External Email - Use Caution
Thank you so much for sharing the ideas, Bruce!
------------------
Best regards,
Yezhe
------------------ Original ------------------
From: "freesurfer-request";<freesurfer-requ...@nmr.mgh.harvard.edu>;
Date: Dec 1, 2020
To: "freesurfer"<freesurfer@nmr.mgh.harvard.edu>;
Subject: Freesurfer Digest, Vol 201, Issue 45
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://secure-web.cisco.com/1z9iluK8C-0HIf0UFksBm0ZUhHli5Vc4eifBra2dUWisaOTx6GJWpI7L5vFYKrsOJvFTSsH3wh5e2ljfhrTbUnCD9E6DNV2w_ova8xc-qUpitfYGbPxqwyBzYiI5Cz4OOYLwy6Tn3zlOEbEE_01HdnQ2ZMF0dKBwCUMpc6F6wZEq6uH7euBNXmrZbEODJMFfVfAwAgT1yVVEjb_UcIEBGYe4PIzgoEuVqn82hCDhuwi3GMcEaemBH5i6A_F-1voHfrCKufDqdyFkS0FFr8ejbLg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: Freesurfer skullstripping error (Fischl, Bruce)
2. Re: arguments to use after pial edits (Darko Komneni?)
3. Re: arguments to use after pial edits (Glasser, Matthew)
4. Fwd: Issue with custom label (Catherine Tallman)
5. Re: Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed} {Disarmed}
{Disarmed}
{Disarmed} {Disarmed} {Disarmed} {Disarmed} (???)
6. Freesurfer skullstripping error ( LIN, Yezhe )
----------------------------------------------------------------------
Message: 1
Date: Mon, 30 Nov 2020 22:18:08 +0000
From: "Fischl, Bruce" <bfis...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer skullstripping error
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<bl0pr04mb66093563136717d2c5c0029bef...@bl0pr04mb6609.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Hi Yezhe
It depends a lot on what your resolution, read out direction, bandwidth and
field strength are. We generally fix these with T2 or FLASH scans at the same
resolution/geometry/readout as the T1. Otherwise they are pretty tough as the
dura is close enough to the gray matter that you can?t see any space between
them
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of LIN, Yezhe
Sent: Monday, November 30, 2020 5:10 PM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer skullstripping error
External Email - Use Caution
Dear Freesurfer users,
Hope this finds you well.
I preprocessed our dataset with recon-all <subj> -s <subj> -all -qcache
and found a number of our subjects had different levels of skullstrip errors. I
tried fixing them by a couple of different approaches, such as -gcut and
adjusted watershed threshold, but they both failed to fix the overlapping of
dura mater (Fig1 and 2). I tried two methods on different subjects and received
the same outcome. I wonder if you have any ideas to fix this error. At this
point, for some who had less skullstripping, I can erase them manually and run
-autorecon-pial or -make. But for the others with multiple locations of
skullstripping (like Fig 3 and 4), do you have any ideas on how to approach to
them at a systemic level? Also I found the skullstripping error in over half of
our subjects, is it normal that we have a such proportion?
Thank you so much!
