what do you mean by functional connectivity if it is not seed based?

On 8/2/17 5:01 PM, John Anderson wrote:

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/FsFastFunctionalConnectivityWalkthr...

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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---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I still don't understand what you mean. in any event, fsfast is set up only to do seed-based FC.

On 8/2/17 5:14 PM, John Anderson wrote:

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.anderso@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/FsFastFunctionalConnectivityWalkthr...

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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�o-�r

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.anderso@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.anderso@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/FsFastFunctionalConnectivityWalkthr...

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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�o-�r

---

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