[Freesurfer] How to convert surface-based atlas to annotation?

[Andy Kim]

External Email - Use Caution

Dear FreeSurfer Developers,


To analyze functional connectivity, I first got Shen 268 surface-based atlas 
from Neurovault. Now I want to extract average time series data from my 
subjects based on the atlas but I have no idea how to make annotation.

All I have is .gii left and right hemispheres atlas files. When I tried 
mris_convert, it says: DA[0] has coordsys with intent NIFTI_INTENT_NONE (should 
be NIFTI_INTENT_POINTSET).

Could you please give me any tips for making an annot file from surface-based 
atlas? Thank you in advance.


Kind Regards,
Andy (Junghyun) Kim
___
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 .
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Re: [Freesurfer] How to convert surface-based atlas to annotation?

[Andy Kim]

External Email - Use Caution

Hi Yujing,

I got the surface-based shen 268 atlas GIFTI file from Neurovault: 
https://secure-web.cisco.com/1nc6gfn6VjjKigEYqWc-8kv59k1M4P4KJsOZNG-wzL9VI7sGz6VtoXvG_MRPd7n1hHecU3LLS5w43aE-t57NFuRIBnv_tzk-0nsXBcpiQ77ZmSTbj2GQVhLK-IB4_Wk3xKYdv4HdSgHx7rjDXvJ5LTWRcOvOKQd8ZFcyhsUVfKTxErlLqydo83AQsb0G4bzx8eRxlK3GbQqE6F2unEOJNs4o7BJbGItXJOSNHKjq-WowGK42iSTozlMFE-bZvVOc1K0TgbWsibZ4E3jwKydRbUsfrTEWlJEoxfxzmHetsxCU1oTcmvcqoEWHB8jjIa8VgsfEyyq3lnHupc-JgRD7NfQ/https%3A%2F%2Fneurovault.org%2Fimages%2F395091%2F
 It is supposed to have specific values within specific regions like any other 
atlases.

What I want to do is to convert the GIFTI file (surface-based atlas) to 
annotation, so that I can extract mean time series.

I saw some methods to convert volume-based atlas to annotation, but I haven't 
found any ways to do it with surface-based atlas. I actually tried volume-based 
shen 268 atlas (recon-all MNI152 -> mri_vol2surf -> mri_vol2label with surf 
option), but I can't trust the result - I will send another email regarding 
this issue. So I want to cross-check with surface-based atlas, which is 
supposed to be easier and more accurate since the atlas itself is on the 
surface.

Could you let me know how to convert the atlas of GIFTI file to annotation or 
how to extract mean time series using a GIFTI atlas file?

Kind Regards,
Andy (Junghyun) Kim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Thursday, January 5, 2023 10:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?


Hi Andy,



Based on my understanding from GIFTI specification, your .gii are functional 
files. I’m not sure if mris_convert supports it.



I’m curious how you got the .gii files.



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andy Kim
Sent: Thursday, January 5, 2023 3:05 AM
To: freesurfer 
Subject: [Freesurfer] How to convert surface-based atlas to annotation?



External Email - Use Caution

Dear FreeSurfer Developers,





To analyze functional connectivity, I first got Shen 268 surface-based atlas 
from Neurovault. Now I want to extract average time series data from my 
subjects based on the atlas but I have no idea how to make annotation.



All I have is .gii left and right hemispheres atlas files. When I tried 
mris_convert, it says: DA[0] has coordsys with intent NIFTI_INTENT_NONE (should 
be NIFTI_INTENT_POINTSET).



Could you please give me any tips for making an annot file from surface-based 
atlas? Thank you in advance.





Kind Regards,

Andy (Junghyun) Kim
___
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. 

Re: [Freesurfer] How to convert surface-based atlas to annotation?

[Andy Kim]

External Email - Use Caution

Hi Yujing,

Yes they are the files I downloaded.

I tried:
mris_convert 395091.R.func.gii rh.shen.atlas.mgh

and I got:
** DA[0] has coordsys with intent NIFTI_INTENT_NONE (should be 
NIFTI_INTENT_POINTSET)
mrisreadGIFTIfile; mris is NULL! found when parsing file 395091.R.func.gii
error: mris_convert: could not read surface file 395091.R.func.gii.

