spec2nii

https://github.com/wtclarke/spec2nii
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spec2nii is a tool for multi-format conversion of in vivo magnetic resonance spectroscopy (MRS) data...
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### Install spec2nii

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Standard installation commands for the spec2nii package.

```bash
conda install -c conda-forge spec2nii
```

```bash
pip install spec2nii
```

```bash
pixi run spec2nii ...
```

--------------------------------

### Install FSLeyes plugin

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Commands to install the NIfTI-MRS plugin for FSLeyes.

```bash
conda install -c conda-forge fsleyes-plugin-mrs
```

```bash
pip install fsleyes-plugin-mrs
```

--------------------------------

### Manual Build and Upload Commands

Source: https://github.com/wtclarke/spec2nii/blob/master/build_process.md

Legacy commands for tagging, cleaning the workspace, building the package, and uploading to PyPI.

```bash
git tag -m VX.X.X X.X.X
git push github master --tags
git clean -fdxn -e prototyping -e *.code-workspace
git clean -fdx -e prototyping -e *.code-workspace
pixi run build
python -m twine upload dist/*
```

--------------------------------

### Run local development tasks with Pixi

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Commands for linting, testing, and building the project locally.

```bash
pixi run lint
pixi run test
pixi run build
```

--------------------------------

### Create Conda environment

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Commands to set up a dedicated environment for spec2nii.

```bash
conda create -c conda-forge -n my_env python=3.8
    conda activate my_env
    conda install -c conda-forge spec2nii
```

--------------------------------

### Dump NIfTI headers

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Outputs the NIfTI headers and header extension to standard output.

```bash
spec2nii dump FILE
```

--------------------------------

### GE File Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts GE p-files to NIfTI-MRS.

```bash
spec2nii ge FILE
```

--------------------------------

### Convert Varian format

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts Varian fid directories to NIfTI-MRS. Requires a fid directory containing fid and procpar files.

```bash
spec2nii varian /path/to/fid.fid
```

--------------------------------

### Philips SPAR/SDAT Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts Philips SPAR/SDAT files to NIfTI-MRS.

```bash
spec2nii philips SDAT_FILE SPAR_FILE
```

--------------------------------

### Philips Data/List Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts Philips data/list files alongside a matching SPAR file.

```bash
spec2nii philips_dl DATA_FILE LIST_FILE SPAR_FILE
```

--------------------------------

### Calculate read and phase position offsets

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Calculates read and phase position offsets, applying a voxel shift if the matrix size is even.

```C++
m_d_read_pos = m_fov.getSliceOffCenterRO();
m_d_phase_pos = m_fov.getSliceOffCenterPE();
if( !( (n = rMrProt.getsSpecPara().getlFinalMatrixSizeRead()) % 2 ) )
        m_d_read_pos += voxelshift_read * rMrProt.sliceSeries().front().readoutFOV() / (double) n;

if( !( (n = rMrProt.getsSpecPara().getlFinalMatrixSizePhase()) % 2 )
        m_d_phase_pos += voxelshift_phase * rMrProt.sliceSeries().front().phaseFOV() / (double) n;
```

--------------------------------

### Convert Raw, jMRUI, and Text formats

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts processed formats to NIfTI-MRS. The text format requires additional imaging frequency and bandwidth parameters.

```bash
spec2nii raw -a AFFINE_FILE FILE
```

```bash
spec2nii jmrui -a AFFINE_FILE FILE
```

```bash
spec2nii text -a AFFINE_FILE -i imaging_freq -b bandwidth FILE
```

--------------------------------

### Initialize voxel shift constants

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Sets the voxel shift constants to 0.5.

```C++
voxelshift_read = voxelshift_phase = voxelshift_slice = .5;
```

--------------------------------

### Twix Format Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Commands for interacting with Siemens Twix files, including viewing flags and specifying conversion parameters.

```bash
spec2nii twix -v FILE
```

```bash
spec2nii twix -e image FILE
```

--------------------------------

### Automatic Format Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Attempts to automatically detect and convert Twix, RDA, SPAR/SDAT, GE p-file, or DICOM formats.

```bash
spec2nii auto FILE
```

--------------------------------

### Extract and Insert header extensions

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Extracts the header extension to a JSON file or inserts a JSON file into the NIfTI-MRS header extension.

```bash
spec2nii extract FILE
```

```bash
spec2nii insert FILE JSON_FILE
```

