-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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Hello,
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Discussion started by: vinoo128
10 Replies
LEARN ABOUT ULTRIX
uuaids
uuaids(8c)uuaids(8c)Name
uucompact, uumkspool, uurespool, uupoll - uucp utilities
Syntax
uucompact -ssystem
uumkspool system ...
uurespool [ -t# ]
uupoll system ...
Description
All of the commands are located in
The command compacts uucp system spool directories and associated subdirectories. If system is ALL, then all existing uucp system spool
directories are compacted. Otherwise, only the specified system spool directory is compacted. If no system is specified, is compacted.
If is stopped before it is finished, it can be restarted without reprocessing directories. The command continues processing where it left
off during it's previous instantiation.
The command makes a per system spool directory and associated subdirectories for each of the specified systems. For example, if system is
mk3 and if the local system name is penny, the following directories are created:
/usr/spool/uucp/sys/mk3
/usr/spool/uucp/sys/mk3/C.
/usr/spool/uucp/sys/mk3/X.
/usr/spool/uucp/sys/mk3/D.
/usr/spool/uucp/sys/mk3/D.penny
/usr/spool/uucp/sys/mk3/D.penny
The command moves files from old spool directories to new spool directories. Because the structure of the spool directories has changed
from older versions of it is necessary to respool old spooled files to new spool directories in at least two instances:
o When installing the current version of
o When creating a new system spool directory for each system.
In the latter case, it is necessary to move files from to the new spool directories. To ease this task, moves files that have been spooled
in one of 4 formats and respools them under the new spooling structure. The format is specified by the -t# option, where the number sign
(#) can be any one of the following:
o Original spool - All files are in
o Split spool - Contains the subdirectories
o Modified split spool - Contains all subdirectories listed in split spool, and
o Used when a new system directory has been created and spool files must be moved from the DEFAULT directory to the new system directory.
The command forces a connect attempt to the named systems even if recent attempts have failed, but not if the file prohibits the call. For
example, the file will prohibit the call if it is the wrong time of day. Thus, the should be monitored for messages about the connection.
Files
Spool directory
Logfile
See Alsomail(1), uucp(1c), uux(1c)uuaids(8c)