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MANUAL_INTERACTIVE
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MANUAL_INTERACTIVE
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[General]
dcminteractive contains numerous commands to help you organize
and eventually convert your data. Each of the following can be done:
help: print help information from the manual
undo: undoes your latest change
redo: redoes your latest undo
convert: convert your dicoms to nifti format via dcm2niix
forceconvert: convert your dicoms, allowing overwrite (DANGEROUS)
ignore: ignore a series for viewing and conversion
rename: rename a series description to something else
inspect: print key information for a series
scrutinize: print all dicom heder information for a series
specify: specify values of protected characters (such as %s)
template: create a template to apply to other datasets
reset: resets to the original dicom table
For more information, you can type help COMMAND for more information
Each command's manual contains information on how to use it.
Commands which will use series numbers will also allow you to specify
ranges of series numbers in the following way with the syntax START:END
(as an example, 1:5 would be 1 2 3 4 5). A typical workflow will involve
ignoring dicom series which you are not interested in, such as scouts, and
then renaming series you are interested in. Once you are satisfied, you can
convert the dicoms to the nifti format using Chris Rorden's dcm2niix tool.
(This is a dependency of the software). You may also save your interactive
session's decisions as a "template" which can be applied to other datasets.
Please see MANUAL_TEMPLATE for more information. It is also highly
recommended to read the supplied manual for this program (MANUAL and
MANUAL_INTERACTIVE) before use.
[help]
Help for dcminteractive. Prints help information for the larger
program and for individual program commands. To view the help for an
individual command, use the syntax help COMMAND. For example, to view the
help for undo, type
help undo
and then you will get help text for the undo command. Commands contain both
instructions and examples for you. It is encouraged for you to read the
manual in full, and use the in-session help text as reference.
[undo]
Undoes the latest change.
Syntax:
undo
Undoes your latest change. You can undo changes until you get to
the original dicom table.
undo SERIES
Undoes the last change to the dicom series specified with
standard series specification syntax. Run "help series" for more
information.
Examples:
1 SCOUT
>>rename 1 useless
1 useless
>>undo
1 SCOUT
1 SCOUT
2 GLORIOUS_T1
>>rename 2 okay_t1
1 SCOUT
2 okay_t1
>>undo 1
There are no changes to undo for series 1 (SCOUT)
>>undo okay_t1
1 SCOUT
2 GLORIOUS_T1
>>undo 2
There are no changes to undo for series 2 (GLORIOUS_T1)
[redo]
Redoes your last undo. You can redo changes until you are at the last
undo, or until a new change is made without undo/redo.
Syntax:
redo
Redoes your last undo.
redo SERIES
Redoes the last change to the dicom series specified with
standard series specification syntax. Run "help series" for more
information.
[convert]
Converts your dicom files to the Nifti-1 format. This uses Chris
Rorden's dcm2niix tool. In those mode, nifti files cannot be
overwritten. Paths are created if they are not found.
Syntax:
convert
Converts everything in the table. You are then prompted to enter
a destination for the converted files, and leave it blank to have the
nifti files placed into the same folder as dicoms.
convert PATH
Converts everything in the table, with the resulting nifti files
going to the specified folder.
Examples:
Example 1
---------
1 GLORIOUS_T1
>>convert
Please enter a path (leave blank for in-place):
>>
Conversion complete.
The result would look like:
folder/
dicom1.dcm
dicom2.dcm
...
dicomn.dcm
GLORIOUS_T1.nii.gz
---------
Example 2
---------
1 SCOUT
>>convert niftis
Conversion complete.
The result would look like:
folder/
[force]
Forcefully converts your dicom files to the Nifti-1 format,
allowing file overwrites. In this mode, a file naming collision will
result in the original file being deleted and a new file being written
in its place.
[ignore]
Ignore series in the table.
Syntax: