Hello. I'm having difficulty on the seemingly simple task of converting dcm files to nii files.
I'm using Bash on Ubuntu on Windows.
My Windows version is Windows 10 Pro.
From ~/c9image/NDARAF706DLN/s796950,
I have i796951.MRDC.1 ~ i796951.MRDC.166 files
I want to convert these dcm? image into nii format so that I can start image processing.
However, the command doesn't work the same way as my intuition.
When I entered the following command, it didn't work. (nothing happened)
Even though the instructions appear when using dcm2nii command,
I don't clearly understand as I was unable to find concrete examples of the usage.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN$ dcm2nii -v s796950
Chris Rorden's dcm2nii :: 4AUGUST2014 (Debian) 64bit BSD License
reading preferences file /home/eternal/.dcm2nii/dcm2nii.ini
[b]0 /usr/bin/dcm2nii ERROR: unable to find[/b]
Either drag and drop or specify command line options:
dcm2nii
OPTIONS:
-4 Create 4D volumes, else DTI/fMRI saved as many 3D volumes: Y,N = Y
-a Anonymize [remove identifying information]: Y,N = Y
-b load settings from specified inifile, e.g. '-b C:\set\t1.ini'
-c Collapse input folders: Y,N = Y
-d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = Y
-e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = Y
-f Source filename [e.g. filename.par -> filename.nii]: Y,N = N
-g gzip output, filename.nii.gz [ignored if '-n n']: Y,N = Y
-i ID in filename [filename.dcm -> johndoe.nii]: Y,N = N
-m manually prompt user to specify output format [NIfTI input only]: Y,N = Y
-n output .nii file [if no, create .hdr/.img pair]: Y,N = Y
-o Output Directory, e.g. 'C:\TEMP' (if unspecified, source directory is used)
-p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y
-r Reorient image to nearest orthogonal: Y,N
-s SPM2/Analyze not SPM5/NIfTI [ignored if '-n y']: Y,N = N
-t Text report (patient and scan details): Y,N = N
-v Convert every image in the directory: Y,N = Y
-x Reorient and crop 3D NIfTI images: Y,N = N
You can also set defaults by editing /home/eternal/.dcm2nii/dcm2nii.ini
EXAMPLE: dcm2nii -a y /Users/Joe/Documents/dcm/IM_0116
When I enter the code below, I get the same error as above.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN$ dcm2nii -4 s796950
<span>I would appreciate it if someone knows the correct way of using the dcm2nii code to convert dcm files to nii format. </span>
<span>I've heard that there are also dcm2niigui and also the matlab versions<span id="_plain_text_marker"> </span></span>
<span><span>I can't seem to use dcm2niigui since I'm using Linux command line.</span></span>
<span><span>I would appreciate it if someone knows how to use dcm2niigui on Bash on Ubuntu on Linux.</span></span>
I'm using Bash on Ubuntu on Windows.
My Windows version is Windows 10 Pro.
From ~/c9image/NDARAF706DLN/s796950,
I have i796951.MRDC.1 ~ i796951.MRDC.166 files
I want to convert these dcm? image into nii format so that I can start image processing.
However, the command doesn't work the same way as my intuition.
When I entered the following command, it didn't work. (nothing happened)
Even though the instructions appear when using dcm2nii command,
I don't clearly understand as I was unable to find concrete examples of the usage.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN$ dcm2nii -v s796950
Chris Rorden's dcm2nii :: 4AUGUST2014 (Debian) 64bit BSD License
reading preferences file /home/eternal/.dcm2nii/dcm2nii.ini
[b]0 /usr/bin/dcm2nii ERROR: unable to find[/b]
Either drag and drop or specify command line options:
dcm2nii
OPTIONS:
-4 Create 4D volumes, else DTI/fMRI saved as many 3D volumes: Y,N = Y
-a Anonymize [remove identifying information]: Y,N = Y
-b load settings from specified inifile, e.g. '-b C:\set\t1.ini'
-c Collapse input folders: Y,N = Y
-d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = Y
-e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = Y
-f Source filename [e.g. filename.par -> filename.nii]: Y,N = N
-g gzip output, filename.nii.gz [ignored if '-n n']: Y,N = Y
-i ID in filename [filename.dcm -> johndoe.nii]: Y,N = N
-m manually prompt user to specify output format [NIfTI input only]: Y,N = Y
-n output .nii file [if no, create .hdr/.img pair]: Y,N = Y
-o Output Directory, e.g. 'C:\TEMP' (if unspecified, source directory is used)
-p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y
-r Reorient image to nearest orthogonal: Y,N
-s SPM2/Analyze not SPM5/NIfTI [ignored if '-n y']: Y,N = N
-t Text report (patient and scan details): Y,N = N
-v Convert every image in the directory: Y,N = Y
-x Reorient and crop 3D NIfTI images: Y,N = N
You can also set defaults by editing /home/eternal/.dcm2nii/dcm2nii.ini
EXAMPLE: dcm2nii -a y /Users/Joe/Documents/dcm/IM_0116
When I enter the code below, I get the same error as above.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN$ dcm2nii -4 s796950
<span>I would appreciate it if someone knows the correct way of using the dcm2nii code to convert dcm files to nii format. </span>
<span>I've heard that there are also dcm2niigui and also the matlab versions<span id="_plain_text_marker"> </span></span>
<span><span>I can't seem to use dcm2niigui since I'm using Linux command line.</span></span>
<span><span>I would appreciate it if someone knows how to use dcm2niigui on Bash on Ubuntu on Linux.</span></span>