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)
10.0
2772.5
365.0
4837.5
5127.5
6900.0
7192.5
8965.0
9257.5
101030.0
11322.5
121092.5
13385.0
141157.5
15450.0
161222.5
17515.0
181287.5
19580.0
201350.0
21642.5
221415.0
23707.5
240.0
25772.5
2665.0
27837.5
28127.5
29900.0
30192.5
31965.0
32257.5
331030.0
34322.5
351092.5
36385.0
371157.5
38450.0
391222.5
40515.0
411287.5
42580.0
431350.0
44642.5
451415.0
46707.5
470.0
48772.5
4965.0
50837.5
51127.5
52900.0
53192.5
54965.0
55257.5
561030.0
57322.5
581092.5
59385.0
601157.5
61450.0
621222.5
63515.0
641287.5
65580.0
661350.0
67642.5
681415.0
69707.5
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. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
_______________________________________________
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
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