As far as I know, the surface files are converted from MNI152 space. Please 
check Q16 
https://secure-web.cisco.com/1FPjk5lSGgnEhveM5WlL4zKWglLvHWna-h08axP_sAaQzH_BkMS_zr90PX8BUNGvWAw-YU0QqSTjv4eMkR7lUJA6Bic23Czl89dOCnGB7TFJBSceG-VMxjiPR93PDP59FtnvyYS8JgkDd0LF0VtyIVeCqoaQGyyGANQ0I6WwXMQ3vnJzSM2ZjP_drZWMMvebn39zlpYcmDYTepBkloAHMmdocLvNjOqMIT5p_QGHNUX0eBOWou5soOpIoPaOvYUHbSlokzHqSqgCrGJtwIKlp3b6JgSn_qB_1dQ7FKv9jKpnrvFIZ3K6OM6MdwkTEZiTF/https%3A%2F%2Fneurovault.org%2FFAQ

And there is an update. When I tried: mri_vol2label --c 395091.R.func.gii --id 
1 --l rh.shen.atlas.1.label --surf fsaverage rh, it seemed to work fine without 
converting it to freesurfer-friendly file like .mgh.

Kind Regards,
Andy (Junghyun) Kim


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 6, 2023 11:19 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?


Hi Andy,



Thanks for the information.



The error message that you are getting is actually from GIFTI library. I’m 
wondering if any other programs using the same library can parse the .gii 
correctly.



I downloaded these files from the site:

shen_2mm_268_parcellation.nii.gz

395091.R.func.gii

395091.L.func.gii



Can you confirm these are the same files you downloaded? To debug it a little 
more, can you also let me know your mris_convert command line?



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andy Kim
Sent: Thursday, January 5, 2023 9:15 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



External Email - Use Caution

Hi Yujing,



I got the surface-based shen 268 atlas GIFTI file from Neurovault: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://secure-web.cisco.com/17RWlqgnemBfnRNNLgiBsfHWqcXdKKz4kMi-VfXjFMMpi6CZhk0DexQ2yoh9sKS-FES6LLTjF7l5MehFEd1TeqvAnmUl-6QXP_GFdcamPMqraeGJPnkom5t0FkCoVWGReDEb06A4808MczrLRSgLsUsF5m9ETkftifkBCIRFyUzxHZOcgP78mt1OgsCef458vDI-rp0V-GmJ-lAut49y76mkaAFtTB1goOa7iMWA-oCeYZCj9bapst51rNUYBmSsSBCqkiPv19AHpVEPo7PyOP_nlWD8PLX5eusLee_U3OK0xPwNBZrFnsfsKoVjJ6UhI/https%3A%2F%2Fneurovault.org%2Fimages%2F395091%2F<https://secure-web.cisco.com/1nc6gfn6VjjKigEYqWc-8kv59k1M4P4KJsOZNG-wzL9VI7sGz6VtoXvG_MRPd7n1hHecU3LLS5w43aE-t57NFuRIBnv_tzk-0nsXBcpiQ77ZmSTbj2GQVhLK-IB4_Wk3xKYdv4HdSgHx7rjDXvJ5LTWRcOvOKQd8ZFcyhsUVfKTxErlLqydo83AQsb0G4bzx8eRxlK3GbQqE6F2unEOJNs4o7BJbGItXJOSNHKjq-WowGK42iSTozlMFE-bZvVOc1K0TgbWsibZ4E3jwKydRbUsfrTEWlJEoxfxzmHetsxCU1oTcmvcqoEWHB8jjIa8VgsfEyyq3lnHupc-JgRD7NfQ/https%3A%2F%2Fneurovault.org%2Fimages%2F395091%2F>.
 It is supposed to have specific values within specific regions like any other 
atlases.



What I want to do is to convert the GIFTI file (surface-based atlas) to 
annotation, so that I can extract mean time series.



I saw some methods to convert volume-based atlas to annotation, but I haven't 
found any ways to do it with surface-based atlas. I actually tried volume-based 
shen 268 atlas (recon-all MNI152 -> mri_vol2surf -> mri_vol2label with surf 
option), but I can't trust the result - I will send another email regarding 
this issue. So I want to cross-check with surface-based atlas, which is 
supposed to be easier and more accurate since the atlas itself is on the 
surface.



