_e3 and _e4 (as well as _e1 and _e2 and _ph) from Siemens fieldmaps

[holmeslabra]

Hi all,
I’m having trouble with BIDS-formatting from siemens when I get lots of files for my fieldmaps. I’ve looked through the threads below and none mention having _e3 and _e4 like I do. (I’ve also tried many different things, none will pass bids, listed below)

Threads of similar problems that I’ve looked through:

Siemens fieldmap mixed echo magnitude image

Follwing up from this discussion sometime ago: When you have half the magnitude image data because of downstream processing that dropped what was deemed to be duplicate slices when in reality they came from a different echo, is it legitimate to combine the available data into a single “complete” volume as the lone magnitude image to use for fieldmap correction ? dcm2niix -m 1 will produce an image which has every slice, albeit some come from one echo, others come from the other. In this case,…

fMRI Prepv1.2.5_distortion correction using GRE field map on ME data

Hi Neurostars, I’m trying to have fMRI Prep v1.2.5 perform distortion correction on ME-data using gradient field maps acquired during data collection. Data was acquired using a Siemens scanner with “Sequence Name: *fm2d2r”. Below are the steps I’ve done: Used dcm2niix to convert to BIDS format. Gradient field maps were directed to the ‘rawdata/sub-PILOT010/fmap’ All files in the anat, fmap, and func folders passed BIDS compatibility. This was checked using the command line, web version, …

FMRIPREP: field mapping data

Dear Siemens users, So- what is the standard way to split these combined 4d series to magnitude and phasediff? Going through the whole sequence, getting the indices (of changes from phase to magnitude) and splitting by them is the only way, or there is some shortcut for this? @Chris_Rorden Sorry for the newbie question, but- When converting Siemens gre_field_mapping sequences to the nifti format by running dcm2niix, one finds: _e1 _e1_eq_1 _e2 _e2_eq_1 _e2_ph How does one should trans…

Field mapping ( Siemens scanners)- dcm2niix output 2 BIDS

Thanks for your answer. Regarding _eq: no missing dicoms, as far as I’ve checked*, but I’ve noticed a very weird behavior: the same Siemens fmap sequence (fm2d2r) was executed two times in the experiment. The number of dicoms in the executions are the same for all field maps series. For one run- an _eq file was created by dcm2niix and for another fmap run- no _eq file was created. Do you have any explanation for such a behavior? (no missing dcms, same sequence, different handling by dcm2ni…

I’ve also scoured the BIDS specification and examples and can’t find anything

Here’s a screenshot of folder of fmap files (of one subject, one session) post-dcm2niix. How would I convert this to BIDS? I’ve tried a bunch of things, including:

• putting the e3 e4 etc. into the ‘acq-’ section and making the ending just phasediff/magnitude
• making the endings phase1, phase2, phase3, / magnitude1, magnitude2…
• making the endings phasediff1, phasediff2, phasediff3 / magnitude1, magnitude2…
• not differentiating and just using ‘run-1’ ‘run-2’ etc

How do I differentiate these files?

Thanks so much for any help,
Kaley