You can give mkanalysis-sess the slice order with -stc as you would with
an ordinary non-accellerated scan. Then give it the number of slice
groups with -ngroups nSliceGroups
I don't quite remember what nSliceGroups means, but I think it means the
number of simultaneously acquired slices.
On 3/
External Email - Use Caution
Are there any suggestions regarding this topic?
Am Montag, 28. März 2022 09:21 CEST, "Laura Doll"
schrieb:
> External Email - Use Caution
>
> Hi everyone,
>
> We are currently piloting an fMRI measurement with multiband sequenc
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 abo
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
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 fou
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 corr
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
they are the files named like "fmcpr.odd.nii.gz"
On 09/04/2015 08:17 AM, std...@virgilio.it wrote:
> Hi using Philips scanner (interleaved)
> Therefore, I'm running
>
> preproc-sess -sf sessid -fwhm 5 -surface fsaverage lhrh -mni305-1mm
> -fsd rest -per-run -sliceorder odd
>
> However, as you c
Hi using Philips scanner (interleaved)Therefore, I'm running
preproc-sess -sf sessid -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest
-per-run -sliceorder odd
However, as you can see below stc has been not produced.
file:///Applications/freesurfer/subjects/Sess101/rest/001/f.niifile:///Appli
what slice order was the data created with? Find out and then use that
slice order in the command
On 8/26/15 4:14 AM, std...@virgilio.it wrote:
Hi list,
I'm performing slice time correction on preproc-sess -s Sess201 -fwhm
5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run.
I have acqui
See preproc-sess -help
On 07/27/2015 02:30 PM, std...@virgilio.it wrote:
> Hi list,
>
> preproc-sess -s Sess101 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd
> rest -per-run
> produces fmc file but fmcstc and fmcstcsm are lacking.
> A- The slice timing correction is performed with the command repo
gt; Thanks,
>
>
> Meryem
>
>
> Message: 11
> Date: Fri, 29 Mar 2013 13:40:42 -0400
> From: "MCLAREN, Donald"
> Subject: Re: [Freesurfer] slice timing
> To: Douglas N Greve
> Cc: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> prtm2htz12fn74vtp2
the calibration scan. I
> pre-process the data and then either surround-subtract or just subtract
> tag from control to get CBF, would it still be a problem to use slice time
> correction?
>
>
> Thanks,
>
>
> Meryem
>
>
> Message: 11
> Date: Fri, 29 Mar 2013 13:40:4
If you are using ASL, you do not want to use Slice timing. You must compute
the CBF maps and keep the slice timing intact.
Removing the time delay between slices will lead to the wrong CBF values as
the CBF equations have the time delay in the equation.
Best Regards, Donald McLaren
==
what are you using to do STC? I think by default FSL will move it to the
middle slice, but there is probably a way to make take into account the
fact that the slices are not uniform over the TR. You should contact the
list of the software you are using to get a definative answer.
doug
On 03/29
Yes, it does MC then STC. This is a chronic problem that has never been
solved. If you do STC first and there is significant motion, then the
STC will be wrong. They really need to be done simultaneously. However,
if you use an ascending or descending slice acq (instead of
interleaved), then th
On 01/31/2013 03:09 PM, Maryam Vaziri Pashkam wrote:
> Hi Doug,
>
> Two questions:
> 1) In fsfast preprocessing is STC done first or MC? is there a way to
> control the order?
MC is done first, then STC. There is not an easy way to control the
order, though it may be possible.
>
>
> 2) Also if S
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