Could you let me know how to convert the atlas of GIFTI file to annotation or 
how to extract mean time series using a GIFTI atlas file?



Kind Regards,

Andy (Junghyun) Kim



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, January 5, 2023 10:39 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



Hi Andy,



Based on my understanding from GIFTI specification, your .gii are functional 
files. I’m not sure if mris_convert supports it.



I’m curious how you got the .gii files.



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andy Kim
Sent: Thursday, January 5, 2023 3:05 AM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] How to convert 

Re: [Freesurfer] How to convert surface-based atlas to annotation?

[Andy Kim]

External Email - Use Caution

Hi Yujing,

rh.shen.atlas.1.label is just an output name. It can be anything. Is this what 
you are asking?

So here is how things have been going. 395091.R.func.gii is a surface version 
of Shen 268 atlas in GIFTI format, so I thought it needed to be converted into 
.mgh and I tried mris_convert which failed.
Then I directly tried mri_vol2label and it seems to work fine. mri_vol2label 
still produces the same error message("DA[0] has coordsys with intent 
NIFTI_INTENT_NONE (should be NIFTI_INTENT_POINTSET)"), but at least 
mri_vol2label command did not fail.

It would be appreciated if you could confirm mri_vol2label works fine after you 
reproduce the command line yourself.
Thanks for your efforts.

Kind Regards,
Andy Junghyun Kim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Tuesday, January 10, 2023 12:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?


Hi Andy,



I would like to reproduce ‘mri_vol2label --c 395091.R.func.gii --id 1 --l 
rh.shen.atlas.1.label --surf fsaverage rh’.  Would you mind letting me know how 
you created rh.shen.atlas.1.label?



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andy Kim
Sent: Sunday, January 8, 2023 1:00 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



External Email - Use Caution

Hi Yujing,



Yes they are the files I downloaded.



I tried:

mris_convert 395091.R.func.gii rh.shen.atlas.mgh



and I got:

** DA[0] has coordsys with intent NIFTI_INTENT_NONE (should be 
NIFTI_INTENT_POINTSET)

mrisreadGIFTIfile; mris is NULL! found when parsing file 395091.R.func.gii

error: mris_convert: could not read surface file 395091.R.func.gii.



As far as I know, the surface files are converted from MNI152 space. Please 
check Q16 MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1BecThDJwbNztud3oC1lsZIyZGkmA_JWqPi7RkFJ5SLWGEFhywI-9mAIio4x3gqnw8yYphDI7zWrFd6e4MIzL5wzXWEvUDw-oMxkziOJb41uwffqmojKj_TE74b4S-sHXLBFERe1-VIMMSv6V9OoIbY9AFIMgvKrnGE6S4d9iDD_8y6yrNCj_7kc3INIA1UKnKEXACM5IrZwcLCXo1aY4GeLKKrR8ED8s8VSRnlfWbBHnW3ttYODnSAXAY9ro7sodpx910OPzjulJ5yxBIHPFNphYN5VHdJ82A5aDOrYYEhzSpGHzhT6fpODOHaSJm7cw/https%3A%2F%2Fneurovault.org%2FFAQ<https://secure-web.cisco.com/1FPjk5lSGgnEhveM5WlL4zKWglLvHWna-h08axP_sAaQzH_BkMS_zr90PX8BUNGvWAw-YU0QqSTjv4eMkR7lUJA6Bic23Czl89dOCnGB7TFJBSceG-VMxjiPR93PDP59FtnvyYS8JgkDd0LF0VtyIVeCqoaQGyyGANQ0I6WwXMQ3vnJzSM2ZjP_drZWMMvebn39zlpYcmDYTepBkloAHMmdocLvNjOqMIT5p_QGHNUX0eBOWou5soOpIoPaOvYUHbSlokzHqSqgCrGJtwIKlp3b6JgSn_qB_1dQ7FKv9jKpnrvFIZ3K6OM6MdwkTEZiTF/https%3A%2F%2Fneurovault.org%2FFAQ>.



And there is an update. When I tried: mri_vol2label --c 395091.R.func.gii --id 
1 --l rh.shen.atlas.1.label --surf fsaverage rh, it seemed to work fine without 
converting it to freesurfer-friendly file like .mgh.



Kind Regards,

Andy (Junghyun) Kim





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 6, 2023 11:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



Hi Andy,



Thanks for the information.



