Hello Jodie,
                     This matches what I ran my test with - I will send you a test script to run.

Kind Regards 

Matthew

> Hi Matthew,
> 
> Below is the text from the command you asked me to run. So what have I done wrong?!...
> 
> Thanks again for this - I really appreciate it,
> Jodie
> 
> 
> [brain1@localhost ~]$ more ${FSLDIR}/bin/imglob
> #!/usr/bin/env python
> #   imglob - expand list of image filenames
> #   Stephen Smith, Mark Jenkinson and Matthew Webster FMRIB Image Analysis Group
> #   Copyright (C) 2009 University of Oxford
> #   Part of FSL - FMRIB's Software Library
> #   http://www.fmrib.ox.ac.uk/fsl
> #   [log in to unmask]
> #
> #   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
> #   Imaging of the Brain), Department of Clinical Neurology, Oxford
> #   University, Oxford, UK
> #
> #
> #   LICENCE
> #
> #   FMRIB Software Library, Release 5.0 (c) 2012, The University of
> #   Oxford (the "Software")
> #
> #   The Software remains the property of the University of Oxford ("the
> #   University").
> #
> #   The Software is distributed "AS IS" under this Licence solely for
> #   non-commercial use in the hope that it will be useful, but in order
> #   that the University as a charitable foundation protects its assets for
> #   the benefit of its educational and research purposes, the University
> #   makes clear that no condition is made or to be implied, nor is any
> #   warranty given or to be implied, as to the accuracy of the Software,
> #   or that it will be suitable for any particular purpose or for use
> #   under any specific conditions. Furthermore, the University disclaims
> #   all responsibility for the use which is made of the Software. It
> #   further disclaims any liability for the outcomes arising from using
> #   the Software.
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> #   University harmless from and against any and all claims, damages and
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> #   transmitted product. You may be held legally responsible for any
> #   copyright infringement that is caused or encouraged by your failure to
> #   abide by these terms and conditions.
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> 
> import sys
> import os
> import glob
> 
> setAvailable=True
> if sys.version_info < (2, 4):
>   import sets
>   from sets import Set
>   setAvailable=False
> 
> def usage():
>    print "Usage: $0 [-extension/extensions] <list of names>"
>    print "       -extension for one image with full extension"
>    print "       -extensions for image list with full extensions"
>    sys.exit(1)
> 
> def removeExt(input):
>    output=input.replace(".nii.gz","")
>    output=output.replace(".nii","")
>    output=output.replace(".hdr.gz","")
>    output=output.replace(".hdr","")
>    output=output.replace(".img.gz","")
>    output=output.replace(".img","")
>    output=output.replace("*","")
>    return output
> 
> 
> if len(sys.argv) <= 1:
>    usage()
> 
> deleteExtensions=True
> singleImage=True;
> startingArg=1
> 
> if sys.argv[1] == "-extensions":
>   singleImage=False
>   deleteExtensions=False
>   startingArg=2
> if sys.argv[1] == "-extension":
>   deleteExtensions=False
>   startingArg=2
> 
> filelist=[]
> for arg in range(startingArg, len(sys.argv)):
>      output=removeExt(sys.argv[arg])
>      filelist.extend(glob.glob(output+".nii.gz"))
>      filelist.extend(glob.glob(output+".nii"))
>      filelist.extend(glob.glob(output+".hdr"))
>      filelist.extend(glob.glob(output+".hdr.gz"))
>      if not singleImage:
>         filelist.extend(glob.glob(output+".img.gz"))
>         if not singleImage:
>            filelist.extend(glob.glob(output+".img"))
> 
> if deleteExtensions:
>    for file in range(0, len(filelist)):
>        filelist[file]=removeExt(filelist[file])
> if setAvailable:
>   filelist=list(set(filelist))
> else:
>   filelist=list(Set(filelist))
> filelist.sort()
> 
> 
> for file in range(0, len(filelist)):
>    print filelist[file],
>    if file < len(filelist)-1:
>       print " ",
> [brain1@localhost ~]$
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 16:19:17 +0000
> From:    Matthew Webster <[log in to unmask]>
> Subject: Re: fsl 5.0.2 higher-level analysis crashes
> 
> Hello Jodie,
>                      Thank you for your upload - I've been looking at your data, can you send me the full text from typing
> 
> more ${FSLDIR}/bin/imglob
> 
> in your terminal?
