mriconvert: basic usage, dti reordering and fsl nifit question

[Chr. Rossmanith]

Hi Michael,

maybe an example for file name creation is helpful:

mcverter --fnformat="My_%PN_%SN" -f fsl -n ...

creates files with names like My_Foo_001_0001.nii, My_Foo_001_0002.nii, 
... , My_Foo_002_0001.nii

i.e. format elements are a combination of some fixed strings ("My") and 
variables taken from the image header prepended with '%' (%PN or %SN).

Christina Rossmanith
--
Dept. of Neurology
University Medicine Mannheim
University of Heidelberg
Germany


On 23.08.2016 09:51, Scheel, Michael wrote:
> Dear all,
>
> i am a new user of mriconvert (dcm2nii previously) and i am very happy 
> about the functionality (e.g. about the output of the info.txt file)
> and also all the background information that I found in the programm 
> itself and on this mailing list  (e.g. to File formats especially the 
> details to fsl nifti)
>
> I have some very basic questions that I hope the mriconvert experts 
> can help me with
>
> 1) Usage of --fnformat=<str>
> I am unsure on how to provide format strings for custom naming of 
> output files
>
> Usage: mcverter [-h] -o <str> -f <str> [-v] [-q] [-V] [-j] [-x] [-d] 
> [-a] [-n] [-b] [-r] [-u] [-s <str>] [-m <str>] [-F <str>] Input 
> directory or file(s)...
>   -h, --help Show this help message
> ……..
>  -F, --fnformat=<str>Use this format for name of output file:
> format = {format element} ;
> some text = {filesystem-legal characters} ;
> format element = {some text} , {"%" "PN" | "PI" | "SD" | "ST" | "SI" | 
> "TD" | "SN" | "SQ" | "PR" | "RD"} , {some text} ;
> or
> format = {"+" | "-" , "PatientName" | "PatientId" | "SeriesDate" | 
> "SeriesTime" | "StudyId" | "StudyDescription" | "SeriesNumber" | 
> "SequenceName" | "ProtocolName" | "SeriesDescription"
>
> I would like to have a custom output filename but I am unsure on how I 
> should provide the format elements.
> Could you give me some examples for actual commands
> I tried the following but this will rename the file into 
> {"PatientName”}.hdr/img
> mcverter -o conversion_fsl_3 -v --fnformat={"PatientName"} dicom
>
>
> 2) DTI conversion - volumes reordered
> I have a DTI dataset with 1b0 volume and 12 directions with 8 repetitions.
> It was originally acquired
> b0_rep1 dir1_rep1 dir2_rep1 dir3_rep1 dir4_rep1 dir5_rep1 dir6_rep1 
> dir7_rep1 dir8_rep1 dir9_rep1 dir10_rep1 dir11_rep1 dir12_rep1 b0_rep2 
> dir1_rep2  …. dir12_rep8
> after conversion the volumes and also the respective bvals and bvecs 
> entries in my case get resorted
> b0_rep1 b0_rep2 b0_rep3 b0_rep4 b0_rep5 b0_rep6 b0_rep7 b0_rep8 
> dir1_rep1 dir1_rep2 dir1_rep3 dir1_rep4 dir1_rep5 dir1_rep6 dir1_rep7 
> dir1_rep8 dir2_rep1 dir2_rep2 ….
> Is this intended and if so why?
>
>
> 3) FSL Nifti - 16bit unsigned
> I have seen that there has been a discussion on FSL supporting 16bit 
> unsigned. As this led to any results?
>
>
> Best wishes, Michael
>
>
> Michael Scheel, MD
> Neurodiagnostics Laboratory
> and Clinical Neuroimmunology Group
> NeuroCure Clinical Research Center
> Charité - Universitätsmedizin Berlin
> Charitéplatz 1
> 10117 Berlin, Germany
>
>
>
> _______________________________________________
> mriconvert mailing list
> mriconvert at lists.uoregon.edu
> https://lists-prod.uoregon.edu/mailman/listinfo/mriconvert


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