------------------
Best regards,
Yezhe
Yezhe Lin, MD MMed (she/her/hers)
Postdoctoral Associate, Department of Psychiatry
University of Rochester Medical Center
yezhe.lin....@gmail.com<mailto:yezhe.lin....@gmail.com>
Twitter<https://secure-web.cisco.com/17wBDBOCFmouG2s48nVWmz-vtBr4ZdcKyF8LdUP3ubrRwDQczpm4GpOeJX8y9BVGMRDS3hknZ-VHMl7Mpew7MEMYptkhA86r0KsD3iwPADFZYwCP0wxhuxurWl7QVvY-iKE9rh-IjjIqsk-tgiFqsn1hWbEH81U5odkPQ55wh4CEqMgfm-cSZSuaDsqkZKqwZUEozlWj1ZaRsw8-u0HAfV0dr1to__qlJ3caSexRdjxciXDNNso4HC-jOlPghIUXCedxdkrpeD-QiAcrCzB-gJg/https%3A%2F%2Ftwitter.com%2FLinYezhe>:
@LinYezhe |
LinkedIn<https://secure-web.cisco.com/11z7MNr4cmxXqrne4KcsfCzlNqe69kxiyCzG4wHKz5Ap2hkVCq7WQE3bUD0nxI3_devi7THRad8MWIkFCE8TIJsGs63B1KKBwx8i16T9hRbwmWuZi1-8rDjYgn8fXpWJ6UHh2TQ4hr199_npMHLrGZcY0k1LHUXCIoTxLlrzhbcMLqsMHFUpNs7rbXmCIijBujwG_V-SFYHX0ZQgm_P6tvN_6l2TuqIGq51X2K0M489TLi7tilzKUefrQ7rs_rIOsZDL0UF35gildP4UD5s_vLg/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fyezhe-lin-md-mm-7063b2a1%2F>
|
Researchgate<https://secure-web.cisco.com/1izwT1sMSoKIcMU2d5YWspFhUDtyiXLrkLArb2WuhXY_thz7lEEHjRyirwimP3Vugr6-mte-mOTSXr5fF83_ci3Qfe_rxFYckK5SaisS5HzmQ3bxMPDMOYNqvng1DS9OgDGAiXb-i17FzeUpR5j_DiuNd5mYs33onTXfi3d4EddqwCOEfjj6m4LbeQAomOMxs06OQ2d8r
IPlUPGjELGFQz8xsHlNuDNzKt-daYiJYAs1kgHgxtEF9vM-ssT2gYGaIzf2_qdHfnThVsbwdgrKCeQ/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FYezhe_Lin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://secure-web.cisco.com/1f0DvXyGg-hMt-t89X5AELnPczD7CgpmxvOQ3mVYZuvrF9z4twJqYbU2ccJadfv8cHM3HBGtte-EZ53zc9SWLQfx5GHGg6Q1-XCUKmrEFHn-tuQbiPGQcAxiGqrI3PR-vKKa0gaVeDZqgNd87igQINTa_bB0WfEva0y679OLfl0AbDXrOjOia-R58eh7Udo3m7bwevnPYvmX05MqsOBXQNEcleOHAQdpDjYNvEfGIS7QNkzqKOC3xQ4d-DdSOD13E-o5nVzx7XGczvwO0-yVilA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201130%2F884a92bc%2Fattachment-0001.html
------------------------------
Message: 2
Date: Tue, 1 Dec 2020 01:23:00 +0100
From: Darko Komneni? <komnen...@gmail.com>
Subject: Re: [Freesurfer] arguments to use after pial edits
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAL-_js1WYLPtgefg5A0NHLaaHcRv=efj4kxuaktewyp8p9o...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use
Caution
Thanks Matt!
Should I also add the -autorecon3 flag, or does that get performed
automatically if I put in "autorecon2"?
Best,
Darko
> Message: 4
> Date: Mon, 30 Nov 2020 19:16:06 +0000
> From: "Glasser, Matthew" <glass...@wustl.edu>
> Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed}
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <274fd511-f94f-4bc1-ae0c-804f1a6a3...@wustl.edu>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use
Caution
>
> I find the recon-all table to be helpful:
>
>
>
http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc0VC-s7rH5tRIiUV_kHXR7CsV_-uoWR6y_oPuNxiCAZCmbkgfSfUxHd4oB4gX7XvLCt40MlQR_Ejq0tpN0lnJJt1uO1jl_1XWYZQv92-3NGME0PKZPC51_qjOKHk9cLfcojjN-AssGWAZ7y0t-UJXooxg2G2tzrQqm9emqIASj8_asI8t84TuQRjHEjkEj7KDq8IvfbXNQIT5xDLxB5A7a-aT2IrgX3QZs0Stdt7Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0
>
> In this case, you probably need to run -autorecon2, as all subsequent
> steps are affected by the brainmask.mgz file.
>
> Matt.
