Dear Leonardo,
it seems like this option has been rarely used until Torben mentioned
it... (the help text is rather discouraging). I got it running by
replacing size(.,1) with size(.) in spm_uw_estimate.m l.630-632:
[nx,mx1] = size(Bx1); [nx,mx2] = size(Bx2);
[ny,my1] = size(By1); [ny,my2] = size(By2);
[nz,mz1] = size(Bz1); [nz,mz2] = size(Bz2);
This will be available in the next update of SPM12.
Best regards,
Guillaume.
On 27/06/16 10:17, Torben Lund wrote:
> That was indeed the one I was thinking about, but I have never tried
> this option, and I am sorry to se it fail.
>
> Best Torben
>
>
> Den 27. jun. 2016 kl. 11.12 skrev Leonardo Tozzi <[log in to unmask]
> <mailto:[log in to unmask]>>:
>
>> Dear Torben,
>>
>>
>> Thank you very much for your swift and thorough reply.
>>
>> Sadly, the dataset has been already acquired and passed to me for
>> analysis. Therefore, I would be especially interested in how to
>> correct for these effects post-acquisition if possible.
>>
>> When you talk about Jacobian modulation, do you mean using the
>> "Realign and Unwarp" dialog and setting the Jacobian deformations
>> option to Yes? If I do that and leave the other settings as default,
>> the unwarping fails and I get the following error:
>>
>>
>> Unwarp terminated abnormally.
>> Failed 'Realign & Unwarp'
>> Error using size
>> Too many output arguments.
>> In file "/Users/tozzil/Documents/MATLAB/Apps/spm12/spm_uw_estimate.m"
>> (v6456), function "uwAtA2" at line 630.
>> In file "/Users/tozzil/Documents/MATLAB/Apps/spm12/spm_uw_estimate.m"
>> (v6456), function "build_AtA" at line 580.
>> In file "/Users/tozzil/Documents/MATLAB/Apps/spm12/spm_uw_estimate.m"
>> (v6456), function "spm_uw_estimate" at line 353.
>> In file
>> "/Users/tozzil/Documents/MATLAB/Apps/spm12/config/spm_run_realignunwarp.m"
>> (v6554), function "spm_run_realignunwarp" at line 90.
>>
>> The following modules did not run:
>> Failed: Realign & Unwarp
>>
>>
>> Are there any settings that should be manually changed for this
>> procedure?
>>
>> Thank you very much,
>>
>>
>>
>>
>> Leonardo Tozzi, MD
>>
>> PhD Student
>>
>> Trinity College Institute of Neuroscience
>>
>> College Green, Dublin 2
>>
>> Ireland
>>
>> ------------------------------------------------------------------------
>> *From:* Torben Lund <[log in to unmask] <mailto:[log in to unmask]>>
>> *Sent:* Monday, June 27, 2016 10:42:50 AM
>> *To:* Leonardo Tozzi
>> *Cc:* [log in to unmask] <mailto:[log in to unmask]>
>> *Subject:* Re: [SPM] Hyperintensity artefact close to edge of field of
>> view
>>
>> Dear Leonardo
>>
>> It looks like signal pile-up near air tissue interfaces due to B0
>> inhomogenieties. You can reduce this at the acquisition stage by using
>> in-plane acceleration e.g. GRAPPA, smaller voxels or different
>> angulation of the slices. Modulation with the jacobian during unwrap
>> might reduce this.
>>
>> Best
>> Torben
>>
>>
>> Sendt fra min iPhone
>>
>> Den 27. jun. 2016 kl. 08.43 skrev Leonardo Tozzi <[log in to unmask]
>> <mailto:[log in to unmask]>>:
>>
>>> Dear experts,
>>>
>>> I am currently working on a task fMRI dataset (TR: 2s, TE: 35ms,
>>> voxel size: 3x3 mm2, 4.8 mm slice thickness, 550 dynamic scans, 23
>>> slices per volume).
>>> While preprocessing the data on SPM, I noticed that it shows a
>>> hyperintensity in the anterior cingulate cortex and inferior temporal
>>> lobes, close to the edge of the field of view. This looks like an
>>> artefact to me: it seems to be common across subjects (see screenshot
>>> 1: 5 subjects after warping at volume 1) and within the time series
>>> of each subject (see screenshot 2, one subject volumes 100:108).
>>> I was wondering if someone had any suggestions on how to correct this
>>> artefact (if possible) and, otherwise, some insight on how it might
>>> impact the analysis of task related activity using a GLM. In
>>> particular, I am concerned it might affect the detection of task
>>> effects in the subgenual portion of the ACC, especially after smoothing.
>>>
>>> Thank you for your help.
>>> Yours faithfully,
>>>
>>>
>>> Leonardo Tozzi, M.D.
>>>
>>> /PhD Candidate/
>>> /Discipline of Psychiatry
>>> Trinity College Institute of Neuroscience/
>>> /College Green
>>> Dublin 2/
>>> /Ireland/
>>> /
>>> /
>>> /Office: +35318964234/
>>> /Mobile: //+353851026166/
>>> <1.png><2.png>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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