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 <dgreve@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

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