Dear Gian Marco,
Yes, exactly, you may use "spm_file_merge" to combine multiple 3D volumes into a single 4D volume if necessary (e.g. creating a single 4D NIFTI file per functional run/session)
Best
Alfonso
On Wed, 12 Apr 2023 12:34:42 +0200, Gian Marco Duma <[log in to unmask]> wrote:
>Dear Alfonso thank you so much for this useful suggestion. In this case the
>functional data should be a 4D file created from all the slices, correct?
>Thanks
>
>Il mar 11 apr 2023, 19:21 Alfonso Nieto-Castanon <[log in to unmask]> ha scritto:
>
>> Dear Gian Marco,
>>
>> You may first convert the .mgz files to NIFTI (.nii) format, and then use
>> any regular ROI extraction tool to obtain the BOLD timeseries from those
>> locations. For example, if you are using CONN (one of the SPM toolboxes,
>> see conn-toolbox.org), you could start using a Matlab command like:
>>
>> conn_mgh2nii /mydata/mri/aparc.a2009s+aseg.mgz;
>>
>> to convert your .mgz to .nii format, and then something like:
>>
>> [data, labels] = conn_rex('/mydata/functional/aurest.nii',
>> '/mydata/mri/aparc.a2009s+aseg.nii', 'level', 'clusters');
>>
>> to extract a #timepoints x #rois matrix with the BOLD timeseries within
>> each ROI. Note that your functional data (in this example the file
>> aurest.nii) is expected to be already preprocessed, and in particular
>> co-registered to your anatomical data (to the same anatomical volume that
>> was analyzed by freesurfer); e.g. in the CONN toolbox you may use one of
>> the default subject-space pipelines for that but you can of course also do
>> that in any number of different ways directly from SPM.
>>
>> Hope this helps
>> Alfonso
>>
>> On Thu, 6 Apr 2023 20:18:45 +0100, Gian Marco Duma <[log in to unmask]>
>> wrote:
>>
>> >Dear SPM experts, I have a resting state data in fMRI. I have segmented
>> with freesurfer the anatomy. So now I would like to extract the ROI
>> timeseries based on the the aparc2009 segmentation atlas from Freesurfer.
>> Is there a simple way to extract the BOLD time series from ROI based on
>> freesurfer atlas? I would only need to obtain a matrix n (regions) x m
>> (time point of the BOLD).
>> >Thanks
>>
>>
>>
>
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