indi > NKI/Rockland - Slice-timing and field-mapping
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Oct 26, 2011  03:10 AM | Jonathan O'Muircheartaigh
NKI/Rockland - Slice-timing and field-mapping
Quick questions on the NKI sample:

The acquisition parameters say interleaved for the fMRI - is this ascending or descending?
Also what format/scale are the fieldmap images?

Thanks a lot and apologies if I've missed the answers elsewhere,
Jonathan
Oct 27, 2011  07:10 AM | Maarten Mennes
RE: NKI/Rockland - Slice-timing and field-mapping
Hi Jonathan,

The NKI scanner is a siemens scanner, in that case interleaved is by definition ascending. Whether is starts at slice 1 or slice 2 depends on the number of slices. In this case the resting state scan has 38 slices, so the interleaved sequence will go 2,4,6,..38,1,3,5,...,37.

Could yoy maybe clarify your question regarding the fielmap images?

Maarten
Oct 27, 2011  10:10 AM | Jonathan O'Muircheartaigh
RE: NKI/Rockland - Slice-timing and field-mapping
Hi Maarten,

Thanks a lot - assumed ascending but wanted to be sure.

I'm afraid the question on fieldmaps isn't clear because I don't know a huge amount about them but I'll try to be specific...

There are two magnitude (I think) images available for most subjects:
fieldmapBOLDA_1/fieldmapBOLD.nii.gz
fieldmapBOLDA_1/fieldmapBOLDA.nii.gz
They appear to be an asymmetric split of the acquisition (22 slices in one image and 16 in the other) - how are they combined? (same question for the DTI acquisition)

Apologies if this is a bit of a naive question - I don't have any experience with field-maps.

All the best,
Jonathan
Nov 1, 2011  01:11 PM | Maarten Mennes
RE: NKI/Rockland - Slice-timing and field-mapping
Hi Jonathan,

Yes, the two images in fieldmapBOLDA_1 are both magnitude images. It looks like dcm2nii split the phase image into fieldmapBOLD_1.

I'll follow-up when I get an answer about the split into the different slices...

Maarten
Nov 1, 2011  03:11 PM | Jonathan O'Muircheartaigh
RE: NKI/Rockland - Slice-timing and field-mapping
Don't spend too much time - I think I figured it out for 1 dataset at least (DTI and fMRI) last Friday - Ill see if I it generalises and post a fslsplit + fslmerge command tomorrow when I'm back at my desk.
Nov 25, 2011  06:11 AM | Jonathan O'Muircheartaigh
RE: NKI/Rockland - Slice-timing and field-mapping
Always delayed (this time by a month - a new record...).

The distribution of slices seem to be a bit random - in the fieldmapBOLDA folder the two created images have between 9 and 27 slices per image for fieldmapBOLDA.nii.gz and therefore between 29 and 11 slices per image for fieldmapBOLD.nii.gz. - they do go together but I'd need to figure out how manually for 200 odd datasets.


Is it possible to package up just the DICOMs of the fieldmap images and I'll try to put them together to nifti and send back?

All the best, 
Jonathan
Mar 5, 2013  11:03 AM | Dylan Nielson
RE: NKI/Rockland - Slice-timing and field-mapping
Hi all,

Sorry to resurrect a zombie thread here, but was the issue with the split fieldmaps that Jonathan describes ever resolved?

Thank you,

Dylan
Mar 5, 2013  01:03 PM | Jonathan O'Muircheartaigh
RE: NKI/Rockland - Slice-timing and field-mapping
Kind of - I have them in a big tar file.

I reconstructed them back in 2011 and then changed jobs, forgetting to upload. I still have them so I'll try and get in contact with someone to upload them to the indi site.
Jan 20, 2014  02:01 PM | Basile Pinsard
RE: NKI/Rockland - Slice-timing and field-mapping
Hi,

sorry to resurrect this post again,
my question is pretty simple, where are the fieldmaps stored in dicoms? It does not seems to be included in the big tars. Or maybe this is only for a subset of NKI_RS?
Many thanks for your help.
Cheers.
basile
Jan 30, 2014  08:01 AM | Jonathan O'Muircheartaigh
RE: NKI/Rockland - Slice-timing and field-mapping
I uploaded the fieldmaps stored as niftis to someone at NKI last March but they may have gone awol somewhere in between. I don't see them on the website.

