Just wanted to update this - I was able to resolve my problem.
The q/s matrices were indeed off. I'm almost certain this was because the images were obtained obliquely, as we had a similar problem w/ a dog project I've been working on - that derailed registration.
I was able to use ITK-Snap to determine what the appropriate orientation and matrix numbers should be, then fixed each sequence using the fslorient -set(s/q)form command. After having done this, I was successfully able to complete my group analysis.
Thanks for the help, and just wanted to put this out there for anyone else dealing w/ oblique acquisitions (e.g., other people imaging non-humans with new protocols).
Peter
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Cook, Peter F.
Sent: Monday, December 16, 2013 1:56 PM
To: [log in to unmask]
Subject: Re: [FSL] Confusing errors in higher level feat analysis
Sorry, quick correction - in my FIRST-level analysis I included time courses from the masks/CSF/WM - obviously second-level was just comparing statistical maps from first-level.
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Cook, Peter F.
Sent: Monday, December 16, 2013 1:34 PM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [FSL] Confusing errors in higher level feat analysis
Thanks for the reply Mark,
When I ran the first level analyses, in feat, each subject was registered first to its own structural image (acquired w/ the same parameters as the EPIs) w/ 6 degrees of freedom, then to the standard space using 12 dof.
These are sea lion brains, so there is no standard atlas - the "standard space" was made prior by registering the structural of each of the brains to one of the brains, then registering all the brains to the output of that. I'm still a little confused on the s and q matrix readouts - should the actual numbers be identical (qto and sto 1-3)?
My second-level analysis included time courses extracted from hippocampal masks, CSF masks, and WM masks - these had each been registered to the structural and the template space as well (although since these EVs were just time course files, I don't believe that could be my problem here).
As a side note, I believe the scans were all acquired in an oblique plane. W/ some dog work I've been doing recently this has caused some problems and we've had to reorient images before proceeding. Could that be throwing me off?
Thanks much,
Peter
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
Sent: Sunday, December 15, 2013 5:02 PM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [FSL] Confusing errors in higher level feat analysis
Dear Peter,
Have you run standard registration for the first level analyses?
Which files are you showing the qform matrices for?
The files that need to be merged together are the COPE and VARCOPE files after registration, and so should all be in the standard space and hence all have the same qform and sform matrices. So when the registrations are done and have worked correctly then you should not see this warning/error message when merging.
All the best,
Mark
On 13 Dec 2013, at 01:44, "Cook, Peter F." <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi, sorry to pester, just wondering what route I should explore next....
Thanks much,
Peter
From: Cook, Peter F.
Sent: Monday, December 09, 2013 3:31 PM
To: 'FSL - FMRIB's Software Library'
Subject: RE: [FSL] Confusing errors in higher level feat analysis
Thanks for getting back to me Matthew,
I've attached the relevant readout from these for my 12 subjects (cope files from first-level analyses). Voxel size and TR are the same for all subjects.
In brief, the qform and sform orientations are the same for each file. The qto_xyz:4 and sto_xyz:4 are also the same for each subject.
However, the qto_xyz and sto_xyz 1-3 values are different between each subject. The first value for the qto and sto xyz:1 values is very close for each subject.
Is this a problem? And, if so, what might explain it? (Given that they were all normalized to the same template).
Thanks much,
Peter
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matthew Webster
Sent: Friday, December 06, 2013 5:13 AM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [FSL] Confusing errors in higher level feat analysis
Hello Peter,
Can you run fslhd on some of the copes in the reg_standard directories of your lower-level inputs and check that there are no differences in the s/q-form matrices?
Kind Regards
Matthew
Hi Stephen,
I've looked into Ram/swap and I really don't think that's the issue. This is running on a 16-core cpu w/ tons of ram and swap memory. Have looked at readouts of these values while trying to run analysis and they're not getting close to maxing out.
The error (always the same as noted below) seems to occur following these warnings:
WARNING:: Inconsistent orientations for individual images when attempting to merge.
Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
All the scans have the same parameters and were normalized to the same group template.
If it would be possible to upload the data set it would be greatly appreciated. How might I proceed?
Thanks much,
Peter
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stephen Smith
Sent: Thursday, November 28, 2013 8:31 AM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [FSL] Confusing errors in higher level feat analysis
Hi - I can't think of a reason why larger analyses would be failing unless you are having disk space / quota / NFS mounting/access / RAM /swap problems. If you can check that those would not explain this first, and still things are not working, feel free to upload the failing analyses and we can take a look. See the FSL wiki for details on RAM/swap problems (in the FAQ) and uploading info.
Cheers.
On 27 Nov 2013, at 12:52, Cook, Peter F. <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi,
First time using the list, so my apologies if not submitting this question through the appropriate channel.
I successfully ran a first-level feat connectivity analysis on a series of hippocampal seeds in 12 subjects.
I have an anterior and posterior seed, and want to look for network differences at the group level.
When running the higher level analysis, using a simple paired t-test design, I'm getting some strange errors.
When I try to run all 12 subjects, I get an error at the post-stat stage:
"child process exited abnormally
While executing
"if { [ catch {
For { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
Switch - [ lindex $argv $argindex ] {
-I {
Incr argin..."
(file "/usr/share/fsl/5.0/bin/feat" line 119)"
Haven't been able to find anything online regarding this error.
What's particularly odd is that I'm able to run smaller numbers of my subjects in the same higher-level analysis with no error. Up to 9 it seems (have looked at subsets of subjects to make sure it's not one bad apple that's throwing things off).
This is on a laptop running Ubuntu 11.4.
I've also tried doing the analysis on a mainframe running Ubuntu 12.4.
There, I get the same error message, but it can successfully run even FEWER subjects w/out spitting an error (4 or 5 it seems).
Any idea what's going on here? Operating system problem?
Any help would be greatly appreciated....
Thanks much,
Peter Cook
Post-Doctoral Fellow
Center for Neuropolicy
Emory University
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