Those are two different things. The --seg is the name of the segmetation
(eg, aparc+aseg.mgz). --segid is the index in that segmentation to use
On 8/2/17 5:23 PM, John Anderson wrote:
Thank you Doug,
One last question please
in the command
fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg
mean.L_Posteriorcingulate.config
Instead of using segid. it is suggested in the help of fcseed that I
can use the flag "seg segmentation" which is aparac+aseg by default.
if I run the command this way
fcseed-config -seg aparc+aseg -fcname
aparc+aseg.dat -fsd bold -mean -cfg mean.aparc+aseg.config
the command always asks for a seedid? what I am doing wrong?
I still don't understand what you mean. in any event, fsfast is set up
only to do seed-based FC.
-------- Original Message --------
Subject: Re: fsfast
Local Time: August 2, 2017 5:14 PM
UTC Time: August 2, 2017 9:14 PM
From: john.ande...@protonmail.com
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
I mean instead of using seed like cingulate gyrus. Can I use the
whole brain (e.g. wmparc.mgz)?
what do you mean by functional connectivity if it is not seed based.
-------- Original Message --------
Subject: Re: fsfast
Local Time: August 2, 2017 5:01 PM
UTC Time: August 2, 2017 9:01 PM
From: john.ande...@protonmail.com
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Hi Doug,
thank you for your response.
The steps in link that you provided is for a seed based functional
connectivity analysis.
I aim to compare the functional connectivity between two groups
without using seeds similar to what we do in surface based analysis
between two groups to compare volume of or cortical thickness.. Is
this possible with fMRI? Or FSfast can only run fMRI analysis
depending on a seed of interest?
If FSFAST can compare functional connectivity between two groups
then how can I create then I don't need the command fcseed-sess. As
a result how the contrast will be created?
Thank you very much for any clarification.
Are you following these steps?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
When you make your analysis, you need to include something like
-taskreg L_Posteriorcingulate.dat
Then when you run isxconcat-sess, you include this as the contrast.
See the wiki for more details
On 8/2/17 12:34 PM, John Anderson wrote:
Dear Dr Greve,
I am new to FSFAST so I highly appreciate your response.
I have resting state fMRI data and I am following the steps as
reported in wiki. I want to study the difference in functional
connectivity between two groups
My questions are regarding motion evaluation and the contrasts.
1. The attached figure is an output of "plot-twf-sess". Given the
plotted data can we say that including run 003 is more reliable that
all the other runs?
2. In the attached figure the command "plot-twf-sess" provides the
maximum and minimum motion for every run on Y axes. I am wondering
if there is any way to create a cutoff value of motion parameters
for all the runs in the study were data can be included/excluded
depending on lower/upper than this cutoff?
3. I used the following commands to study the differnc ein
functional connectivity between two groups (each group has one run):
## preprocessing
preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh
-mni305-2mm -fsd bold -per-run -init-spm
###**First-Level (Group) Analysis
mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
#####Analyze First Level
selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok
selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok
selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok
Now for the next step I need to concatenate the sessions using
isxconcat but this command needs a contrast which I didn't create it
in the previous step. Given that I am looking for a differnce in the
functional connectivity between two groups how can I create the
contrast for this anlaysis.
Thank you for any help and feedback!!
John
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