I'm happy to upload again if needed - I think I found slice identifiers in the dicom headers and reconstructed them with an elaborate for loop but it was a few years ago so I don't entirely remember. If I remember, dcm2nii split the fieldmaps unpredictably.


Originally posted by Basile Pinsard:
Hi,

sorry to resurrect this post again,
my question is pretty simple, where are the fieldmaps stored in dicoms? It does not seems to be included in the big tars. Or maybe this is only for a subset of NKI_RS?
Many thanks for your help.
Cheers.
basile
Jan 30, 2014  08:01 AM | Basile Pinsard
RE: NKI/Rockland - Slice-timing and field-mapping
Hi Jonathan,

yes I would be greatly interested by the fieldmaps, the test-retest data only would be nice if they exists, the purpose is to try to the benefit of use of fieldmap in preprocessing of both regular and multiband imaging, and reproducibility is always interesting to assess.

I would rather the dicoms than nifti converted, I personally used dcmstack to convert to nifti or even just for ordering the dicom slices, and I am quite happy with it. The fact is that you can create some specific ordering class to handle different constructor fields and also this enables to handle vendor specific scaling of the values which are meaningful in the case of fieldmaps contrary to other mri acquisitions.

Many thanks for you answer.
Cheers.

basile
Jan 31, 2014  03:01 PM | Paul Geha
RE: NKI/Rockland - Slice-timing and field-mapping
Hi 

I would also be very interested in getting the fieldmap magnitude image correct to using in pre-proprocessing.

I also have a question about slice timing correction: this is a multi-slice parallel acquisition if i am not mistaken?  Which slices are acquired together? Where can we find this information?

Thank you!
Paul
Feb 1, 2014  01:02 AM | Basile Pinsard
RE: NKI/Rockland - Slice-timing and field-mapping
Hi Paul

the way I found to get the slicetiming as this is Siemens data is to look in the csa header for the MosaicRefAcqTimes field.
for example using python nibabel you can do:

import nibabel.nicom.dicomwrappers
dw=nibabel.nicom.dicomwrappers.wrapper_from_file('NKI_enhanced/2475376/session1/RfMRI_mx_1400/IM-0001-0001.dcm')
dw.csa_header['tags']['MosaicRefAcqTimes']

{'items': [0.0,
615.00000001000001,
1230.0000000099999,
437.5,
1052.5000000099999,
262.50000001000001,
877.5,
87.500000009999994,
702.5,
1317.5,
527.50000001000001,
1140.0,
350.00000001000001,
965.00000001000001,
175.0,
790.00000001000001,
0.0,
615.00000001000001,
1230.0000000099999,
437.5,
1052.5000000099999,
262.50000001000001,
877.5,
87.500000009999994,
702.5,
1317.5,
527.50000001000001,
1140.0,
350.00000001000001,
965.00000001000001,
175.0,
790.00000001000001,
0.0,
615.00000001000001,
1230.0000000099999,
437.5,
1052.5000000099999,
262.50000001000001,
877.5,
87.500000009999994,
702.5,
1317.5,
527.50000001000001,
1140.0,
350.00000001000001,
965.00000001000001,
175.0,
790.00000001000001,
0.0,
615.00000001000001,
1230.0000000099999,
437.5,
1052.5000000099999,
262.50000001000001,
877.5,
87.500000009999994,
702.5,
1317.5,
527.50000001000001,
1140.0,
350.00000001000001,
965.00000001000001,
175.0,
790.00000001000001],
'last3': 77,
'n_items': 66,
'syngodt': 4,
'tag_no': 80,
'vm': 0,
'vr': u'FD'}

which seems to give the precise timing of each slice of the mosaic volume.

Cheers.

basile
Sep 9, 2016  06:09 AM | Bruno Hebling Vieira
RE: NKI/Rockland - Slice-timing and field-mapping
Was this ever sorted? I'm working with the NKI - Rockland Sample (NIfTI) and I have to combine the slices of the magnitude images. The NIfTI header apparently gives no information on this.

Also, what are the two Echo times used? The header contains only one echo time.