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://secure-web.cisco.com/1JC9bGmfD8ICPWLEYWuztA9d0Bavk-ouMj0Eb9TYCm3uUqZ7oO6OddUCOricW30AKoM3NneCw9-MeSr8SNPe8e7ucJ0Vz28n_Hxw7TT-TKR6emohCE53Eh-LmrqbR9op1oa_cY6fkVwEtAHy9jH0n6FKspQU2SVGthSou_QoEJD51bQxVHqCmQ2K2hBDZc2pMgEi0Y-pjlE-iOItysf08xPEpGPX-xJy6uI4Ig3ZaO-H950EUK9-Q8LRrkpX3ROnCcvgjPikC1x4yTiatqChQZA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201201%2F6f1311f8%2Fattachment-0001.html
------------------------------
Message: 3
Date: Tue, 1 Dec 2020 00:25:57 +0000
From: "Glasser, Matthew" <glass...@wustl.edu>
Subject: Re: [Freesurfer] arguments to use after pial edits
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <c985cc68-34cb-4788-81eb-7b912105a...@wustl.edu>
Content-Type: text/plain; charset="utf-8"
External Email - Use
Caution
I think so.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Darko Komneni?
<komnen...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, November 30, 2020 at 6:23 PM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] arguments to use after pial edits
External Email - Use Caution
Thanks Matt!
Should I also add the -autorecon3 flag, or does that get performed
automatically if I put in "autorecon2"?
Best,
Darko
Message: 4
Date: Mon, 30 Nov 2020 19:16:06 +0000
From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed}
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<274fd511-f94f-4bc1-ae0c-804f1a6a3...@wustl.edu<mailto:274fd511-f94f-4bc1-ae0c-804f1a6a3...@wustl.edu>>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
I find the recon-all table to be helpful:
http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc0VC-s7rH5tRIiUV_kHXR7CsV_-uoWR6y_oPuNxiCAZCmbkgfSfUxHd4oB4gX7XvLCt40MlQR_Ejq0tpN0lnJJt1uO1jl_1XWYZQv92-3NGME0PKZPC51_qjOKHk9cLfcojjN-AssGWAZ7y0t-UJXooxg2G2tzrQqm9emqIASj8_asI8t84TuQRjHEjkEj7KDq8IvfbXNQIT5xDLxB5A7a-aT2IrgX3QZs0Stdt7Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0
In this case, you probably need to run -autorecon2, as all subsequent steps are
affected by the brainmask.mgz file.
Matt.
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://secure-web.cisco.com/1UWwFkBGY57eHrVJmdzlE9t0-f_sYBqRvDMW4W5WqqYu13JmJcZylcUGwnb3c2Y04PKtCW0dstuyRO4JHxr0cdhXrPa1UZJFyDfSDwELWQyw7lJABGBZxgq_mxFvVFGI7xXkk9KoutgMxwbv7KjwdpV2bQCjiYkMMIe_q_NjmcLRc7aHENl1pfjYrOyFH9AgntFtARylKHUK7_PC3wkc2BsRQdHfeVQ_9YXnp4NUByizDxsIcHoKJrPGUH6K5e5ULYvOgCkxp52VgkcKrNxqEFA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201201%2Faead8fd7%2Fattachment-0001.html
------------------------------
Message: 4
Date: Mon, 30 Nov 2020 16:28:07 -0800
From: Catherine Tallman <ctall...@ucsd.edu>
Subject: [Freesurfer] Fwd: Issue with custom label
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+obyhmiXyGfYsdBrB+kqtCb6DGowgCLF0wB=undg7aciv3...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use
Caution
Hello,
I was wondering if there were any updates on this question?
Thank you,
Catherine
---------- Forwarded message ---------
From: Catherine Tallman <ctall...@ucsd.edu>
Date: Thu, Nov 19, 2020 at 8:57 AM
Subject: Issue with custom label
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Hello,
After running mri_vol2label I created a custom label named test.label. When
I try to load the label onto lh.pial, I receive the following error: "Could
not load label from <path>". The file is saved within the path folder
itself. Within the terminal I receive the warning "label has not been
mapped to surface". I was wondering what might be causing this issue?
