Paul,
The command I used to run FIX: /usr/local/fix1.06/fix rest_smooth.feat
/usr/local/fix1.06/training_files/Standard.RData -m 5
Contents of the .ica directory:
eigenvalues_percent
log.txt
mask.nii.gz
mean.nii.gz
melodic_FTmix
melodic_IC.nii.gz
melodic_ICstats
melodic_mix
melodic_PPCA
melodic_Tmodes
report
Contents of the output directory:
dummy.nii.gz
dummyabs.nii.gz
edge1.nii.gz
edge2.nii.gz
edge3.nii.gz
edge4.nii.gz
edge5.nii.gz
fastsg_mixeltype.nii.gz
fastsg_pve_0.nii.gz
fastsg_pve_1.nii.gz
fastsg_pve_2.nii.gz
fastsg_pveseg.nii.gz
fastsg_seg.nii.gz
highres2std.mat
hr2exf.nii.gz
hr2exfTMP.nii.gz
hr2exfTMP.txt
logMatlab.txt
maske1.nii.gz
maske2.nii.gz
maske3.nii.gz
maske4.nii.gz
maske5.nii.gz
std1mm2exfunc0.nii.gz
std1mm2exfunc0dil.nii.gz
std1mm2exfunc0dil2.nii.gz
std1mm2exfunc1.nii.gz
std1mm2exfunc1dil.nii.gz
std1mm2exfunc1dil2.nii.gz
std1mm2exfunc2.nii.gz
std1mm2exfunc2dil.nii.gz
std1mm2exfunc2dil2.nii.gz
std1mm2exfunc3.nii.gz
std1mm2exfunc3dil.nii.gz
std1mm2exfunc3dil2.nii.gz
std2exfunc.mat
std2highres.mat
Thanks!
> Hi Madelyn,
>
> Could you please tell me the following:
>
> - The command you used to run FIX
> - The contents of the input .ica directory
> - The contents of the output directory, after FIX failed
>
> Cheers,
>
> Paul
>
> On 27 August 2015 at 10:27, Madelyn Glymour <[log in to unmask]>
> wrote:
>
>> Dear FSL team,
>>
>> I work with Clark Glymour’s fMRI group at CMU, including, Joe Ramsey
>> and
>> Ruben Sanchez. We’re currently analyzing some resting state data, and
>> we’d
>> hoped to use FSL’s FIX to clean the data, but we’re running into
>> some
>> problems making the process work. After a lot of googling and
>> trial-and-error, we still can’t get it to run, so I was hoping you
>> might
>> be able to shed some light on what’s going wrong.
>>
>> When I run FIX, I get the following command line output:
>>
>> FIX Feature extraction for Melodic output directory: rest_smooth.feat
>> create edge masks
>> run FAST
>> registration of standard space masks
>> extract features
>> FIX Classifying components in Melodic directory: rest_smooth.feat using
>> training file: /usr/local/fix1.06/training_files/Standard.RData and
>> threshold -m
>> FIX features not already generated, so creating them now.
>> FIX Feature extraction for Melodic output directory: rest_smooth.feat
>> create edge masks
>> run FAST
>> registration of standard space masks
>> extract features
>> No valid labelling file specified
>>
>>
>> The logMatlab.txt file gives this output:
>>
>> < M A T L A B (R) >
>> Copyright 1984-2014 The MathWorks, Inc.
>> R2014b (8.4.0.150421) 64-bit (maci64)
>> September 15, 2014
>>
>> [ Warning: Name is nonexistent or not a directory:
>> /Users/user/Documents/ROI]
>> [ Warning: Name is nonexistent or not a directory:
>> /Users/user/Documents/ROI/Coordinates]
>> [ Warning: Name is nonexistent or not a directory:
>> /Users/user/Documents/ROI/Normal]
>> [ Warning: Name is nonexistent or not a directory:
>> /Users/user/Documents/ROI/Original]
>>
>> For online documentation, see http://www.mathworks.com/support
>> For product information, visit www.mathworks.com.
>>
>> ----------------------------------------------------
>> Your MATLAB license will expire in 44 days.
>> Please contact your system administrator or
>> MathWorks to renew this license.
>> ----------------------------------------------------
>> rest_smooth.feat/
>> 29 1
>>
>>
>> Error Time: 08/18/2015 00:40:02
>> Error using horzcat
>> Dimensions of matrices being concatenated are not consistent.
>>
>>
>> My guess, based on what I’ve seen online about other users who’ve
>> received
>> similar errors, is that there is an incorrect setting in the settings.sh
>> file, or possibly that a folder has been misplaced somewhere. But I
>> can’t
>> figure out what that setting/folder might be. Do you have any sense of
>> what might be going wrong? I am, of course happy to send you any other
>> logs/output files that might help illuminate the issue.
>>
>> Thank you very much for your time,
>> Madelyn Glymour
>>
>
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