Hi,
I'm trying to use the FEAT GUI prestats to correct my DTI data distortion with FSL
4.1.2. It started running fine with the following stated on the feat html page and folders
created. However, the status is "still running" after several days. I'm not sure if the
problem lies in my input files/parameters or with the fsl I've installed. I have also used
the same dataset and tried running it on FSL4.1.0 and 4.1.1 and the same thing happens.
The other tools on fsl ( bet, eddy, tbss, fdt and tracking and fslview) have worked fine.
I have pasted here the output file/folders and feat report log from running the FEAT GUI.
On the fsl FEAT GUI, i then turn off all options except the prestats and put in my 4D
eddycorrected data.nii.gz, the calculated fieldmap, my betted_magnitude_brain.nii.gz and
the required parameters effective EPI echo spacing 0.282ms and EPI TE 102ms.
The output files and folders are:
design.con mc
design.frf prefiltered_func_data.nii.gz
design.fsf prefiltered_func_data_mcf.nii.gz
design.mat report.html
design.png report_log.html
design.ppm report_poststats.html
design.trg report_prestats.html
design_cov.png report_reg.html
design_cov.ppm report_stats.html
example_func.nii.gz unwarp
logs
The progress report is :
Feat main script
/bin/cp /tmp/feat_AQIvE7.fsf design.fsf
/Applications/fsl/fsl/bin/feat_model design
mkdir .files;cp /Applications/fsl/fsl/doc/fsl.css .files;ln -s /Applications/fsl/fsl/doc/images
.files/images
/Applications/fsl/fsl/bin/fsl_sub -T 11 -l logs -N feat2_pre /Applications/fsl/fsl/bin/feat
/Users/siewmingan/Desktop/DATASET/sharon/fsl/trydistortion/data.feat/design.fsf -D
/Users/siewmingan/Desktop/DATASET/sharon/fsl/trydistortion/data.feat -I 1 -prestats
Prestats
/Applications/fsl/fsl/bin/fslmaths
/Users/siewmingan/Desktop/DATASET/sharon/fsl/trydistortion/data prefiltered_func_data
-odt float
Total original volumes = 35
/Applications/fsl/fsl/bin/fslroi prefiltered_func_data example_func 17 1
/bin/mkdir -p unwarp
Secondly, I would like to ask if I have done these calc correctly and if it matters that the
range of intensity of my fieldmap has changed from (-4096 to 4096) to (0 to 4094) when
it is converted from dicom to nii format:
I have a magnitude map and a real field map from the scanner.
The real field map dicom file has intensity -4096 to +4094.
When the dicom file is converted to nifti, the real field map.nii has intensity 0 to 4094.
I rescale it 2 ways to try it out as the range of my real fieldmap is not from -pie to pie.
1. real fieldmap.nii -mul 3.142 -div 4096 fieldmap1.nii -odt float
(this output file has intensity 0 to 3.142)
2. real fieldmap.nii -mul 6.284 -div 4096 fieldmap2.nii -odt float
(this output file has intensity 0 to 6.284)
I did not divide by the TE echo time difference between the phase maps in seconds (i.e
real fieldmap.nii -mul 6.284 -div 4096 -div 0.00246 newfieldmap.nii odt float).
It is recommended to use the FEAT gui to do the distortion correction. If unfortunately, for
some reasons I cannot run the FEAT gui, is it possible to run command line with the
realfieldmap data and the magnitude map data that I have? I found commands lines for
phase maps but am not sure how to do the distortion correction with a realfieldmap of
intensity 0 to 4094 and a magnitude map. Is there a sample command line for me to
perform the distortion correction?
Many Thanks
Siewmin
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