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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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?
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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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