Great to know that this would not cause any problems. After I did stc first and named the file with the stc stem, I tried to use -mcin, -mcout, -smin, and -smout to specific the input and output file stems for motion correction and spatial smoothing in preproc-sess. I received error messages about some files not being there, etc. So I just renamed the stc files back to f.nii.gz files and then ran preproc-sess. Everything seemed to work. So I think renaming seems to work the best if one does not want to disturb things too much.
On Jun 6, 2018, at 12:46 AM, Douglas Greve <dgr...@mgh.harvard.edu<mailto:dgr...@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 Freesurfer 5.3 and not 6.0. Once I was running under the correct version, things were running as intended. I was told that in fs-fast, motion correction (mc) has to go before slice timing correction (stc). For my data, I need to run stc before mc. So I found this work around method: What I did was to run slice timing correction by running stc-sess on the .nii files, rename these stc corrected files back to its original name (and thus pretended they were the original files), and then run preproc-sess without stc. Everything seemed to run through 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 <yaod...@wjh.harvard.edu<mailto:yaod...@wjh.harvard.edu>> wrote: I tried to use preprocess-sess with -sdf, here is the error message: ERROR: Flag -sdf unrecognized. I attach here the slice timing. I saved it in a .txt file and tried “-sdf slicetimingfile” but got the above error message. Instead of using preproc-sess directly, I tried to use stc-sess to correct for timing and then planned to rename the file to the appropriate name to use preproc-sess. But stc-sess would not take -sdf either. In theory, these steps should allow me to do STC first and then MC in fs-fast, right? Here is the slice timing: slice time no. (ms) 1 0.0 2 772.5 3 65.0 4 837.5 5 127.5 6 900.0 7 192.5 8 965.0 9 257.5 10 1030.0 11 322.5 12 1092.5 13 385.0 14 1157.5 15 450.0 16 1222.5 17 515.0 18 1287.5 19 580.0 20 1350.0 21 642.5 22 1415.0 23 707.5 24 0.0 25 772.5 26 65.0 27 837.5 28 127.5 29 900.0 30 192.5 31 965.0 32 257.5 33 1030.0 34 322.5 35 1092.5 36 385.0 37 1157.5 38 450.0 39 1222.5 40 515.0 41 1287.5 42 580.0 43 1350.0 44 642.5 45 1415.0 46 707.5 47 0.0 48 772.5 49 65.0 50 837.5 51 127.5 52 900.0 53 192.5 54 965.0 55 257.5 56 1030.0 57 322.5 58 1092.5 59 385.0 60 1157.5 61 450.0 62 1222.5 63 515.0 64 1287.5 65 580.0 66 1350.0 67 642.5 68 1415.0 69 707.5 Thanks, - Yaoda On Jun 1, 2018, at 5:21 PM, Douglas Greve <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote: You will need to know how many slice groups were used in the acquisition, fsfast will not know that. preproc-sess should accept a slice-timing with with -sdf (though this is not listed in the 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 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 it accordingly? I have the actual slice timing file. I tried to use "-sdf slicedelayfile”, but it does not seem to be a recognized flag. It appears that fs-fast does slice timing correction after motion correction. If the volume is going to be resliced after motion correction, thus each slice will no longer have its original timing, shouldn’t slice timing correction be done before motion correction? Is there a way in fs-fast to run slice timing correction before motion correction? I guess instead of running “preproc-sess”, I could first run “sts-sess” and then “mc-sess”? Any suggestions would be greatly appreciated. Thank you! - Yaoda Xu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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