The error message that you are getting is actually from GIFTI library. I’m 
wondering if any other programs using the same library can parse the .gii 
correctly.



I downloaded these files from the site:

shen_2mm_268_parcellation.nii.gz

395091.R.func.gii

395091.L.func.gii



Can you confirm these are the same files you downloaded? To debug it a little 
more, can you also let me know your mris_convert command line?



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andy Kim
Sent: Thursday, January 5, 2023 9:15 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



External Email - Use Caution

Hi Yujing,



I got the surface-based shen 268 atlas GIFTI file from Neurovault: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://secure-web.cisco.com/1NDp7O6WwguCMv8yGmBuQ3g0GyMlcCsqdZR38E26wtLIXEFwKfVdGhUANokOx0-SQWZ8VHOY_p1rBFoJipvMg_lzrAy4JAasggN-ZUR90KlUizlqd5ww03oGiuSoJA5wDP1K7yJWPi2mNTvweudT1cdB2XzDKiys2tb7yLI-9eBPr20bBLzdrTpZr0_OIo2WFJNpqRDT7pDukePozkvzB8jXBrXgKOhkYHcvCJbcPkw9-rlrOdNcDhKiHXIpOxwJI1wrsJz3ZkZgxfvTWM4aRkb2UO7fmRf7sKz2kLH_4A8

Re: [Freesurfer] How to convert surface-based atlas to annotation?

[Andy Kim]

External Email - Use Caution

Hi Yujing,

I got it. Thank you Yujing.

Kind Regards,
Andy Junghyun Kim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Thursday, January 12, 2023 5:04 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?


Hi Andy,



I found out that mris_convert has  ‘-f’ flag to specify functional file. The 
syntax is

mris_convert -f 395091.R.func.gii  rh.shen.atlas.mgh



You also need to specify a valid surface file as the 3rd argument., or it will 
fail argument check.



Best,



Yujing





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andy Kim
Sent: Monday, January 9, 2023 8:25 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



External Email - Use Caution

Hi Yujing,



rh.shen.atlas.1.label is just an output name. It can be anything. Is this what 
you are asking?



So here is how things have been going. 395091.R.func.gii is a surface version 
of Shen 268 atlas in GIFTI format, so I thought it needed to be converted into 
.mgh and I tried mris_convert which failed.

Then I directly tried mri_vol2label and it seems to work fine. mri_vol2label 
still produces the same error message("DA[0] has coordsys with intent 
NIFTI_INTENT_NONE (should be NIFTI_INTENT_POINTSET)"), but at least 
mri_vol2label command did not fail.



It would be appreciated if you could confirm mri_vol2label works fine after you 
reproduce the command line yourself.

Thanks for your efforts.



Kind Regards,

Andy Junghyun Kim



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Tuesday, January 10, 2023 12:17 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



Hi Andy,



I would like to reproduce ‘mri_vol2label --c 395091.R.func.gii --id 1 --l 
rh.shen.atlas.1.label --surf fsaverage rh’.  Would you mind letting me know how 
you created rh.shen.atlas.1.label?



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andy Kim
Sent: Sunday, January 8, 2023 1:00 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



External Email - Use Caution

Hi Yujing,



Yes they are the files I downloaded.



I tried:

mris_convert 395091.R.func.gii rh.shen.atlas.mgh



and I got:

** DA[0] has coordsys with intent NIFTI_INTENT_NONE (should be 
NIFTI_INTENT_POINTSET)

mrisreadGIFTIfile; mris is NULL! found when parsing file 395091.R.func.gii

error: mris_convert: could not read surface file 395091.R.func.gii.



