You can just average the runs together, then concatenate the averaged
runs, ie,
mri_concat sess01/bold1/analysis1/contrast/ces.nii.gz \
sess01/bold2/analysis2/contrast/ces.nii.gz \
sess01/bold3/analysis3/contrast/ces.nii.gz
--mean --o sess01/contrast.ces.nii.gz
then concatenate/staack the sessions:
mri_concat sess01/contrast.ces.nii.gz \
sess02/contrast.ces.nii.gz ...
--o contrast.ces.nii.gz
Then run mri_glmfit, etc, on the contrast.ces.nii.gz file
On 04/19/2016 11:15 AM, Shea, Conor wrote:
> One of the tasks we use has three runs, and so each run has a specific B0
> map. We're wondering how we can concatenate the three runs back together
> again for the Group analysis, since FSFAST is technically now considering
> each run to be a separate "task."
>
> -----Original Message-----
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Tuesday, April 12, 2016 6:22 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Preprocessing task data with multiple B0-corrected
> runs
>
> Can you tell me more about your design? Does each run have a separate task?
> Do you want to test across tasks?
>
> On 04/12/2016 11:53 AM, Shea, Conor wrote:
>> Thanks so much. So, then, how does the Group Level Analysis work? How do I
>> concatenate the runs together again, now that we've separated them into
>> different tasks?
>>
>> Conor
>>
>> -----Original Message-----
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: Friday, April 08, 2016 12:05 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Preprocessing task data with multiple
>> B0-corrected runs
>>
>> Unfortunately, I only programmed it assuming that you would have only one B0
>> map per session. There are a couple of work-arounds. One is to create a
>> different session for each run. This is probably easiest but makes the group
>> analysis a little trickier.
>>
>> On 04/05/2016 04:48 PM, Shea, Conor wrote:
>>> Dear Doug,
>>>
>>> I'm trying to use FSFAST to analyze task data with multiple runs. Before
>>> using the preproc-sess pipeline, I ran B0 correction on each of the runs,
>>> so I have 3 different b0dcmap files. I'm trying to figure out the best way
>>> to run preprocessing on the three runs simultaneously using preproc-sess,
>>> but I don't know how to get FSFAST to use each run's specific b0dcmap in
>>> the preprocessing of each run's data. FSFAST wants the b0dcmap files to be
>>> in the task folder, but how can it differentiate between the three b0dcmap
>>> files if they're not in the run folders?
>>>
>>> Thanks,
>>> Conor
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
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>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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