Attached is the label file.
mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l label/lh.test.label
Thank you,
Catherine
--
------------------------------------------------
Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego
--
------------------------------------------------
Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://secure-web.cisco.com/1ADsfVKK3Kh87OVDYLZsPT1BgApEfEROyPNmisM7ZNiCDudMiTSyL8tmV5SjdiDnMOTyx6grpRCWBzednjeYgHr9egDuWwndyRnSPF2n_mmfNBWa5G8Ay9s9XnwZmzF8TwGNs7Lqgu0Qn4ZsHA1sFYZG8AxoC5y0oRZGgFAZhSiFH5wDee5BkSLoF0ZNq9W6NfchW_4KprIb3EGuTvTtXTMRyL-AuNv-yEfJoatzD45f7Z9Mdq3SlgcNNE4QAVZiqjQx5pnwiYobSJxMkR-DwLQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201130%2Fa08bb956%2Fattachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test.label
Type: application/octet-stream
Size: 95213 bytes
Desc: not available
Url :
http://secure-web.cisco.com/18YtCGuex1cbsFPLqZD5387KH1EoR7ZcSwB7RlG2qMTmSM4EFm2DnUy6jxnlTKgyjA4TOd5Mb_ui39v8N-zkWppGhpOW-LOtB-jsuRpjEB3sXwN1AC8PusetKJgHj0LYspE1VwoFLJVoFF8VtGxpk0GP_Ehcs1jNRs-Yg5iYGu0Y0vutdt2SCC807NMA7t129-qIlUpQ091u3Gprgw0yb0QA4okPoEHdd2oUr86MNzXF6xAa-rbcn21j9R8RqFCj3U7wxOCKytfuGA2FJTALtow/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201130%2Fa08bb956%2Fattachment-0001.obj
------------------------------
Message: 5
Date: Tue, 1 Dec 2020 08:59:19 +0800 (GMT+08:00)
From: ??? <meng...@csu.edu.cn>
Subject: Re: [Freesurfer] Extract he value of area and volume in the
fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}
{Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6d642f90.29e3.1761bcf9ccf.coremail.meng...@csu.edu.cn>
Content-Type: text/plain; charset="utf-8"
External Email - Use
Caution
Yes, what should I do if there is something wrong
-----????-----
???:"Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
????:2020-11-30 01:22:22 (???)
???: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
{Disarmed}
You mean that you are getting a different result between the voxel wise
analysis and the ROI-wise analysis? And you created the ROI from the region
that is significant in the voxel-wise analysis? If so, then I think something
is wrong
On 11/17/2020 8:08 PM, ??? wrote:
External Email - Use
Caution
I got the sum area and average area of the label, there is no significant
difference between the mTBI group and health control, either.However, the label
was significant different in the fsaverage between mTBI group and health
control after multiple control. Did this correct?
-----????-----
???:"Douglas N. Greve" <dgr...@mgh.harvard.edu>
????:2020-11-16 23:48:37 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
The lh_areapial.avgwf.dat has a value for each subject. That value will be
whatever the y.mgh is. If you want a different value, then create a new y.mgh
file. Also, I forgot to tell you to include --sumwf so that the avgwf file has
the sum and not the average.
On 11/14/2020 5:24 AM, ??? wrote:
External Email - Use
Caution
I am sorry for that my presentation was not that good, the
lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the
lh_areapial.sum file
with the following command.
mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh lh.areapial.label
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0
My question was that how can I get the value of the area and volume in the
standard space for every TBI and health control subjects.
-----????-----
???:"Douglas N. Greve" <dgr...@mgh.harvard.edu>
????:2020-11-13 23:03:50 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, ??? wrote:
External Email - Use
Caution
Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh lh.areapial.label
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0
(1)Should I extract the area and volume one by one with the following command
for each subject:
mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped
to every subject from the fsaverage)
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0
-----????-----
???:"Douglas N. Greve" <dgr...@mgh.harvard.edu>
????:2020-11-12 22:23:13 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing.
