Dear Michael,
yes, I believe it should work fine with SPM8 as well.
All the best,
Guillaume.
On 30/07/14 17:07, Michael Bannert wrote:
> Hi,
>
> Thanks both of you for your help. Do you believe the two functions would
> also work with SPM8?
>
> I’d rather not switch SPM version at this point…
>
> Cheers,
> Michael
>
> On 30 Jul 2014, at 14:12 , Guillaume Flandin <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
>> Dear Michael,
>>
>> please find attached to this email the relevant modified functions for
>> SPM12b (they are indeed not available from the SPM website yet). They
>> correspond to the ones that Michael W is referring to in his response
>> below: with these, you can specify the 'slice order' and 'reference
>> slice' inputs in unit of time (milliseconds) instead of slice indices;
>> in this setting, what you enter for TA is not relevant and will not be
>> used, so you can set it to 0.
>>
>> Best regards,
>> Guillaume.
>>
>>
>> On 30/07/14 12:52, Michael Woletz wrote:
>>> Dear Michael,
>>>
>>> since the TA is only used to get the right spacing between the slices in
>>> cases where there is a waiting period at the end of the acquisition, it
>>> is not needed any more when the correct slice times are supplied in the
>>> multi band version.
>>> Just set it to any value you want (e.g. 0). The correct TA is already
>>> implicitly stored in your slice times vector.
>>>
>>> If you are using spm_slice_timing.m directly, stick to the TA
>>> calculation in the description and ignore that you are using multiband
>>> when specifying the timing vector. For historical reasons, this vector
>>> is used to calculate the TR and this calculation will only work when you
>>> ignore that you are using a multiband sequence.
>>>
>>> Cheers,
>>> Michael
>>>
>>> On 2014-07-30 13:24, Michael Bannert wrote:
>>>> Dear Michael and SPM gang,
>>>>
>>>> (@Guillaume: I just downloaded SPM12b but I’m afraid the slice
>>>> timing correction hasn’t been included in the current release yet.)
>>>>
>>>> Thanks for your code, Michael! I’m about to use that code on my
>>>> multiband data and I started to wonder about how to calculate TA
>>>> (acquisition time) in a multiband scenario where several slices are
>>>> acquired simultaneously. I have the strong intuition that the
>>>> suggested formula TA = TR - (TR / nslices) does not apply anymore.
>>>>
>>>> I’m working with the following values in my dataset:
>>>> TR = .870 s
>>>> nslices = 56
>>>> MB = 4 (multiband factor: number of slices acquired simultaneously)
>>>>
>>>> Now what formula should I use to calculate TA for use with SPM’s
>>>> slice timing correction algorithm? I had the idea in mind that just
>>>> dividing the number of slices by the number of slices measured
>>>> simultaneously should do the trick:
>>>>
>>>> This is what the formula what would look like then:
>>>> TA_MB = TR - (TR * MB / nslices) = .8079 s
>>>>
>>>> The old formula for comparison:
>>>> TA = TR - (TR / nslices) = .8545 s
>>>>
>>>> Could somebody please verify that I’m on the right track with the
>>>> adapted formula?
>>>>
>>>> Thank you in advance for your thoughts on this!
>>>>
>>>> Cheers,
>>>> Michael
>>>>
>>>> On 02 Jun 2014, at 19:37 , Guillaume Flandin <[log in to unmask]
>>>> <mailto:[log in to unmask]>> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> just to let you know that an implementation of multiband slice timing
>>>>> correction will make its way shortly in SPM12b. It is a contribution
>>>>> from Michael Woletz and colleagues from the Medical University of
>>>>> Vienna, Austria. Their work will be described in a poster at HBM next
>>>>> week (number 3484).
>>>>> I haven't looked at your code Michael (thanks for sharing!) but I
>>>>> assume
>>>>> it should be very similar - with perhaps a difference in how the extra
>>>>> parameters are specified.
>>>>>
>>>>> Best regards,
>>>>> Guillaume.
>>>>>
>>>>>
>>>>> On 02/06/14 18:02, Michael Erb wrote:
>>>>>> Hi all,
>>>>>>
>>>>>> here my solution to the Multiband Slice timing. I have changed the
>>>>>> code
>>>>>> so that for multi band the slice order is an array where each row
>>>>>> give
>>>>>> the slices which are measured at the same timepoint
>>>>>>
>>>>>> % Multi-Band: array
>>>>>> % [ [ 1 4] same timepoint 1
>>>>>> % [ 3 6] same timepoint 2
>>>>>> % [ 2 5] ] same timepoint 3
>>>>>>
>>>>>> Hope it works also for you.
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Michael
>>>>>>
>>>>>>
>>>>>> Am 02.06.2014 15:57, schrieb Torben Lund:
>>>>>>> That is right. Looking at the code it seems that nslices is rather
>>>>>>> fundamental for the way the code works, and that extra matlab coding
>>>>>>> will be needed. You could either rewrite the spm_slicetiming.m
>>>>>>> code or
>>>>>>> alternatively split each of the current volumes into (in our example)
>>>>>>> three volumes, and perform the correction on each of the segments
>>>>>>> seperately, and then after the correction merge the volumes
>>>>>>> again. Much
>>>>>>> better would of course be a slice specific designmatrix in which case
>>>>>>> this would not be a problem.
