External Email - Use Caution
Dear Douglas N. Greve,
I see. Thank you!
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: Monday, April 3, 2023 11:26 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Which motion correction parameters are used in FSFAST?
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<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: Friday, March 31, 2023 10:40 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?
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 regressors in
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://secure-web.cisco.com/1GRIZppdm97ltvCJpcifU0sFxe_6_gdygXg-GAsekAEZadAMBY2tstpRq51Q0cN4oHtEa642v5qZUof61vP_t23Z6RecLaMaLWYPUPQTMSe7rVdDde4WSnGf3gcY7uPgch1v15ZVo8ohbVvXtfkv7E_Aj_6WoDLOJ6dKEjLBtcwMomUWRSeOy-YFOdUu51IvI64dUDUVUl3QbgUcu8JeK1sDZtd3X8FLOTpTuKbYDOV-3TwUPkgEFL4Lq-mkks9Dj9t_f64Nyu97C_LZJdEcTNwj8dzH9lH6_Lf5b7y6zbOwFkzlE-vhYJGNxlJfY8VczLJJ-rRG5aNQnTbNsNWUBOw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsFastTutorialV6.0%2FFsFastPreProc%23MotionCorrection.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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1rOkYCz621eTZ7vgMJOfMWYG_oID-8OObBZLU15WniAqKhu42PvNI2QJcXAlLa0COZG6l4Wf4lG4UsXraY5Cnj2l1eApthlUIty5xs4DFIevQehf8xevd5UwIKTFjmyDWjQi0wFdlKHvoM2ChhpwC3B_WkrIRgV9L-zUhAdMPwnVuLHE6A5j70LnXDY0l-YLFyfwx30EEdVtn8WfcdEkfpnQkmzIzK3V0Z2gaXm7h1uxb2tdLKLllp5qDuMIV_p_Kw7pKIeTNijIX2u4euVdC9ovNN4n2rREPbOugKncG5eqBla3R8TzZKRhG8-EDII6F2rvC_Jq8o-SbSW5P3oLPJw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1XAxXa9-2Uaj_PJTSGILNjn4g6kKDxrkKu4lJfZkqPQa9QPsgc0hJ2Bnq19s963YVCJ-d3bbldMQrsKKqlkeFy3RHGz2j0LBKjSUIta-7ym9MwSzw9wpavMjDcBtWFdXVFFYY_B8UG6uuD2Yw7MsGzlR6JXKzHpv1HWkGSpzNkv-0qWT4xWBoY0laFFtq7b_sZB4ES5340CBohDElUQ6dRIVKaBN2LZTbxBVoKX4mYic7ZnlmOk3oXpFQZDPBJyVCslWh1iGUGx269-mJhemAtHqOEw37Uaa6DMz-GB58vKcWgWwUMFoStxuI0nPgOUQBSvFYcR1ozDJ9F-sA9bRuew/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1rOkYCz621eTZ7vgMJOfMWYG_oID-8OObBZLU15WniAqKhu42PvNI2QJcXAlLa0COZG6l4Wf4lG4UsXraY5Cnj2l1eApthlUIty5xs4DFIevQehf8xevd5UwIKTFjmyDWjQi0wFdlKHvoM2ChhpwC3B_WkrIRgV9L-zUhAdMPwnVuLHE6A5j70LnXDY0l-YLFyfwx30EEdVtn8WfcdEkfpnQkmzIzK3V0Z2gaXm7h1uxb2tdLKLllp5qDuMIV_p_Kw7pKIeTNijIX2u4euVdC9ovNN4n2rREPbOugKncG5eqBla3R8TzZKRhG8-EDII6F2rvC_Jq8o-SbSW5P3oLPJw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/11urqkM-G9FB9zRcBAXM5mhqz6YinUD2hKeogtetqKv5OcT98nxRsn2mFwsT_fuBuCMp2Ck8SmwXdLIGXKwDw5yjoEZOPVXtSDsgv6oEJ2KWqP_XukTP94_ZS1KxXZ7w268u7qhw9PVxAMoj4bO5Xd3J-XPYFQtqSGaiYYQ4pRq51xVGIFpSdi1BOgK0IDEcaDKDJelmkR_sUBEt7lhWTTyrcDfA1yF6uh84eiRrqomMNml0UdEynf7NRwQ9NVLwH_uizJgUoYZf5oRIY0gYeLLOXRmDRvWTIb91ngDYwDPDM2CC4zU4U3gm-xpCoscuiAq1yhj-gRPwExxXw_fHKZA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1rOkYCz621eTZ7vgMJOfMWYG_oID-8OObBZLU15WniAqKhu42PvNI2QJcXAlLa0COZG6l4Wf4lG4UsXraY5Cnj2l1eApthlUIty5xs4DFIevQehf8xevd5UwIKTFjmyDWjQi0wFdlKHvoM2ChhpwC3B_WkrIRgV9L-zUhAdMPwnVuLHE6A5j70LnXDY0l-YLFyfwx30EEdVtn8WfcdEkfpnQkmzIzK3V0Z2gaXm7h1uxb2tdLKLllp5qDuMIV_p_Kw7pKIeTNijIX2u4euVdC9ovNN4n2rREPbOugKncG5eqBla3R8TzZKRhG8-EDII6F2rvC_Jq8o-SbSW5P3oLPJw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1yE9gtyVONqF8yr_2fagq7P3WII1wnHwt4dwjLdje1JJ1Ft783NDpWfRvknpIuIp6IYHUuP8ZBg7V38g2FhvvKmQimSl7dqwkS7JYGIL9N1b4jUbGrie3lWWkk14xqN5WFKz24HDgIl6suIKaUxPk3ULoi6ovypqB11JzX9fZlK1XPysg8FNsOqmbwpg9dMWZD1sge0r45w3H1H8SCD36is2rVaIgUUTdfc2qEoQ8x7HvAsVJchKvACxn9Nc05o-VAm1_kRADhU91PdKsLBC11SPuQSr9V6nK10qiP-eLI1VbphlGHlx-maw_jZy-mCyr/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1rOkYCz621eTZ7vgMJOfMWYG_oID-8OObBZLU15WniAqKhu42PvNI2QJcXAlLa0COZG6l4Wf4lG4UsXraY5Cnj2l1eApthlUIty5xs4DFIevQehf8xevd5UwIKTFjmyDWjQi0wFdlKHvoM2ChhpwC3B_WkrIRgV9L-zUhAdMPwnVuLHE6A5j70LnXDY0l-YLFyfwx30EEdVtn8WfcdEkfpnQkmzIzK3V0Z2gaXm7h1uxb2tdLKLllp5qDuMIV_p_Kw7pKIeTNijIX2u4euVdC9ovNN4n2rREPbOugKncG5eqBla3R8TzZKRhG8-EDII6F2rvC_Jq8o-SbSW5P3oLPJw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