As far as I know, the surface files are converted from MNI152 space. Please 
check Q16 MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1ChDKA3EErXiXfzxccBX00lYA8g7SDFBwHh3C_rujWilfD6dRFSz1-6XrDXMrAummOV6-pvbctwr0zo8KbTWCD6IAgoJCGwQpSmSEUKg-mfVeno1Nw4W5Sy1aOg-GTQ1v7Vs1ieIpSh9fqKOPdLrOouOhXOX9CwLKbqY5N8rY2rxXY59C9ynO6P_dm1VZlNfmABp2IcwXsKMCUKjQ_9AQywKi0pZDB0w5TbLKLw3GSPlIuuVN_CUVakXAer0s5V_yodqy8fAi8GHK9PXe_mdCIxEBKck6KI1DmczEn75SpUz-3FTG4GnmwppZllog2lGq/https%3A%2F%2Fneurovault.org%2FFAQ<https://secure-web.cisco.com/1FPjk5lSGgnEhveM5WlL4zKWglLvHWna-h08axP_sAaQzH_BkMS_zr90PX8BUNGvWAw-YU0QqSTjv4eMkR7lUJA6Bic23Czl89dOCnGB7TFJBSceG-VMxjiPR93PDP59FtnvyYS8JgkDd0LF0VtyIVeCqoaQGyyGANQ0I6WwXMQ3vnJzSM2ZjP_drZWMMvebn39zlpYcmDYTepBkloAHMmdocLvNjOqMIT5p_QGHNUX0eBOWou5soOpIoPaOvYUHbSlokzHqSqgCrGJtwIKlp3b6JgSn_qB_1dQ7FKv9jKpnrvFIZ3K6OM6MdwkTEZiTF/https%3A%2F%2Fneurovault.org%2FFAQ>.



And there is an update. When I tried: mri_vol2label --c 395091.R.func.gii --id 
1 --l rh.shen.atlas.1.label --surf fsaverage rh, it seemed to work fine without 
converting it to freesurfer-friendly file like .mgh.



Kind Regards,

Andy (Junghyun) Kim





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 6, 2023 11:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?



Hi Andy,



Thanks for the information.



The error message that you are getting is actually from GIFTI library. I’m 
wondering if any other programs using the same library can parse the .

[Freesurfer] Do you have a specific reason for having only 3 motion regressors for connectivity analysis?

[Andy Kim]

External Email - Use Caution

Dear FreeSurfer Developers,

I am trying to analyze functional connectivity using Freesurfer. When I checked 
FSFAST tutorial, it says:
Sample command: "mkanalysis-sess -analysis fsrest.surf.lh -surface self lh 
-fwhm 5 -notask -nuisreg vcsf.dat 1 -nuisreg wm.dat 1 -mcextreg -polyfit 5 
-nskip 4 -fsd fsrest -TR 4.5 -per-run"
-mcextreg means that only top 3 components (I checked it was first 3 columns of 
mcprextreg) are used out of total 6 components. And indeed there are only 3 
motion regressors in X.mat file.
Freesurfer uses AFNI program to get motion correction parameters and AFNI uses 
all 6 components. 
(https://secure-web.cisco.com/12TJnsSiUh4nUlS0evLlfL-8nA36tqM4rfztjSsg7-3om9_ecCtXvMBvPYqjf0sKuLiZQn8Kc4JVAk2siFc7R9b_03WI4ju9aoZaa3RGNddJ6rWZ77949c6bJObCxos0x--p6-WKy89GVF6NEuQO9XARbvrlbU6PLWE6fc8EKApLIwE4AGMBKvY8GTpm-48nuYCz_feKDKtqo16zRuvxsXg6N2ct9tZ20yPtnCKpIxjhGQCsa02IvnHKdk-8k7CQ1y_BIQqQHk0Qw8k9Rz7Ud2xDKE0T-4U98Ig-DPt_kvVbU8fAPplOTT4aQchdtENcKWfIFk8X9A8PX4HnK3pYsbg/https%3A%2F%2Fafni.nimh.nih.gov%2Fpub%2Fdist%2Fedu%2Flatest%2Fafni_handouts%2Fafni05_regression.pdf)
Do you have any reasons for having 3 as default?

Kind Regards,
Andy Junghyun Kim
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[Freesurfer] How to get individual betas (parameter estimates) in certain ROI?

[Andy Kim]

External Email - Use Caution

Dear FreeSurfer Developers,

Hi. Thanks to FreeSurfer, I finished a group activation analysis with FS-FAST.
Now I want to draw a ROC curve to check how well my task conditions can 
distinguish M1 and S1. (M1 is more activated under certain condition of my task 
and S1 is more activated under another condition.)
To do so, I need to get every betas of individual nodes in certain ROIs (which 
I created my own, but let's just say M1 and S1).
Betas are in beta.mgh file which is a product of mri_glmfit. Then how do I get 
betas of only M1 nodes or only S1 nodes?