>>>>>>>
>>>>>>> Best
>>>>>>> Torben
>>>>>>>
>>>>>>>
>>>>>>> Torben Ellegaard Lund
>>>>>>> Associate Professor, PhD
>>>>>>> Center of Functionally Integrative Neuroscience (CFIN)
>>>>>>> Aarhus University
>>>>>>> Aarhus University Hospital
>>>>>>> Building 10G, 5th floor, room 31
>>>>>>> Noerrebrogade 44
>>>>>>> 8000 Aarhus C
>>>>>>> Denmark
>>>>>>> Phone: +45 7846 4380
>>>>>>> Fax: +45 7846 4400
>>>>>>> http://www.cfin.au.dk <http://www.cfin.au.dk/>
>>>>>>> [log in to unmask] <mailto:[log in to unmask]>
>>>>>>> <mailto:[log in to unmask]>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Den Uge:23 02/06/2014 kl. 13.37 skrev Rajat Thomas
>>>>>>> <[log in to unmask] <mailto:[log in to unmask]>
>>>>>>> <mailto:[log in to unmask]>>:
>>>>>>>
>>>>>>>> Hi Torben,
>>>>>>>>
>>>>>>>> Thank you for your suggestion. I think it is a good compromise
>>>>>>>> because
>>>>>>>> in this case for example, 1 3 5 which should be offset by zero
>>>>>>>> (because its acquired simultaneously) but will be offset by TR/15
>>>>>>>> (using default SPM). Indeed for TRs < 1s, this would be negligible.
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> Rajat
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Rajat Mani Thomas
>>>>>>>> Social Brain Lab
>>>>>>>> Netherlands Institute for Neuroscience
>>>>>>>> Amsterdam
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> *From:*Torben Lund <[log in to unmask]
>>>>>>>> <mailto:[log in to unmask]> <mailto:[log in to unmask]>>
>>>>>>>> *Sent:*02 June 2014 11:48
>>>>>>>> *To:*Rajat Thomas
>>>>>>>> *Cc:*spm Parametric Mapping)
>>>>>>>> *Subject:*Re: [SPM] Multiband Slice timing
>>>>>>>> Hi Rajat
>>>>>>>>
>>>>>>>> This is a wild guess which I have not testet, but have you tried
>>>>>>>> a sliceorder vector which reflects the situation e.g. with 15 slices
>>>>>>>> and multislice acceleration of 3 [1 3 5 2 4 1 3 5 2 4 1 3 5 2 4 ]
>>>>>>>>
>>>>>>>> Best
>>>>>>>> Torben
>>>>>>>>
>>>>>>>>
>>>>>>>> Torben Ellegaard Lund
>>>>>>>> Associate Professor, PhD
>>>>>>>> Center of Functionally Integrative Neuroscience (CFIN)
>>>>>>>> Aarhus University
>>>>>>>> Aarhus University Hospital
>>>>>>>> Building 10G, 5th floor, room 31
>>>>>>>> Noerrebrogade 44
>>>>>>>> 8000 Aarhus C
>>>>>>>> Denmark
>>>>>>>> Phone: +45 7846 4380
>>>>>>>> Fax: +45 7846 4400
>>>>>>>> http://www.cfin.au.dk <http://www.cfin.au.dk/>
>>>>>>>> [log in to unmask] <mailto:[log in to unmask]>
>>>>>>>> <mailto:[log in to unmask]>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Den Uge:23 02/06/2014 kl. 11.08 skrev Rajat Thomas
>>>>>>>> <[log in to unmask] <mailto:[log in to unmask]>
>>>>>>>> <mailto:[log in to unmask]>>:
>>>>>>>>
>>>>>>>>> Dear SPMers,
>>>>>>>>>
>>>>>>>>> Any suggestion on how to perform multiband slice timing in SPM?
>>>>>>>>>
>>>>>>>>> Thanks.
>>>>>>>>>
>>>>>>>>> Rajat
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Rajat Mani Thomas
>>>>>>>>> Social Brain Lab
>>>>>>>>> Netherlands Institute for Neuroscience
>>>>>>>>> Amsterdam
>>>>> --
>>>>> Guillaume Flandin, PhD
>>>>> Wellcome Trust Centre for Neuroimaging
>>>>> University College London
>>>>> 12 Queen Square
>>>>> London WC1N 3BG
>>>>
>>>> --
>>>> Michael Bannert, Dipl.-Psych.
>>>> Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ.
>>>> of Tübingen & BCCN Tübingen
>>>> Otfried-Müller-Str. 25, 72076 Tübingen, Germany
>>>> Phone: +49 - (0)7071 / 29 - 89031
>>>>
>>>>
>>>>
>>>
>>> --
>>> Dipl.-Ing. Michael Woletz
>>> Medizinische Universität Wien
>>> Zentrum f. Medizinische Physik und Biomedizinische Technik
>>> Exzellenzzentrum Hochfeld-MR
>>> Lazarettgasse 14
>>> 1090 Wien
>>> Tel.: +43 1 40400 64650
>>>
>>
>> --
>> Guillaume Flandin, PhD
>> Wellcome Trust Centre for Neuroimaging
>> University College London
>> 12 Queen Square
>> London WC1N 3BG
>> <spm_slice_timing.m><spm_cfg_st.m>
>
>
> --
> Michael Bannert, Dipl.-Psych.
> Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of
> Tübingen & BCCN Tübingen
> Otfried-Müller-Str. 25, 72076 Tübingen, Germany
> Phone: +49 - (0)7071 / 29 - 89031
>
>
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
|