mriconvert: basic usage, dti reordering and fsl nifit question

[Scheel, Michael]

Dear Christina,

thanks so much for you reply. That works!

Do you or someone else has an idea about:

2) DTI conversion - volumes reordered

3) FSL Nifti - 16bit unsigned issue


Thanks, Michael


On 23.08.2016, at 10:30, Chr. Rossmanith <cr at NEURO.MA.UNI-HEIDELBERG.DE<mailto:cr at NEURO.MA.UNI-HEIDELBERG.DE>> wrote:

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




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