They should be the first 3 columns of mcprextreg.dat which are the first 3 PCA components I mentioned below. The actual motion correction parameters are in the .mcdat file

On 3/30/2023 11:39 PM, Andy Kim wrote:

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Dear Douglas N. Greve,

Thank you. I followed your advice and re-ran the codes with -mcextreg. Now there are 3 more columns in X.mat for each run. I assume those 3 additional columns are motion correction parameters.

But what are they? Where do they come from? I couldn't find the same numbers in the mcprextreg files. I'm sorry to bother you, but I don't want to use data that I totally don't have idea. Please help. Thank you.

Kind Regards,

Andy (Junghyun) Kim

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, March 30, 2023 11:06 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Which motion correction parameters are used in FSFAST?
you did not specify to include any motion correction regressors in the design. If that is what you want, then include -mcextreg

On 3/29/2023 11:29 PM, Andy Kim wrote:
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Dear Douglas N. Greve,

My experiment design is block design with 2 conditions.

Here is the mkanalysis command line:

mkanalysis-sess -fsd main -stc siemens \

-surface fsaverage lh -fwhm 0 -event-related -paradigm GLonset.par \

-nconditions 2 -spmhrf 0 -TR 2 -refeventdur 48 -nskip 0 -polyfit 3 \

-analysis GLanalysis01.lh -per-run -force

In addition, I attached the paradigm file, mcprextreg, and X.mat.

I want to know motion correction parameters used as nuisance regressors in FSFAST analysis. I appreciate your help.

Kind regards,
Andy (Junghyun) Kim

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, March 29, 2023 11:01 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Which motion correction parameters are used in FSFAST?
These are not the basic translations and rotations, rather:
mcprextreg - text file of the motion correction parameters assembled into an orthogonalized matrix that can be used as nuisance regressors

I don't know what your design is, please send your mkanalysis command lie

On 3/29/2023 12:45 AM, Andy Kim wrote:
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Dear FreeSurfer Developer,

Hi. Thanks to FreeSurfer, I could perform surface-based activation analysis with FSFAST. Now I want to do surface-based functional connectivity analysis. For the sake of consistency, I want to use the same nuisance regressors as used in FSFAST. Unfortunately I'm stuck in motion correction parameters.

According to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastPreProc#MotionCorrection.28MC.29, motion correction parameters are stored in mcprextreg. Since there are 6 columns, I guess they are 3 translations and 3 rotations. On the other hand, none of them are in mcAll, X.mat. What are the 18 motion correction parameters in X.mat? and which motion correction parameters are used as nuisance regressors in FSFAST?

Thanks in advance.

Kind regards,

Andy (Junghyun) Kim
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