What's the Slice Order of the NKI-RS Lite Releases Data

Submitted by sunnystar2013 on Sat, 08/24/2013 - 15:58

Hi all,

Could anyone give me some information about the R-fMRI Slice Order of NKI-RS Lite Releases. Thank you in advance!

Best regards,

Huangjing

Hi Huangjing,

For sequence of R-fMRI (TR = 2500msec; voxel size = 3mm isotropic; duration = 5 minutes), please input [2:2:38,1:2:37] as slice order in either SPM or DPARSF.

For the other two multiband sequences, 645ms and 1400ms sequences, I don't think SPM can process that kind of multiband sequences at the current stage.

Best,

Chao-Gan

Thank you for your prompt reply. If I would like to deal with the TR=645ms and 1400ms sequences, can DPARSF work well on them? Could you explain more why SPM is supposed unable to process them currently?

In addition, are there any hints about the slice order in the given "Rest_CAP.pdf"? From this document, I got to know nSlices=38 and the multi-slice mode=Interleaved. However, I am not sure whether the slice order is [2:2:38,1:2:37] or [1:2:37,2:2:38]. How can you determine it to be [2:2:38,1:2:37]?

Thank you for your expended time and reply in advance!

Best,

Huangjing

Re

Hi Huangjing,

Because TR=645ms and TR=1400ms sequences are multiband sequences, i.e., several (4) slices were acquired at the same time. AFNI can handle that kind of sequences but not SPM. I asked this question several months ago at SPM maillist, please see here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1209&L=spm&D=0&P=443564

Because this is a SIEMENS scanner. For SIEMENS scanner, if the total slice number is an even number, then will start from the 2nd slice. If the total number is an odd number, then will start from the 1st slice. Thus, for 38 slices interleaved scanning, should be [2:2:38,1:2:37]. If there were 37 slices in total, then will be [1:2:37,2:2:36].

Of note, if it's a GE scanner, then the story is totally different.

Best,

Chao-Gan

Hi Dr. Yan,

Thank you very much for your detailed reply.

BTW, does a Philips scanner follow the rule of [2:2:N,1:2:N-1] for N even slice number and [1:2:N,2:2:N-1] for N odd slice number?

Best,

Huangjing

Re

Hi Huangjing,

To my knowledge, GE should be [1:2:N,2:2:N-1] in such a case. For Philips scanner, I am not quite sure, but should also be [1:2:N,2:2:N-1].

In addistion, here is a note from Qingyang Li:

Hi Chao-gan,

I am bring this email to your attention regarding to the post on R-fMRI network.

Also the slice timing info for the 3 sequences are

645 (40 slices)

0.0 452.5 257.5 65.0 517.5 322.5 130.0 582.5 387.5 195.0 0.0 452.5 257.5 65.0 517.5 322.5 130.0 582.5 387.5 195.0 0.0 452.5 257.5 65.0 517.5 322.5 130.0 582.5 387.5 195.0 0.0 452.5 257.5 65.0 517.5 322.5 130.0 582.5 387.5 195.0

1400 (64 slices)

-- Siemens timing (64 entries): 0.0 615.0 1230.0 440.0 1055.0 262.5 877.5 87.5 702.5 1317.5 527.5 1142.5 352.5 965.0 175.0 790.0 0.0 615.0 1230.0 440.0 1055.0 262.5 877.5 87.5 702.5 1317.5 527.5 1142.5 352.5 965.0 175.0 790.0 0.0 615.0 1230.0 440.0 1055.0 262.5 877.5 87.5 702.5 1317.5 527.5 1142.5 352.5 965.0 175.0 790.0 0.0 615.0 1230.0 440.0 1055.0 262.5 877.5 87.5 702.5 1317.5 527.5 1142.5 352.5 965.0 175.0 790.0

2500 (38 slices)

1255.0 0.0 1320.0 65.0 1385.0 132.5 1452.5 197.5 1517.5 262.5 1585.0 330.0 1650.0 395.0 1717.5 462.5 1782.5 527.5 1847.5 592.5 1915.0 660.0 1980.0 725.0 2047.5 792.5 2112.5 857.5 2177.5 925.0 2245.0 990.0 2310.0 1055.0 2377.5 1122.5 2442.5 1187.5

Yang

Best,

Chao-Gan

Hi Dr. Yan,

Thank you so much for your instructions. It is extremely helpful.

Best,

Huangjing

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