> 
> Kind Regards
> 
> Matthew
>> Dear Matthew,
>> 
>> Thanks for your reply! I'm currently using Centos 6.2, but was previously using Centos 6.0 with no problems. However, at the same time I also changed FSL feat versions, and I have just noticed a difference in the number of files produced at the first-level analysis level. In the older feat version (v5.98) it created 40 files in the main folder, whereas it only created 28 files in the newer feat version (v6.00). So, I'm guessing that it is not the same problem as others were having , though the error produced during the higher-level analysis appears to be the same.
>> 
>> As I wasn’t sure where the problem lies (the zstat files produced in the first-level analysis appear fine), I've uploaded both the group feat folder and an individual feat folder (the one that produces only 28 files) to the server - reference no. 499811.
>> 
>> Sorry for any confusion, and thanks so much for your help with this!
>> 
>> All the best,
>> Jodie
>> 
>> ------------------------------
>> 
>> Date:    Mon, 17 Dec 2012 11:44:54 +0000
>> From:    Matthew Webster <[log in to unmask]>
>> Subject: Re: fsl 5.0.2 higher-level analysis crashes
>> 
>> Hello Jodie,
>>                     This problem should be fixed, can you let me know what OS you are using, and upload a tar of your FEAT directory to:
>> 
>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>> 
>> and let me know the 6-digit reference number?
>> 
>> Kind regards
>> 
>> Matthew
>> 
>>> Dear FSL experts,
>>> 
>>> I’ve seen the previous messages regarding the newer version of FSL ironing out the problems with the ’child process exited abnormally’ error (on line 119) during post-stats higher-level analysis. I recently installed the newer version of FSL (5.0.2) but the problem still persists.
>>> 
>>> Anyone happen to know how to fix this problem? I haven’t been able to successfully run any group analysis for a while now, so any cheats or suggestions for fixing would be very welcomed! When I open the FEAT GUI it still has v6.00 at the top – could this be the reason?
>>> 
>>> All the best,
>>> Jodie
>>> 
>>> -
>>> ---
>>> Jodie Davies-Thompson, Postdoctoral Fellow Department of
>>> Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre
>>> 2550 Willow Street
>>> Vancouver, BC, V5Z 3N9
>>> Canada
>>> Tel: 604-875-4111 ext 69003
>>> 
>> 
>> 
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 10:20:07 -0600
> From:    Jeanette Mumford <[log in to unmask]>
> Subject: Re: mean % signal change
> 
> Hi,
> 
> Yes, it is relatively simple once you figure out how to fix any lower level contrast scaling issues.  It is all in here http://mumford.fmripower.org/perchange_guide.pdf
> 
> Basically, if you have a contrast where the positive parts (when present) do not sum to 1 or the negative parts (when present) do not sum to -1, you need to scale so that they did.  For example, if I ran the [1 1 -1 -1] contrast at level 1.  Then at level 2 I averaged this together within subject and at level 3 I did some sort of model (doesn't matter, but you'll use the filtered_func_data and mean_func from this group analysis).  I need to account for the fact that my level 1 contrast's positive parts sum to 2 and negative parts sum to -2.  The "contrast fix" would be 2.
> 
> Assuming you had an event-related design, next you choose a "ruler" or type of stimulus that you're using as reference.  This doesn't need to actually exist in your design it is just a ruler for measure.  If you have really long trials (duration >5s or so), you can ignore this part, since linearity doesn't hold.  Anyhow, this is to get the min/max range of an isolated trial.  I almost always use an isolated 1s long trial.  Assuming you used a double gamma for convolution the min/max range is .2088 (others are in the pdf I mentioned above).
