Hi MRS experts,
I acquired SVS data on our Philips scanner. However, after converting to nii format using spec2nii in FSL_MRS, I found that the FIDs from 32 channels have been combined. Is there a setting in the prescription to get the data from each channel?
What’s the export format you used? SDAT/SPAR is already coil-combined on the scanner. DATA/LIST preserves the individual coil signals but does not store the spatial geometry of the acquisition, so you’ll need the SPAR header for that, too. Finally, SIN/LAB/RAW also preserves the individual coil signals, but prior to down-sampling, and is frankly a pain to export.
Thank you for your quick response.
I exported it to SDAT/SPAR. What should I do to enable exports to DATA/LIST, or SIN/LAB/RAW formats? Also, as far as I understand, for Philips data, FSL_MRS only supports importing the SDAT/SPAR format. Is that right?
Spec2nii generally supports data/list when combined with a spar file; I suppose the specifics will depend on the exact sequence you’re using, but for product single-voxel it certainly works. What’s the sequence you’re using?
For the Philips raw data, I’m sharing a little how-to that someone in our group at Hopkins made, but I can’t remember for the life of me who it was (I think it was @stevehui but could have also been @khupfeld or @Helge):
You need to select “YES” for the option “Save raw data” under the Postproc tab in the exam card (before the scan!):
Right click on the data > “Reconstruction” > “Raw Export”
- Double-click on the RawExp - this will bring up a parameter editor for the export
- Set the “Output file identification” to a unique number and Accept - this becomes the file name for the exported data:
- Right click start the export step:
- The raw data (.data/.list) will be generated in the export folder, it is g:\temp by default I think:
CAVEAT: If you have more than one MRS scan in your protocol, make sure they have different export IDs. Files with the same IDs overwrite each other.
You can also save the reconstruction step alongside the exam itself in the exam card, so you only really have to do this setup once.
Yap, that’s how we export raw data in data/list format. Just a reminder for the “Output file identification” in step 4, use a UNIQUE number for each output. Otherwise the export files will be overwritten.
@admin @stevehui Thank you, both. I will try it out later today.
@admin Is right. Spec2nii will handle data/list, though I haven’t seen many types of data int hat format, so I expect that it might not be fully functional for all sequences.
Is there a particular reason you want coil uncombined data? I imagine that there isn’t much to be gained over the Philips default coil combination.
I am a novice in MRS, and doing a calibration of the peaks of PVP phantoms on GE/Philips/Siemens scanners. I only have a very rough understanding of what each preprocessing step does, and so am curious to see how each step does offline, e.g. in FSL_MRS.
BTW, do you know which method Philips uses to do coil combinations? Thanks.