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 <surface file> 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
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Andy Kim
Sent: Monday, January 9, 2023 8:25 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Tuesday, January 10, 2023 12:17 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<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>
<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
<freesurfer@nmr.mgh.harvard.edu<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://neurovault.org/FAQ<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>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 6, 2023 11:19 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<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>
<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
<freesurfer@nmr.mgh.harvard.edu<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://neurovault.org/images/395091/<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>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, January 5, 2023 10:39 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<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>
<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
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
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
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