> 
> now you can caclulate the scale factor, which is 10*minmax range/contrast fix = 100*0.2088/2 = 10.44for my case with the lower level contrast of [1 1
> -1 -1]
> 
> then you just do:
> fslmaths filtered_func_data -mul 10.44 -div mean_func perchange_image
> 
> fslmeants -i perchange_image -m roi_mask
> 
> Gives the mean time series for your ROI.  The filtered_func data come from your group analysis directory as does the mean func image.  If your lower level contrast was simply [1 0 0 0] or [-1 0 0 0] or [1 -1 0 0] (ie, passes the rule I mentioned above) your scale factor would be 20.88.
> 
> Of course be careful about double dipping, since you're using a thresholded stat map to obtain your ROI.  There are plenty of papers on this.
> 
> Cheers,
> Jeanette
> 
> On Thu, Dec 20, 2012 at 8:31 AM, Jason Thomas <[log in to unmask]> wrote:
> 
>> Hi all,
>> 
>> I’m looking for a quick way to examine the mean % signal change for
>> each of my COPEs, for a cluster from a higher level analysis. I know I
>> could use featquery and do an ROI with a mask of the cluster, BUT, I
>> was hoping someone might know a quick/crude method of getting some
>> mean values with some code on a command line.
>> 
>> Many thanks if anyone is able to help!
>> 
>> Jason
>> 
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 17:42:00 +0100
> From:    Jesper Andersson <[log in to unmask]>
> Subject: Re: Jacobian of the field - Inverse consistent
> 
> Hi there,
> 
>> I am trying to create a Jacobian of the field using --jout option in fnirt command.
>> What i observed was that the Jacobian maps generated by fnirt' ing  images A-->B and B-->A are not inverse consistent.
>> 
>> For example: when i choose a random voxel on the Jacobian map, i see that the value for that particular voxel in both cases (A-->B and B-->A) are greater than 1. Which means that the same voxel is expanding in both trials.
> 
> there are two issues here.
> 
> 1. Fnirt is not guaranteed to be inverse consistent. However, inverse consistency was a large part of the evaluation we did of fnirt and the errors were quite small (~3mm for most cortical areas).
> 
> 2. I think this is what you see in your case. The Jacobian map is in the space of the reference scan. When you have done A->B and look at the Jacobian in coordinate x,y,z that corresponds to that particular area in B. If you want to know what the Jacobian in the B->A warp is in that location you can not look in x,y,z, because that refers to that location in the space of A. You need to look at the Jacobian for B->A in the location x+dx(x,y,x),y+dy(x,y,z),z+dz(x,y,z) where the displacement fields are those given by the A->B warp.
> 
> Spatial stuff is confusing.
> 
> Good luck Jesper
> 
>> 
>> Is there a way to make it inverse consistent, so that i see expansion in one direction  (A-->B) and contraction in the opposite direction(B-->A)?
>> 
>> BW
>> Jay
>> 
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 16:53:54 +0000
> From:    Matthew Webster <[log in to unmask]>
> Subject: Re: Problem with processing the model
> 
> Hallo Sade,
>                     Can you let know what OS and FSL version your colleague's computer is using?
> 
> Kind Regards
> 
> Matthew
> 
>> Hello,
>> 
>> Yes, I am. It works on my colleague's computer but not on mine.
>> 
>> 
>> On Thu, Dec 20, 2012 at 9:11 AM, Matthew Webster <[log in to unmask]> wrote:
>> Hello Sade,
>>                   Are you able to test this feat design on a different system?
>> 
>> Kind Regards
>> 
>> Matthew
>> 
>>> Hello All,
>>> 
>>> I am trying to run a first level of analysis and when I go to run the analysis, a window pops up that says "Problem with processing the model: libc++abi.dylib: terminate called throwing an exception".
>>> 
>>> If anyone could give assistance on the problem that would be great.
>>> 
>>> -Sade
>>> 
>> 
>> 
>> 
>> --
>> Sade E. Johns
>> Virginia State University
>> Psychology, M.S.
>> Pennsylvania State University Alum
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 17:11:22 +0000
> From:    Jodi Gilman <[log in to unmask]>
> Subject: Re: Problem with 2 groups paired in Feat
> 
> Thank you! I turned off 'outlier detection' and it ran in 4 hours. (My original one, with outlier detection, is still running and it has ben 67 hrs!!!)