Kind Regards,
Andy (Junghyun) Kim
___
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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 
 .
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. 

[Freesurfer] Which motion correction parameters are used in FSFAST?

[Andy Kim]

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 
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
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 
 .
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. 

Re: [Freesurfer] Which motion correction parameters are used in FSFAST?

[Andy Kim]

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 
 on behalf of Douglas N. Greve 

Sent: Thursday, March 30, 2023 11:06 PM
To: 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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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/1SjzUR0jPOynfk3Z0RrgfVtnfBUH-NvVoDsrYf4eEDxqKSXZpFxXr94_MAX-98O6SZl1yTQOGO-CuCgafWWqZOIkPtjTYgNdbC2zr43MfLs11JA-iLHC7Uk5bJMh5UoiIOyA8rHq6k7QyzZJsOPogPOekV-LWlioqeiiKsLHiiF0E1vO87Ja_1TFoMcsKyGdergQUWhDDwR8_p-07xrLwXiDkOIKYozqA4WiHgE5dckzS13KpX3s21mUNfE67CxMfqOdsjQiFbrV7pTHtj9K0o_zWicd8nv3EZ740bvfRx7K7AIZsENZKmHYZMs05YmTiGGWVb7akOtl1efOURV4e8Q/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/11urqkM-G9FB9zRcBAXM5mhqz6YinUD2hKeogtetqKv5OcT98nxRsn2mFwsT_fuBuCMp2Ck8SmwXdLIGXKwDw5yjoEZOPVXtSDsgv6oEJ2KWqP_XukTP94_ZS1KxXZ7w268u7qhw9PVxAMoj4bO5Xd3J-XPYFQtqSGaiYYQ4pRq51xVGIFpSdi1BOgK0IDEcaDKDJelmkR_sUBEt7lhWTTyrcDfA1yF6uh84eiRrqomMNml0UdEynf7NRwQ9NVLwH_uizJgUoYZf5oRIY0gYeLLOXRmDRvWTIb91ngDYwDPDM2CC4zU4U3gm-xpCoscuiAq1yhj-gRPwExxXw_fHKZA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<h

Re: [Freesurfer] Which motion correction parameters are used in FSFAST?

[Andy Kim]

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 
 on behalf of Douglas N. Greve 

Sent: Friday, March 31, 2023 10:40 PM
To: 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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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/1-DOsKOzL3VaovpLNZZabsFH1ew6VZyXv98DqEpZ9MvSWtIutLwbXfBQApKy16e-HbK-2oG0KdU3GQV4P1TRfqSwIV2rQSWrcpVCGn5heV0DM8AUcTtnPN37JGvsNlgfFBmeBYRlA7GUUQzyisspY0XZNRRVOhTonlMx9CJPC5fbUrA-TxLH8XRH3-6GoUtmOX3PTjuZww0P_UkXTO0gZDxCCI5Mv2IYf_LOx2wrDk1xAqV2pspegF7ySJGwcQAqxzerUD31yNeTkC4ujslVylqxpNuvbG224UDKL4cyRFMNTOdYMRSjJBi_q5j7gtyXb/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.

Re: [Freesurfer] Which motion correction parameters are used in FSFAST?

[Andy Kim]

External Email - Use Caution

Dear Douglas N. Greve,

I see. Thank you!

Kind Regards,
Andy (Junghyun) Kim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, April 3, 2023 11:26 PM
To: 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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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_t23Z6RecLaMaLWYPUPQTMSe7rVdDde

[Freesurfer] How to create a functional ROI on surface where activation is peak?

[Andy Kim]

External Email - Use Caution

Dear FreeSurfer developers,

Hi. I've always appreciated your help.

I am writing this email to kindly ask you how to create a functional ROI where 
activation (which is a result of FS-FAST) is peak. In volume-based analysis, 
people often make a "3mm-sphere" seed around peak activation for connectivity 
analysis. But since it is surface based, there is no "3mm-sphere". Then what 
would it be for surface?

