ismrmrd / philips_to_ismrmrd

Philips to ISMRMRD converter

ISMRM Raw Data Format (ISMRMRD)

A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. This repository describes such a common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format. This standard was developed by a subcommittee of the ISMRM Sedona 2013 workshop and is described in detail in:

Inati SJ, Naegele JD, Zwart NR, Roopchansingh V, Lizak MJ, Hansen DC, Liu CY, Atkinson D, Kellman P, Kozerke S, Xue H, Campbell-Washburn AE, Sørensen TS, Hansen MS. ISMRM Raw data format: A proposed standard for MRI raw datasets. Magn Reson Med. 2017 Jan;77(1):411-421.

Please cite this paper if you use the format.

Please the ISMRMRD documentation for details.

philips_to_ismrmrd's Issues

failed to convert

I run something like this

run -f /path/rawdataT1Jacob/raw_007 -x /path/IsmrmrdPhilips.xsl -o out.h5

But I obtain this error:
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Failed to convert SIN file to XML: Unable to open SIN file for XML conversion

My raw data extension are .data and .list, is it not correct??

Thanks

Why TR is set as ETH?

The default xml file sets TR to be ETH. Is there a specific reason for that?

philips_to_ismrmrd/IsmrmrdPhilips.xsl

Lines 184 to 186 in 0e38eb0

	<xsl:for-each select="philips/repetition_times/value">
	<TR>ETH</TR>
	</xsl:for-each>

Need support for 'measurement_sign' to handle reverse direction k-space readout

The 'measurement_sign' entry of the Philips raw data label is not addressed such that raw data acquired with an opposite sign readout direction, e.g. when using bipolar multiple gradient echo (flyback=no), yields "flipped" k-space in the readout (frequency encode) direction.

Parameter XSL stylesheet: does not exist.

Hi,

I have some trouble running the converter..

• Machine: Ubuntu 18.04
• cmake version 3.10.2

After installing ISMRMRD according to the instructions, and installing this package... I tried the example code with some of my data

philips_to_ismrmrd -f v8_19062019_1634512_1_1_surveylrV4 > -x IsmrmrdPhilips.xsl -o philips.h5

Where I get this error

Parameter XSL stylesheet: does not exist.

Another strange effect is when I run

philips_to_ismrmrd --help

I only see the available options.. nothing more. I expected that there would be a bit more information...

In another Issue I found that you recommended to run a debugger against it. You gave the following instructions

cd philips_to_ismrmrd
mkdir build_debug
cd build_debug
cmake -DCMAKE_BUILD_TYPE=Debug ../
make
make install

However, when running make install... it wants to place it in the directory /usr/local/bin/philips_to_ismrmrd, which is of course already occupied.. And thus the installation fails.
Can I somehow say to store it under a different directory? And is this also wise?

Problem when converting data

Dear Michael and Philips users

I have a problem when converting a set of 2D radial raw data from Philips scanner. The command I used is

philips_to_ismrmrd -f aa -x ./IsmrmrdPhilips.xsl -o radial2d.h5

And the error says

Segmentation fault (core dumped)

I'm wondering if you could help take a look at this. The raw data files are attached in the google group thread.

If you need more data, please let me know.

Best Regards!
Yishi

Acquisition time stamp is zero for all acquisitions

Hi,

I wanted to extract the acquisition time for each readout, which I previously performed for Siemens data with:

acq = dset.read_acquisition(acqnum)
time = acq.acquisition_time_stamp

However, when reading Philips data, this entry is 0 for all acquisitions (specified with acqnum). Is this a known issue or might it be related to my data?

Thanks in advance for the help!

incorrect encodedSpace matrixSize entries

The encodedSpace matrixSize entries are not correct. The example MATLAB output below shows the correct size [240, 84, 36] of a 3D k-space loaded with the ismrmrd MATLAB classes. The encodedSpace matrixSize entries are incorrectly set to [448, 156, 35.9996]. IsmrmrdPhilips.xsl needs to be corrected.

%% true size of 3D k-space
nkx = meas.head.number_of_samples(1);
nky = range(meas.head.idx.kspace_encode_step_1(:)) + 1;
nkz = range(meas.head.idx.kspace_encode_step_2(:)) + 1;
nkx

nkx =

240

nky

nky =

 84

nkz

nkz =

 36

%% incorrect encodeSpace sizes
hdr.encoding.encodedSpace.matrixSize.x

ans =

448

hdr.encoding.encodedSpace.matrixSize.y

ans =

156

hdr.encoding.encodedSpace.matrixSize.z

ans =

35.9996