http://www.fmrib.ox.ac.uk/fsl/first/index.html
The following script has been written to automate and simplify all five steps and two Quality Assurance processes. Click her to download script.
Please leave your feedback if you like this tool or a suggestion if you think it needs to be improved!
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6 comments:
In which software did you get these beautiful images?
I created them using FIRST tool (FSL).
Hi, I found the software really useful! Thanks so much for building this.
I noticed that the output of the run_first_all had outputs like these:
vt_t1_all_none_firstseg.nii.gz
vt_t1_all_none_origsegs.nii.gz
vt_t1_to_std_sub.nii.gz
is there supposed to be "FAST" instead of "none"? as a result, I could not check my segmentations.
Hi Mak,
Thank you very much for using this script and for commenting here, telling me about this issue. Word "FAST" will not make any change, I will adapt script to be compatible with your files names and send it to you by email and will change the original one.
Jamaan
Thank you so much! Is there a place for me to check the volume for the subcortical structures so that I could at least be sure that my volumes segmented from FSL FORST are not unusually large or small? Thank you so much! my email: elijahmak@gmail.com
Hi Mak,
I understood that you already had created volume using fslstats command, is that right?
Regarding your previous comment about output file name "vt_t1_all_none_firstseg.nii.gz", could you please verify which did you use for for first run "All or a proper structure"
To find out why you get this name, could you please send one file, so I can test it.
Jamaan
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