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
[]
{\rtf1\ansi\ansicpg1252\cocoartf1265\cocoasubrtf210
{\fonttbl\f0\fmodern\fcharset0 CourierNewPSMT;}
{\colortbl;\red255\green255\blue255;\red26\green26\blue26;}
\paperw11900\paperh16840\margl1440\margr1440\vieww28300\viewh14540\viewkind0
\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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End of Matlab Script}
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