-copy directories to a new location
-perform conversions on the files within the copied directories
-move the newly created files to a new directory
Please see my super basic script and notes below... and thank you thank you thank you in advance !!
Code:
#created 9/4, KZ
subjid=SWJNaudio04 #subject info
value=0*
cd /data2/SWJN/Originals/${subjid}/bold/
cp -r 0* ../../../NIFTI/${subjid}/bold
#these first two lines (above) copy all directories starting with 0 (012, 014, 028, etc.) to the desired new location
cd ../../../NIFTI/${subjid}/bold
#below is where my problem is. mri_convert uses the following format: mri_convert -options /desired/input/path/and/filename /desired/output/path/filename. my problem is that within each /${subjid}/bold/ directory, there are multiple folders (all starting with '0') each containing multiple bshort and hdr files (all starting with 'f_0') and I would like to run the converter/repeat the conversion for every bshort file in each of these directories. I can't just type the actual directory and file numbers because they will differ for each subject. I would ideally like a way to select the numbers from each directory and filename so that the same numbers can be used in the output. I tried to use 0* and f_0*, respectively, to run the converter for all files beginning with 'f_0' in all directories beginning with '0' but this obviously will not work lol
Code:
for f in ${value} ; do mri_convert -it bshort -ot nii /data2/SWJN/Original/${subjid}/bold/${value}/f_${value}.bshort /data2/SWJN/NIFTI/${subjid}/bold/${subjid}_${value}
mkdir NIFTI
mv *.nii /NIFTI/
#this will move the newly created .nii files to new directory
Last edited by Corona688; 09-04-2015 at 12:59 PM..
hai,
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Discussion started by: vinoo128
10 Replies
LEARN ABOUT V7
dh_installdeb
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AUTHOR
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11.1.6ubuntu2 2018-05-10 DH_INSTALLDEB(1)