Dear Jodie,
Yes, if the sw*.nii file is 4D, this should be fine and you can proceed
with model specification. In the file selector, in the entry under
"Filter" called "Frames", replace the default value 1 with NaN to list
entire 4D files (no ",1" at the end of files any more) or Inf to list
all frames (i.e. volumes) within a file.
Best regards,
Guillaume.
On 23/06/2021 15:06, Davies-Thompson J. wrote:
> Hi Guillaume,
>
> Many thanks for your swift response, and for the link. The nii file is
> indeed a 4D dataset. All the pre-processing steps have worked with it so
> far, and when we open it in Mango it says it contains 280 volumes (which
> is correct).
>
> We'll try it in SPM12 and see if that fixes the problem - presumably we
> wouldn't have to run all the pre-processing again, and we can jump
> straight to the model specification stage?
>
> Many thanks,
> Jodie
> ------------------------------------------------------------------------
> *From:* Guillaume Flandin <[log in to unmask]>
> *Sent:* 23 June 2021 14:58
> *To:* Davies-Thompson J. <[log in to unmask]>;
> [log in to unmask] <[log in to unmask]>
> *Subject:* Re: [SPM] Model specification error
>
> Dear Jodie,
>
> I presume you have a 4D NIfTI file (containing a series of 3D volumes
> over time) - if so, have a look at this page on how image files should
> be selected in the batch interface:
>
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikibooks.org%2Fwiki%2FSPM%2FWorking_with_4D_data&data=04%7C01%7CJ.Davies-Thompson%40Swansea.ac.uk%7Cb1369d7f6bc24869542f08d9364f0c90%7Cbbcab52e9fbe43d6a2f39f66c43df268%7C0%7C0%7C637600535403387171%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bZmFhDNwrc6l3V9pRvb%2Fc1BUPjQSmCGkEaUZl5ZNMts%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikibooks.org%2Fwiki%2FSPM%2FWorking_with_4D_data&data=04%7C01%7C%7C5ba6cee05acc42afc10108d936500ffc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637600539765336381%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=0ln%2FKm1GLcxvuuq9xhwagxuPfPR15JL1%2B7uB8i2mD%2F0%3D&reserved=0>
> If that was the source of the problem, I would have expected a more
> explicit error message but I don't remember how it was working for SPM8.
> On that note, I would strongly recommend to switch to SPM12.
>
> Best regards,
> Guillaume.
>
>
> On 23/06/2021 14:49, Davies-Thompson J. wrote:
>> Dear SPM experts,
>>
>> I am attempting to run a basic blocked design analysis, but am having
>> some difficulties at the design specification stage. Below is the error
>> I am getting. I have tried fixing it with the following, but still get
>> the same error message:
>>
>> 1. Running it with and without the motion included as a regressor
>> 2. Only including 2 onsets and durations (in case I made an error with
>> how long the experiment lasts for)
>> 3. Running it using nii, nii.gz, and hdr/img
>>
>> Some notes - it is a simple blocked design, and there is only one swr*
>> file which is an nii file (is this a problem - does it have to be
>> multiple nii files? In which case, how do you unzip to one file per
>> volume using matlab - gunzip only extracts from nii.gz to a singular nii
>> file).
>>
>> ---
>> Failed 'fMRI model specification'
>> Brace indexing is not supported for variables of this type.
>> In file "C:\Users\BoAtMaNeM_CaSsIoPeIa\Desktop\spm8\spm_Ce.m" (v3527),
>> function "spm_Ce" at line 53.
>> In file "C:\Users\BoAtMaNeM_CaSsIoPeIa\Desktop\spm8\spm_fmri_spm_ui.m"
>> (v4421), function "spm_fmri_spm_ui" at line 345.
>> In file
>> "C:\Users\BoAtMaNeM_CaSsIoPeIa\Desktop\spm8\config\spm_run_fmri_spec.m"
>> (v4185), function "spm_run_fmri_spec" at line 301.
>>
>> The following modules did not run:
>> Failed: fMRI model specification
>> ----
>>
>> Are there any other things I could try to fix the problem?
>>
>> Many thanks,
>> Jodie
>
> --
> Guillaume Flandin, PhD
> Wellcome Centre for Human Neuroimaging
> UCL Queen Square Institute of Neurology
> London WC1N 3BG
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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