Also, you will just want to use the 2nd row. You can eliminate the first row
with --exclude 0
On 11/12/2020 5:39 AM, ??? wrote:
External Email - Use
Caution
Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after
the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the
volume is Area_mm2?Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName
Mean
StdDev
Min
Max Range
1 0 161058
81037.1 Seg0000 242940.3281
0.7312 0.0000
3.8885 3.8885
2 1 2784
1182.3 Seg0001
3760.6619 0.2525
0.7136 1.8140 1.1005
Following is the code for extracting volumes
mri_segstats
--i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.volume.label (This was the label extracted from the
fsaverage after multi-correction)
--avgwf lh_volume.avgwf.dat (output file)
--accumulate
--sum lh_volume.sum (output file)
-----????-----
???:"Douglas N. Greve" <dgr...@mgh.harvard.edu>
????:2020-11-11 23:58:20 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed} {Disarmed}
Sorry, try this
mri_segstats
--i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the
fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
On 11/5/2020 10:26 PM, ??? wrote:
External Email - Use
Caution
I tried following codes according to the suggestions, the terminal reported an
error: cannot do frame average without input volume
mri_segstats
--seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the
fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
-----????-----
???:"Douglas N. Greve" <dgr...@mgh.harvard.edu>
????:2020-11-05 22:37:07 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed}
Try
--slabel fsaverage lh /path/to/lh.areapial.label
On 11/2/2020 10:24 PM, ??? wrote:
External Email - Use
Caution
Thank you very much! I tried to extract the areas with the following codes:
mri_segstats
--seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel lh.areapial.label (This was the label extracted from the fsaverage
after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
I did not get a text file including the areas of all subjects. Is this code
correct?
-----????-----
???:"Douglas N. Greve" <dgr...@mgh.harvard.edu>
????:2020-11-02 23:36:14 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
every subject {Disarmed}
I think the reason for this may be that the data in fsaverage space (after
mris_preproc) will have had a jacobian correction which will not be in data on
the native surface. For this reason, I would not use #1. #2 is fine.You can
apply your label in fsaverage space to the y.mgh used as input to mri_segstats
specifying the label using --slabel and using --avgwf output and also use
--accumulate; run it with --help for more info. This will create a text file of
the areas or volumes (depending upon which y.mgh you input) all your subjects
for that label.
On 10/30/2020 10:37 PM, ??? wrote:
External Email - Use
Caution
Dear Professors:
I compared the thickness, area, volume in the mild traumatic brain
injury patients with health control by FreeSurFer, and found statistic
difference region in the cortex area, volume respectively. I defined the
statistic difference regions as a label on the fsaverage and mapped this label
to subjects by Qdec/mri_label2label. The label defined on the fsaverage was
mapped onto all subjects successfully, and the label in subjects matched well
with the inflated cortex of subjects in Freeview Then the value of the
label in every single subjects was extracted, and I found that there is no
statistic difference in the value regarding to the area and volume between the
mild traumatic brain injury patients and health control subjects. Following are
my questions:
(1)Can I carry out correlation analysis between the cortex area and volume with
the behavior scores through these non-statistical extracted values?
(2)Can I extract the value of cortex area and volume in the standard space for
every TBI and health control subjects, and carry out correlation analysis
between the cortex area and volume with the behavior scores. How can I extract
the value of cortex area and volume in the standard space for every TBI and
health control subjects
Best wishes
Mengjun Li
-----????-----
???:"Douglas N. Greve" <dgr...@mgh.harvard.edu>
????:2020-10-30 23:40:30 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for
every subject
Do you mean you compared your TBI subjects against fsaverage? That is not
proper methodology.
On 10/29/2020 9:51 PM, ??? wrote:
External Email - Use
Caution
Dear FreeSurfer Developers:
I compared the cortical thickness, area, volume in the mild
traumatic brain injury patients with health control by FreeSurFer, and found a
statistic difference region in the cortex area and volume after correction. How
can I extract the value of cortex area and volume for every subject in the
fsaverage with the code of mri_segstats
FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra.
Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4YMwk2oU0QyoFaKYhF29vZDjDOc2EbdCGBU5Ae3PqkdcIVav-l__UauXqCsilEzQvT_zLUnqfP6wEBq9idW0oLVE0Iavnu-IApFzHCy5-qQcrn5Yg2ynbO7w-aON1HwbuFFKkaVkL1LerJ179cNagxY_fiFzFqityYi4zbDxg_TTId4tSzFbF7hXvbmasJCz3mMyh1l5hPvWwc74DOgwPT7929stAfAgvYH3UHSknA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4YMwk2oU0QyoFaKYhF29vZDjDOc2EbdCGBU5Ae3PqkdcIVav-l__UauXqCsilEzQvT_zLUnqfP6wEBq9idW0oLVE0Iavnu-IApFzHCy5-qQcrn5Yg2ynbO7w-aON1HwbuFFKkaVkL1LerJ179cNagxY_fiFzFqityYi4zbDxg_TTId4tSzFbF7hXvbmasJCz3mMyh1l5hPvWwc74DOgwPT7929stAfAgvYH3UHSknA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4YMwk2oU0QyoFaKYhF29vZDjDOc2EbdCGBU5Ae3PqkdcIVav-l__UauXqCsilEzQvT_zLUnqfP6wEBq9idW0oLVE0Iavnu-IApFzHCy5-qQcrn5Yg2ynbO7w-aON1HwbuFFKkaVkL1LerJ179cNagxY_fiFzFqityYi4zbDxg_TTId4tSzFbF7hXvbmasJCz3mMyh1l5hPvWwc74DOgwPT7929stAfAgvYH3UHSknA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4YMwk2oU0QyoFaKYhF29vZDjDOc2EbdCGBU5Ae3PqkdcIVav-l__UauXqCsilEzQvT_zLUnqfP6wEBq9idW0oLVE0Iavnu-IApFzHCy5-qQcrn5Yg2ynbO7w-aON1HwbuFFKkaVkL1LerJ179cNagxY_fiFzFqityYi4zbDxg_TTId4tSzFbF7hXvbmasJCz3mMyh1l5hPvWwc74DOgwPT7929stAfAgvYH3UHSknA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4YMwk2oU0QyoFaKYhF29vZDjDOc2EbdCGBU5Ae3PqkdcIVav-l__UauXqCsilEzQvT_zLUnqfP6wEBq9idW0oLVE0Iavnu-IApFzHCy5-qQcrn5Yg2ynbO7w-aON1HwbuFFKkaVkL1LerJ179cNagxY_fiFzFqityYi4zbDxg_TTId4tSzFbF7hXvbmasJCz3mMyh1l5hPvWwc74DOgwPT7929stAfAgvYH3UHSknA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4YMwk2oU0QyoFaKYhF29vZDjDOc2EbdCGBU5Ae3PqkdcIVav-l__UauXqCsilEzQvT_zLUnqfP6wEBq9idW0oLVE0Iavnu-IApFzHCy5-qQcrn5Yg2ynbO7w-aON1HwbuFFKkaVkL1LerJ179cNagxY_fiFzFqityYi4zbDxg_TTId4tSzFbF7hXvbmasJCz3mMyh1l5hPvWwc74DOgwPT7929stAfAgvYH3UHSknA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4YMwk2oU0QyoFaKYhF29vZDjDOc2EbdCGBU5Ae3PqkdcIVav-l__UauXqCsilEzQvT_zLUnqfP6wEBq9idW0oLVE0Iavnu-IApFzHCy5-qQcrn5Yg2ynbO7w-aON1HwbuFFKkaVkL1LerJ179cNagxY_fiFzFqityYi4zbDxg_TTId4tSzFbF7hXvbmasJCz3mMyh1l5hPvWwc74DOgwPT7929stAfAgvYH3UHSknA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://secure-web.cisco.com/1xBvUCYKavZVolKahDBlsMBn8_ooFbaO2RPlPXr9QF7bJuL7UAqh21cCCSaOtwAf3mbb25R_7owLv9_2NVkeDCXQ8SVxfwa5o-41Ob7CAwTeoUCH0wHzgX6P0k2nYgjxcAjbn6f4SSkn4N4tWlS8xYqzkgeYGpe9oSPgiY3IOVm8j3xzBvArhRGUKb92drSim6vHLlWW2F4webejdETlFbHKLna6jE5rgUvD1BxP-fPFFL-sMcIMAEsUBnFvXPYHiqHYnEx9Lg3J79pWqVY7uqg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201201%2F5563c32f%2Fattachment-0001.html
------------------------------
Message: 6
Date: Tue, 1 Dec 2020 09:24:44 +0800
From: " LIN, Yezhe " <yezhe....@foxmail.com>
Subject: [Freesurfer] Freesurfer skullstripping error
To: " freesurfer " <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <tencent_98ca21ce342ad20e07070c068c2f226b7...@qq.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use
Caution
Dear Freesurfer users,
Hope this finds you well.
