are some automatically > commands that can do this flatten projects for 140 subject? Any reply > would be really appreciated! Qiongmin > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer I don't think so, though I think bruce was working on something. You could just flatten fsaverage and then map everyone to fsaverage (as you have already done). Why do you want to map everyone to a flat map? doug

2 1

Cortical Lesions
by Maia Pujara 19 May '14

19 May '14

Hi all, I'm having similar issues that were brought up in this post regarding subjects with cortical lesions: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-January/004359.h… Would these lesions would affect the way the brain is labeled and the measurements for cortical thickness? If so, how would this affect group comparisons of lesion patients to healthy controls? I've attached an example of what one of the lesion subjects looks like. Thanks, Maia

2 1

automatically expand surface label along the surface
by Martha Shiell 19 May '14

19 May '14

Hello Freesurfer users, Does anyone know a command to automatically expand (grow/dilute) a label file along the surface, e.g. add neighbouring vertices to the label? Thanks, Martha Shiell Ph.D. Candidate, Neuroscience McGill University

3 2

labels of surface vertices
by Tanya 19 May '14

19 May '14

Hi Freesurfers, I'm confused about surface vertices labels. One of the tutorial mentions that: " There is a one-to-one correspondence between surfaces which allows the user to cross-reference vertices from one surface to another (even across subjects) and to the volume." So there is a map between vertex index and label and it is universal for all subjects and all surfaces? Where can I find this map and is there a script to use it? Thank you! Tanya

2 1

Contrast vector in Qdec terminal and DOSS vs DODS
by Santosh Yadav 19 May '14

19 May '14

Dear FS Experts, I am asking same question again since did not get any reply. I processed my data with FS 5.3 version and running analysis in Qedc GUI with DODS that include 2 groups (control and heart Failure). I want to see the cortical thickness difference between these 2 groups, with age and gender as a covariate. In Qdec GUI, model factors have three options that include the fixed factor, continuous factor (covariate) and nuisance variable. So group (control and heart failure) belongs to fixed factor while age and gender belongs to both continuous factor and nuisance variable. When I am running this analysis in Qdec by selecting the model that include only group the contrast vector in the Qdec terminal is 1, -1, and I believe its fine. But when I am designing the model that includes age and gender as a nuisance factor, the contrast vector showing 1, -1, 0, 0, 0, 0, on the Qdec terminal. So my question is why we have two extra 0, 0 in contrast vector, as per my understanding it should be 1, -1, 0, 0, please explain. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display again. Another question: When I finished the analysis in Qdec and got the state data tables, that have 18 files, with volume, area, curv and thickness from both left and right sides. I am interested in cortical thickness and it's have four files with left and right with two versions. for example for left side one is lh.aparc.a2009s and one is lh.aparc. I am not sure which file should I used for the analysis. I believe for left side qdec is using lh.aparc, Is I am right? With Regards, Santosh K. Yadav -- With Best Regards, Post Doctoral Fellow, Department of Anesthesiology University of California, Los Angeles, CA 90034 Phone No. 808-5896940

1 0

Rotated structurals
by Tudor Popescu 18 May '14

18 May '14

Hi everyone Are structurals that come out of the scanner somewhat rotated (a few degrees, but still visible, example - attached) processed normally by recon-all, or do they first have to be manually corrected (rotated)? Thanks! Tudor

2 1

Re: [Freesurfer] using multiple cores
by Lukas.Scheef＠ukb.uni-bonn.de 16 May '14

16 May '14

3 3

mri_convert frame error in tracula
by Pedro Rosa 16 May '14

16 May '14

Dear All, As suggest, I am reposting a previous question. I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148, for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the trac-all.log that comes with the following error: ERROR: fMRIframe: frame >= frames Can anyone help me? Thank you in advance! Regards, Pedro Rosa.

1 0

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