The regressors have been demeaned; other than that, they should be the same.
On 3/31/2023 6:59 PM, Andy Kim wrote:
External Email - Use Caution
Dear Douglas N. Greve,
But the 3 additional columns in X.mat file (which is result of
-mcextreg option in mkanalysis-sess command) are not the first 3
columns of mcprextreg file. They are totally different numbers. You
are saying they (3 additional columns in X.mat file and the first 3
columns of mcprextreg file) should be the same, right? Or am I
misunderstanding what you're saying?
Kind Regards,
Andy (Junghyun) Kim
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Friday, March 31, 2023 10:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Which motion correction parameters are
used in FSFAST?
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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Thursday, March 30, 2023 11:06 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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:
External Email - Use Caution
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
regressorsin FSFAST analysis. I appreciate your help.
Kind regards,
Andy (Junghyun) Kim
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Wednesday, March 29, 2023 11:01 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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:
External Email - Use Caution
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
<https://secure-web.cisco.com/10LyHLSQ2Psfux7V-2TqU0TpTUpRE9gROQ8dm_KryluL_QNU55nhxXetOytBet_fQTG2A2PoLAke5cI9GoJ_eOzKwcQtM7JYw9WYkhhQtt4s_DvZSfuBoKyguaDrK0mk0JuETegFDP3ZyvD9qyw4cHTRZQb4vlDoArkNwd9vCCghIRn9t4xKTpeh9V8rLHllL_HSPRV5m0aF_axLuq8MDNrWo5dzq5hejqIK9sN2xGbSggauWRBsUhLpwYiivhVBn7KdQOMfU5Fu6_mxwrCIiNvR4h-Ppkv4hJ0XwVF4Yl9PZKclgLeYyDKzb_0D9qDTnFRh9CGp5eFa_0qD3zHhSSA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsFastTutorialV6.0%2FFsFastPreProc%23MotionCorrection.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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