[Freesurfer] Freesurfer v6.0 + edit in v5.3.0 then rerun v6.0

[Tiril Pedersen Gurholt]

Dear Freesurfer Experts,

It is my understanding that Freesurfer v6.0 is at the verge of being released. 
Do you have a tentative v6.0 release data? Also, there is a beta version of 
Freesurfer v6.0. How stable is it? (Mostly thinking of the recon-all pipeline.)

Some of our data has been processed in Freesurfer v5.3.0 (recon-all to 
structural T1 data) and then manually edited. Is there a downside to rerun this 
data processed in v5.3.0 (after manual edit) in v6.0? Or is it best (or 
advisable) to rerun this data from the original T1 data in v6.0 and then do a 
new round of manual edit?

Best regards,

Tiril ??



--
Tiril Gurholt

Postdoctoral Fellow - Psychosis Research Centre

University of Oslo, Norway
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[Freesurfer] Fw: FreeSurfer group analysis: mri_glmfit-sim

[Silas]

Dear FS team,


I'm currently making a group analysis using the "command-line" group analysis 
stream in freesurfer.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng

[https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]

FsTutorial/GroupAnalysisDng - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Introduction. This tutorial is designed to introduce you to the "command-line" 
group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), 
including ...



1) I would like to do a surface based analysis where i'm only investigating a 
certain area or label - instead of doing a whole brain analysis. This can be 
done by introducing --label surface_area_of_interest.label when running 
mri_glmfit. Would this (in theory) give me different results from doing a whole 
brain analysis - or would it just exclude the results from outside the label? 
And how about after clusterwise correction for multiple comparisons?

-> is there a better way to do this than following the command-line group 
analysis stream in freesurfer?


2) When running mri_glmfit-sim i'm investigating the output ending with 
-voxel.mgh - how do i interpret the results of this file? When investigating 
the file in freeview what is the meaning of the units when configuring the 
overlay?


Best, Silas
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[Freesurfer] Paired analysis FSFAST

[Thục Trinh]

Hello,

I'm working on group analysis in fMRI activation using FSFAST. I tend to
test whether any significant changed in fMRI activation within group across
two time points ( pre-training vs post). I ran first level already.  I
still confuse about the concat data and the mri_glmfit command. Here are
the command lines, I'm wondering if it runs exactly what I want it to do.

--  idlist

Input NCP140005_1
Input NCP140005_2
Input NCP140012_1
Input NCP140012_2
Input NCP140071_1
Input NCP140071_2
Input NCP140079_1
Input NCP140079_2
Input NCP140082_1
Input NCP140082_2
Input NCP140543_1
Input NCP140543_2
Input NCP140556_1
Input NCP140556_2
Input NCP140558_1
Input NCP140558_2

-- concat data
isxconcat-sess -sf idlist -analysis work.sm5.lh -contrast con-v-arrow -o
group2

-- FSGD file

GroupDescriptorFile 1
Title Con-arrow Gr2
Class Defi
Input NCP140005 Defi
Input NCP140012 Defi
Input NCP140071 Defi
Input NCP140079 Defi
Input NCP140082 Defi
Input NCP140543 Defi
Input NCP140556 Defi
Input NCP140558 Defi

-- run glm analyisis

mri_glmfit --glmdir lh.paired.gr2-diff --y ces.nii  --fsgd
con-arrow_group2.fsgd --C mean.mat

-- content in matrix contrast
 C = [ 1 0 ]

Thank you,
Trinh
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Re: [Freesurfer] Freesurfer v6.0 + edit in v5.3.0 then rerun v6.0

[Bruce Fischl]

Hi Tiril

we continue to work hard on getting V6 out. As of now there is no beta. 
There was one previously, but it turned out we had to make too many 
changes to it and so now are getting ready for another beta. We are 
hoping to release it before April. Manual edits done in 5.3 should be ok if 
rerun in v6 I think


cheers
Bruce
On Sat, 6 Feb 2016, Tiril Pedersen 
Gurholt wrote:



Dear Freesurfer Experts, 

It is my understanding that Freesurfer v6.0 is at the verge of being
released. Do you have a tentative v6.0 release data? Also, there is a beta
version of Freesurfer v6.0. How stable is it? (Mostly thinking of
the recon-all pipeline.) 

Some of our data has been processed in Freesurfer v5.3.0 (recon-all to
structural T1 data) and then manually edited. Is there a downside to
rerun this data processed in v5.3.0 (after manual edit) in v6.0? Or is
it best (or advisable) to rerun this data from the original T1 data in
v6.0 and then do a new round of manual edit? 

Best regards, 

Tiril ​​



--
Tiril Gurholt

Postdoctoral Fellow - Psychosis Research Centre

University of Oslo, Norway

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