> 
> Still have no idea why cope5 didn't run, but I ran it separately in a different Feat, and it ran fine.  Strange.
> 
> Thanks for your help.
> 
> Jodi
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 18:35:36 +0000
> From:    jie yu <[log in to unmask]>
> Subject: Re: Demean Problem
> 
> Thanks so much!
> And does it matter if that sum of the demeaned new EVs is not zero?
> 
> Thanks
> JIe-Yu
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 19:14:23 +0000
> From:    Jason Thomas <[log in to unmask]>
> Subject: Re: mean % signal change
> 
> Excellent, thanks Jeanette!
> 
> Jason
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 21:09:48 +0100
> From:    "Jacobs H (NP)" <[log in to unmask]>
> Subject: interpretation of contrast
> 
> Dear FSL developers
> 
> I am a bit confused about my model that I have used for the dual regression of my resting state data.
> I have two groups (patients and controls) and two measurements (pre and post).
> In order to compare them I subtracted pre from post and ran the dual regression on this difference.
> So now I have the following contrasts:
> patients > controls: 1 -1
> controls > patients: -1 1
> mean patients: 1 0
> mean controls: 0 1
> 
> I do understand that the first two contrast reflect group differences for the post-pre difference (so to speak the interaction group x timepoint).
> But I was a little confused about the latter two: is this actually giving me the result of patients post - patients pre ; controls post - controls pre respectively?
> Would that mean that if I would run a dual regression on one group and compare post with pre, that my results would be comparable?
> Or should I interpret this differently?
> 
> Thanks for helping me out on this!!
> 
> Best
> Heidi
> 
> ================================================
> Dr. Heidi Jacobs
> Postdoc researcher
> Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg [log in to unmask] www.maastrichtuniversity.nl www.heidijacobs.nl
> 
> 
> Dr. Tanslaan 12, 6229 ET Maastricht
> P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================
> 
> ------------------------------
> 
> Date:    Thu, 20 Dec 2012 21:47:30 +0000
> From:    Niels van Strien <[log in to unmask]>
> Subject: Parametric modulation of EV’s using custom 3 file format.
> 
> [Message contains invalid MIME fields or encoding and could not be processed]
> 
> ------------------------------
> 
> Date:    Fri, 21 Dec 2012 00:26:05 +0100
> From:    "Christian F. Beckmann" <[log in to unmask]>
> Subject: Re: melodic command line does not output filtered_func_data
> 
> Hi,
> 
> first, melodic does _not_ convert to %BOLD signal change unless you switch this on - are you sure you're running a recent version of FSL?
> Wrt fsl_regfilt: this is designed to allow you to use the _time series output_ from melodic to denoise the original data. The further processing within melodic simply improves the characterisation of the temporal modes. These will then be regressed out of the _original_ data or any version thereof that you've prepared by any means you fancy. Please see the fslcourse and go through the course if you are unsure about how to use this.
> 
> hth
> Christian
> 
> 
> 
> 
> On 18 Dec 2012, at 17:57, Joseph Viviano <[log in to unmask]> wrote:
> 
>> I think you fail to understand my question... how am I supposed to do this properly? I could variance normalize all of my data pre melodic, but I would rather do that after averaging. But the prewhitening step eludes me.
>> 
>> So, what should I do? Input registered, non normalized data into melodic, then independently convert to % signal change and variance normaize, and THEN use fsl_regfilt? Is there no way to apply melodic results to non-variance normalized data? What, exactly, should I do before I run melodic the first time, and before the second time? Especially since the --varnorm and --pbsc flags fail to actually turn off mean/variance normalization, so occasionally the program gets stuck trying to divide by 0...
>> 
>> Please provide some sort of information on how to use your tool properly. There is so little documentation and I have no clear idea of what is actually happening to my data...
> 
> ------------------------------
> 
> End of FSL Digest - 19 Dec 2012 to 20 Dec 2012 (#2012-357)
> **********************************************************