Re: [Freesurfer] slice timing correction with mulit-band

2018-06-05 Thread Xu, Yaoda
...@mgh.harvard.edu>> wrote: That sounds ok, I don't think it will cause problems. You can also do whatever preprocessing you want and then specify the input data with the -funcstem option to mkanalysis-sess On 6/5/18 8:16 PM, Xu, Yaoda wrote: OK, I realized that I was running under Fre

Re: [Freesurfer] slice timing correction with mulit-band

2018-06-05 Thread Xu, Yaoda
so far to the GLM stage. Does this work around sound OK? Would it cause any problem in the analysis down the line? Thanks a lot, - Yaoda On Jun 1, 2018, at 6:43 PM, Xu, Yaoda mailto:yaod...@wjh.harvard.edu>> wrote: I tried to use preprocess-sess with -sdf, here is the error message:

Re: [Freesurfer] slice timing correction with mulit-band

2018-06-01 Thread Xu, Yaoda
e help). What is the error that you are getting? There is no way to do STC before MC in fsfast. When you have interleaved slices, there are arguments for each order (when the slices are acquired continguously, then MC should always go first). On 5/31/18 11:42 PM, Xu, Yaoda wrote: Dear all, I am

[Freesurfer] slice timing correction with mulit-band

2018-05-31 Thread Xu, Yaoda
Dear all, I am trying to do slicing timing correcting with Siemens’s 3T Prisma data at acceleration 3. I am told that I can use “-ngroups” when running "preproc-sess”. How do I use the “-ngroups” flag? Should I do “-ngroups 3”? Would fs-fast automatically compute the slice timing file and apply