--------------------------------

### Bruker Data Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts Bruker 2dseq or fid files to NIfTI-MRS.

```bash
spec2nii bruker -m 2DSEQ 2DSEQ_FILE_or_DIR
```

```bash
spec2nii bruker -m FID FID_FILE_or_DIR
```

--------------------------------

### Siemens DICOM Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts Siemens DICOM files or directories to NIfTI-MRS.

```bash
spec2nii dicom DCM_FILE_or_DIR
```

--------------------------------

### Calculate excitation phase for CSI sequence

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Calculates the excitation phase based on CSI address and FOV parameters.

```C++
excit_phase =  360. * (
    - m_sh_1st_csi_addr[i] * m_d_read_pos / rMrProt.sliceSeries().front().readoutFOV()
    - m_sh_2nd_csi_addr[i] * m_d_phase_pos / rMrProt.sliceSeries().front().phaseFOV()
    - m_sh_3rd_csi_addr[i] * m_d_slice_pos / rMrProt.sliceSeries().front().thickness() );
```

--------------------------------

### UIH DICOM Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts UIH DICOM files or directories to NIfTI-MRS.

```bash
spec2nii uih DCM_FILE_or_DIR
```

--------------------------------

### Siemens RDA Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts Siemens RDA files, compatible with CSI and SVS data.

```bash
spec2nii rda RDA_FILE
```

--------------------------------

### Calculate position offset for VB reconstruction

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Calculates the position offset based on slice thickness and indices.

```C++
posOffset = sliceThickness * ( c3rd - .5 * n3rd + .5 )
```

--------------------------------

### Set 3D CSI position vector in VB reconstruction

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Calculates and sets the position vector for 3D CSI in VB reconstruction.

```C++
dPosVec_vector[0] = m_vfPosition_Sag[0] + m_vfNormal_Sag[0] * posOffset;
dPosVec_vector[1] = m_vfPosition_Cor[0] + m_vfNormal_Cor[0] * posOffset;
dPosVec_vector[2] = m_vfPosition_Tra[0] + m_vfNormal_Tra[0] * posOffset;
pMiniHeader->setArrayValues("PosVec", dPosVec_vector);
```

--------------------------------

### Set 2D CSI position vector in VB reconstruction

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Sets the position vector for 2D CSI in VB reconstruction.

```C++
dPosVec_vector[0] = m_vfPosition_Sag[cSlc];
dPosVec_vector[1] = m_vfPosition_Cor[cSlc];
dPosVec_vector[2] = m_vfPosition_Tra[cSlc];
pMiniHeader->setArrayValues("PosVec", dPosVec_vector);
```

--------------------------------

### Anonymize NIfTI-MRS files

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Removes sensitive header keys and user-defined private parameters from the NIfTI-MRS file.

```bash
spec2nii anon FILE
```

--------------------------------

### Check SliceLocation DICOM tag

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Calculates the dot product to verify the slice location.

```C++
dPosVec_vector[0] * dRowVec[0] + dPosVec_vector[1] * dRowVec[1] + ...
```

--------------------------------

### Philips DICOM Conversion

Source: https://github.com/wtclarke/spec2nii/blob/master/README.md

Converts Philips classic or enhanced DICOM files or directories.

```bash
spec2nii philips_dcm DCM_FILE_or_DIR
```

--------------------------------

### Calculate slice position offset

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Calculates the slice position offset, applying a shift if the matrix size is even.

```C++
m_d_slice_pos = m_fov.getSliceShift();

if( !( (n = rMrProt.getsSpecPara().getlFinalMatrixSizeSlice()) % 2 ) )
        m_d_slice_pos += voxelshift_slice * rMrProt.sliceSeries().front().thickness() / (double) n;
```

--------------------------------

### Set SVS position vector in VB reconstruction

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Sets the position vector for SVS in VB reconstruction.

```C++
dPosVec_vector[0] = m_fVoI_Position_Sag;
dPosVec_vector[1] = m_fVoI_Position_Cor;
dPosVec_vector[2] = m_fVoI_Position_Tra;
pMiniHeader->setArrayValues("PosVec", dPosVec_vector)
```

--------------------------------

### Set position vector in VE reconstruction

Source: https://github.com/wtclarke/spec2nii/blob/master/notes/siemens.md

Sets the slice position vector for VE reconstruction.

```C++
sVec dPosVecPCS(m_dVoI_Position_Sag, m_dVoI_Position_Cor, m_dVoI_Position_Tra);
SodaPointer->setSlicePosVec(dPosVecPCS)
```
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