If you don't believe what Michael Harms wrote, you can make a test
acquisition with a phantom. Remove the phantom after about 0.6*TR and
see which slices disappear.
Michael.
Am 01.12.2011 18:25, schrieb Michael Harms:
> If this is Siemen's EPI, and you collected an even number of slices with
> an Interleaved acquisition (and assuming that the other conditions I
> mentioned hold), then the order of slice acquisition is [2 4 6 ... 1 3
> 5 ...]. Siemen's states this very clearly in their fMRI Users Guide
> (which I'll forward to you as a separate communication).
>
> Best,
> -MH
>
> On Thu, 2011-12-01 at 19:16 +0200, zeynep basgoze wrote:
>> Hmmm now I have two different answers and I'm confused again :( What I
>> used in my analysis was "1,3,5,....30,32,34" Why this one does not
>> work I did not quite understand :( I am sure that we have 34 slices
>> and nifti file is ordered "I -> S". I doubt about "F -> H" scheme
>> though...But we use Siemens, so is it "F -> H" by default, when it's
>> interleaved?
>>
>>
>>
>>
>> On Thu, Dec 1, 2011 at 7:05 PM, Michael Harms<[log in to unmask]>
>> wrote:
>>
>> It sounds like your technician is giving you faulty advice.
>>
>> With Siemen's EPI, if you collect an interleaved acquisition
>> with an
>> even number of slices, then even slices are acquired first,
>> followed by
>> the odd slices! So, assuming an axial acquisition, and that
>> you used an
>> "F -> H" scheme for Image Numbering during the acquisition,
>> and that the
>> slice axis in your nifti file is ordered "I -> S", then the
>> order of
>> slice acquisition is:
>>
>> [2:2:n 1:2:n-1]
>>
>>
>> which should be ("2 4 6 ... 1 3 5 ...")
>> You say that you somehow got a "34, 32 ..." order with that
>> specification?? That makes no sense...
>>
>> cheers,
>> -MH
>>
>>
>> On Thu, 2011-12-01 at 16:06 +0200, zeynep basgoze wrote:
>> > Hi Vladimir,
>> >
>> >
>> > I have a problem with slice timing optionsin SPM. We have 34
>> slices,
>> > and our scanner (Siemens 3T)'s acquisition mode is
>> interleaved and
>> > scans from 1 to 34. I used [1:2:n 2:2:n-1] and got something
>> like
>> > "1,3,5....". Later, I read in a poster that since I have
>> even no of
>> > slice (34) I should use [2:2:n 1:2:n-1]. However when I use
>> this one
>> > it goes like "34, 32 ...". But our technician said that it
>> should be
>> > like: "1,3,5...". What should I do now? I am so confused.
>> >
>> >
>> > Thank you in advance for helping me out :)
>> >
>> >
>> >
>>
>>
>>
>
--
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Dr. Michael Erb
Dep. Neuroimaging and MR-Physics
University Hospital Tübingen
Hoppe-Seyler-Str. 3
72076 Tübingen, Germany
Tel.: +49(0)7071/2987753 priv. +49(0)7071/61559
Fax.: +49(0)7071/294371
e-mail: <[log in to unmask]>
www: http://www.medizin.uni-tuebingen.de/nrad/sektion/
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