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
External Email - Use Caution
Hi everyone,
We are currently piloting an fMRI measurement with multiband sequence on a 3T
Siemens scanner to increase resolution, but I don't know how to do the slice
timing correction:
I assume, that I have to use a slicedelay file instead of the
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
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
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
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 acquired data
using a Philipps scanner (interleaved). Thefore, shuold I use "-sliceorder
siemens"?The command line:preproc-sess -s Sess201 -fwhm 5 -surf
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 acquired data
using a Philipps scanner (interleaved). Thefore, shuold I use "-sliceorder
siemens"?The command line:preproc-sess -s Sess201 -fwhm 5 -surfa
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
Hi list,
preproc-sess -s Sess101 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest
-per-runproduces fmc file but fmcstc and fmcstcsm are lacking.A- The slice
timing correction is performed with the command reported above? Or I should add
to command line -stc (furthemore, where I should put it? S
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
be a problem to use slice time
correction?
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:
Content-Type: text/plain; charset=&
be a problem to use slice time
correction?
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:
Content-Type: text/plain; charset=&
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
Hi,
I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am
wondering when I do slice time correction does that move all slices to the
mid of TR that is 1.5 s prior in time or, it moves them to the timing of
the mid slice, which would be the mid of image acquisition aorund 0.6 sec
prior
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
Can you tell me the order of the slice timing and motion correction steps
in preproc-sess (freesurfer v 4.5)? From the wiki it looks like motion
correction is done first (For MC the input will be f and the output will be
fmc For STC the input will be fmc and the output will be fmcstc". However,
w
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
Hi Doug,
Two questions:
1) In fsfast preprocessing is STC done first or MC? is there a way to
control the order?
2) Also if STC is not mentioned in the analysis line and only done in the
preprocessing would the analysis be run on the STC data automatically? or
should I specify STC in the analysi
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