Dear Steve,
Thanks for your quick response!
You mention adjusting the threshold. We have used a threshold of 20 as advised on the FIX website. Do you recommend lowering that threshold (<20) or increasing it (>20)? What would produce the most reliable results given your expertise in using this tool?
Also, I as mentioned in my previous message, do you think that the way we preprocessed the data (e.g bandpass filter, slice time correction) and the warnings we got in the logMatlab.txt regarding Octave could be a problem?
Any assistance would be more than welcome!
Regards,
Mauricio
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Hi - it looks like none of the ICA components are getting classified as noise, which seems unlikely! So the easiest thing to do would be to change the threshold you are using....see the FIX documentation for more details.
Cheers.
On 30 Dec 2014, at 07:13, Mauricio Delgado <[log in to unmask]> wrote:
Dear FSL experts,
We are using the newly developed FIX tool for the first time and are encountering some problems. After running the standard FIX command as outlined on the FIX website using the Standard.RData data we don't end up with the expected filtered_func_data_clean.nii.gz file. Moreover the content of the fix4melview_Standard_thr20.txt (see below) and logMatlab.txt (see attachment) looks odd/troubling.
Could you be so kind and provide us with some assistance in resolving this issue.
Thanks in advance.
All the best,
Mauricio
We have preprocessed our data using FEAT with ICA exploration on. Data is preprocessed with the following parameters: Bandpass filter (50 and 2.8 sigma), slice time corrected, intensity normalisation, 5 mm smoothing, non-brain tissue removal, and motion correction. The TR is 2.1
This is the Fix command as was run:
/usr/local/fsl/fix1.061/fix Subj_18/Preproc.feat /usr/local/fsl/fix1.061/training_files/Standard.RData 20
These were the FIX steps that were shown on my screen after running the command:
FIX Feature extraction for Melodic output directory: Subj_18/Preproc.feat
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: Subj_18/Preproc.feat using training file: /usr/local/fsl/fix1.061/training_files/Standard.RData and threshold 20
FIX Applying cleanup using cleanup file: Subj_18/Preproc.feat/fix4melview_Standard_thr20.txt and motion cleanup set to 0
Content of fix4melview_Standard_thr20.txt:
filtered_func_data.ica
1, Signal, False
2, Signal, False
3, Signal, False
4, Signal, False
5, Signal, False
6, Signal, False
7, Signal, False
8, Signal, False
9, Signal, False
10, Signal, False
11, Unknown, False
12, Signal, False
13, Signal, False
14, Signal, False
15, Signal, False
16, Signal, False
17, Signal, False
18, Unknown, False
19, Unknown, False
20, Signal, False
21, Signal, False
22, Signal, False
23, Signal, False
24, Signal, False
25, Signal, False
26, Signal, False
27, Signal, False
28, Signal, False
29, Signal, False
30, Signal, False
[]
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\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural
\f0\fs24 \cf2 \cb1 \CocoaLigature0 warning: function /usr/local/octave/octave-3.8.2/share/octave/packages/specfun-1.1.0/expint.m shadows a core library function\
warning: function /usr/local/octave/octave-3.8.2/share/octave/packages/specfun-1.1.0/ellipke.m shadows a core library function\
warning: function /usr/local/octave/octave-3.8.2/share/octave/packages/specfun-1.1.0/erfcinv.m shadows a built-in function\
warning: function /usr/local/octave/octave-3.8.2/lib/octave/packages/specfun-1.1.0/x86_64-unknown-linux-gnu-api-v49+/ellipj.oct shadows a built-in function\
Subj_18/Preproc.feat\
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warning: corrcoef is not equivalent to Matlab and will be removed from a future version of Octave; for similar functionality see corr\
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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