I tried: mri_surfcluster --in ./masked_sig1.nii.gz --hemi lh --subject 
fsaverage --thmin 5 --sum ./summary1.txt, but its output is not actually what I 
want. It tells peak X, Y, Z coordinates, but I want a fixed size of small 
cluster (like 3mm-sphere in volume) for creating a ROI in different masks (like 
peak ROI in V1, peak ROI in V2, etc). In addition, minimum threshold may be 
diffrent depending on masks. By this I mean, if I choose thmin of 5 for both V1 
and V2, V1 may have a huge cluster where vertices have values greater than 5, 
where as V2 may have a small cluster. I just want to get a fixed size of ROI 
around "peak".

How should I make a functional ROI around peak activation on surface?

Kind Regards,
Andy (Junghyun) Kim
___
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 
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Re: [Freesurfer] How to create a functional ROI on surface where activation is peak?

[Andy Kim]

External Email - Use Caution

Thanks! I will try it.

Kind Regards,
Andy (Junghyun) Kim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, April 6, 2023 11:43 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] How to create a functional ROI on surface where 
activation is peak?

If you know what the vertex number is, you can do something like
mri_volsynth --dim-surf fsaverage/surf/lh.white --pdf delta --delta-crsf 
vertexno 0 0 0 --o delta.mgh
mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh
mri_binarize --i delta.sm3.mgh --min 0.5 --o delta.sm3.bin.mgh
delta.sm3.bin.mgh will be a binary disk approximately 3mm in radius

On 4/4/2023 7:24 AM, Andy Kim wrote:

External Email - Use Caution

Dear FreeSurfer developers,

Hi. I've always appreciated your help.

I am writing this email to kindly ask you how to create a functional ROI where 
activation (which is a result of FS-FAST) is peak. In volume-based analysis, 
people often make a "3mm-sphere" seed around peak activation for connectivity 
analysis. But since it is surface based, there is no "3mm-sphere". Then what 
would it be for surface?

I tried: mri_surfcluster --in ./masked_sig1.nii.gz --hemi lh --subject 
fsaverage --thmin 5 --sum ./summary1.txt, but its output is not actually what I 
want. It tells peak X, Y, Z coordinates, but I want a fixed size of small 
cluster (like 3mm-sphere in volume) for creating a ROI in different masks (like 
peak ROI in V1, peak ROI in V2, etc). In addition, minimum threshold may be 
diffrent depending on masks. By this I mean, if I choose thmin of 5 for both V1 
and V2, V1 may have a huge cluster where vertices have values greater than 5, 
where as V2 may have a small cluster. I just want to get a fixed size of ROI 
around "peak".

How should I make a functional ROI around peak activation on surface?

Kind Regards,
Andy (Junghyun) Kim



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[Freesurfer] How can I increase radius of a binary disk?

[Andy Kim]

External Email - Use Caution

Dear Dr. Douglas N. Greve,

Thanks to you, I could have a binary disk approximately 3mm in radius by the 
codes you told me 
(https://secure-web.cisco.com/1z0F3-vP1KDJI6B_AsTyKAaKNmMd0vO7tGkwv_YiAe4mgtFL1QdTiYs_dYZa0SNYmBNh1h2ge_bd6h98_TjHFMZx8lfVf63LrKeca6bpHJqS3efsPrABmWu40PwE_1bXSb2a1Mtv0R2-CjohzV52lOG68h2lN3pBTXfpuar6V01OlX-ZOuMA0aMQl0OxzxU7uGWZRbNeUFiUdR2dqlzLBm98JI_0xPxY7tVbtcYEGfmjJ4NRcdsEjFHhLRp6JVv4h241u3JIeOcZrWmJ69BHaQm7ygPDdDOpDsxQNHVOTHeJVBDigROxNKREccAKsjdVP/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74761.html):

mri_volsynth --dim-surf fsaverage/surf/lh.white --pdf delta --delta-crsf 
${vertexno} 0 0 0 --0 delta.mgh
mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh
mri_binarize --i delta.sm3.mgh --min 0.5 --o delta.sm3.bin.mgh

I have sincerely appreciated your help.

Now I'm wondering how to modulate the radius. I guess I can do it by adding 
--fwhm option to mris_fwhm command, for example:
mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh --fwhm 5
At the end, I will get a binary disk with 5mm in radius. Am I right? And does 
this mean that --fwhm 3 is default for mris_fwhm? How could you define 3mm?

Kind Regards,
Andy (Junghyun) Kim

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Re: [Freesurfer] How can I increase radius of a binary disk?

[Andy Kim]

External Email - Use Caution

Dear Dr. Douglas N. Greve,

I see. Thanks!

Kind Regards,
Andy (Junghyun) Kim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Saturday, May 20, 2023 7:08 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] How can I increase radius of a binary disk?


External Email - Use Caution

oh, you should have used --fwhm 3 on that first command, and if you want 5mm 
then use --fwhm 5


On 5/19/2023 7:15 AM, Andy Kim wrote:

External Email - Use Caution

Dear Dr. Douglas N. Greve,

Thanks to you, I could have a binary disk approximately 3mm in radius by the 
codes you told me (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1wUlJQ4uIaCCKMh9cnv1QSFKTfG1tVIqA2Hu1BVMXjeePssYF4Gdrxj5YOuZPTyJ48jSP1gO-HL_gkwbuSRHEno192j3wNYaZDt32wzd1h-zvtDLliCkQi_dKbye33cnpEt1G4pIDu1bgXruOlVb_lDKnmnTTnhw3yLZ6HlfANeI-pJaCCI5HrUEeVIR0_oOxnbJzzlq8vTIUOyk_DLf4vn3OzMS6NHzE8WisvCHxOUpC_Jd1LnJF3SOwKqkNUUUpnVnGzuOkClHM3gS_hY1PRPI24PVl-yz2InMNvo3ODG3i_S7diUfzHHGD_iUHcS7y/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74761.html<https://secure-web.cisco.com/1z0F3-vP1KDJI6B_AsTyKAaKNmMd0vO7tGkwv_YiAe4mgtFL1QdTiYs_dYZa0SNYmBNh1h2ge_bd6h98_TjHFMZx8lfVf63LrKeca6bpHJqS3efsPrABmWu40PwE_1bXSb2a1Mtv0R2-CjohzV52lOG68h2lN3pBTXfpuar6V01OlX-ZOuMA0aMQl0OxzxU7uGWZRbNeUFiUdR2dqlzLBm98JI_0xPxY7tVbtcYEGfmjJ4NRcdsEjFHhLRp6JVv4h241u3JIeOcZrWmJ69BHaQm7ygPDdDOpDsxQNHVOTHeJVBDigROxNKREccAKsjdVP/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74761.html>):

mri_volsynth --dim-surf fsaverage/surf/lh.white --pdf delta --delta-crsf 
${vertexno} 0 0 0 --0 delta.mgh
mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh
mri_binarize --i delta.sm3.mgh --min 0.5 --o delta.sm3.bin.mgh

I have sincerely appreciated your help.

Now I'm wondering how to modulate the radius. I guess I can do it by adding 
--fwhm option to mris_fwhm command, for example:
mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh --fwhm 5
At the end, I will get a binary disk with 5mm in radius. Am I right? And does 
this mean that --fwhm 3 is default for mris_fwhm? How could you define 3mm?

Kind Regards,
Andy (Junghyun) Kim




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[Freesurfer] Can I use Freeview (tksurferfv) Tools on surface?

[Andy Kim]

External Email - Use Caution

Dear FreeSurfer Developers,

Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine 
voxel draw" of ROI edit tool 
(https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D8qAugBQR0S6zkInLYQn1Xl3TOY0oJFkbI6RPoALUmxV8oGNWxHym5WLqi_7QJGx6lX_2lR2STOnJi8s5vxdZ04_fp6b35pehxBr4-l3lWS9mctgTSjBy8AoiErcgueL8xMXgwARppZnFQsp5XATWNDB0WoToTsJF83bHPyUNGu6Y5lPXBkaByhwQCqmvt868YGR7krXkrVJxtOzaK6CXTOosaqrURervPHT_5_uQcCLb2pTXaSosaJebFrwRElEgl4lxY-KXxNejDq39JdB4yHXidLiBk2g2KtN7BJOhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeviewGuide%2FFreeviewTools%2FRoiEdit).

On the other hand, unfortunately, it seems that it only works in 3d volume 
space.

So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make 
Closed Path". But this time, the vertices were not connected straight. The 
lines were zigzag.

Could you tell me how to draw a rectangular ROI with straight lines. 
Furthermore, if possible, could you explain how zigzag lines form?

Thank you in advance.

Kind Regards,
Andy (Junghyun) Kim
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