I preprocessed our dataset with recon-all <subj&gt; -s <subj&gt; -all
-qcache and found a number of our subjects had different levels of skullstrip
errors. I tried fixing them by a couple of different approaches, such as -gcut
and adjusted watershed threshold, but they both failed to fix the overlapping
of dura mater (Fig1 and 2). I tried two methods on different subjects and
received the same outcome. I wonder if you have any ideas to fix this error. At
this point, for some who had less skullstripping, I can erase them manually and
run -autorecon-pial or -make. But for the others with multiple locations of
skullstripping (like Fig 3 and 4), do you have any ideas on how to approach to
them at a systemic level? Also I found the skullstripping error in over half of
our subjects, is it normal that we have a such proportion? ?
Thank you so much!?
------------------
Best regards,
Yezhe
Yezhe Lin, MD MMed&nbsp; (she/her/hers)
Postdoctoral Associate, Department of Psychiatry
University of Rochester Medical Center
yezhe.lin....@gmail.com
Twitter: @LinYezhe | LinkedIn&nbsp;| Researchgate
&nbsp;
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://secure-web.cisco.com/1WaLSLli8-xxlWr0PLad30vFeAwS4XWtwf6rsb_V838ARzUlDwnqPNHjC2pokwXZaas4Bt37yEliAGq1WlMpWr2tPmpLUqmpP-rXebfqV_KVJANQuqnuR6RUhWkp3TlezO_h0VxGO-w4gxU0ioYbCxGxQ46VqqgEZRletg8Wa5MOXc-cajwkrcAH81-esKaBGxQ0deaV8tTLZ9f3x6UozzdNbgHPhVRQte-eX8oOGYZGOh2rNKwF_44oipVEgng-7eovP4ulJuF0jlaMukz8JRA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201201%2Fe8603f45%2Fattachment.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fig.2 After running recon-all -skullstrip -clean-bm -gcut -s subj.png
Type: application/octet-stream
Size: 115736 bytes
Desc: not available
Url :
http://secure-web.cisco.com/1xPithPGi6qFor7IcbrAXJILT6reMdb7Uz-4VMkm3cl7RQPf2xaRlBjj1aI675HeLyoPTrdywGF5qjUCJ2lu0BC81vybDkLxpjhQnX0O5GNRi1kIfkWNXPZKjVJw8R8gO9R9040x5lw8-TmUuQzbLj_T5Wv81uVWV0ZoAqyBz5QO439b7sPIEUlAFCgrvs7Sb6xr_IG1UNSkfFDHuX4hkqLrqw8DYYMDfJ9GJvsrcLFiZkw7FnV6wDooLMlXm5gQTRboh3QbxoPcjgCQIJF7dSA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201201%2Fe8603f45%2Fattachment.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fig 3. Another subject before ?gcut.png
Type: application/octet-stream
Size: 166493 bytes
Desc: not available
Url :
http://secure-web.cisco.com/1_8e4pPmg-UyONGCtsGyB8WGWoB6-g9SQMi5Ut2gpieVsrPTj8fOcxQkP9pfbSu0bpL9Qp2popWrOEY4PAclqQxrW8mEmJ9eky9LEe38dTLeDFbchRZ-kSOYV86JRxC_XOxOoRAuYSVWZbsRujgySOub99PGEUnW-7Q23LPbr4AHZSQUbfMBqDtwPmRqPeL3RIPmyooz66xG07ecxFf3FOVE0PbcU7iOxuIc0WbArt9AO0vkhIKBXZC_WUmXKjzi4owEOlxLRR1n7b9t7LnJtZQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201201%2Fe8603f45%2Fattachment-0001.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fig 4. Another subject after ?gcut.png
Type: application/octet-stream
Size: 179439 bytes
Desc: not available
Url :
http://secure-web.cisco.com/17typU6f-PGiUwLeuCDhLiqaQL8jj89UTj4H44s2dvuMXqXAMuk1Kw9SNoLpGqkJ7jInUd9Vii5aw5N-AtGovAGh7R7KmH3KZ4goub9CICUGbFOonJagmchFpuwSiqzDwXeWxPQjI4huDRF2OfITzyO1kut1voNS3UbmyAbnH5hfBGvoDNr327mOoYh6U6UwyVao9qpB1Uv1byVyAlg0HtelOOgxYAM9rPk27nsiM2XYRZVS9FqAV3YsJ-fXXC302D4SML8n-F7YO6CLl_lDwWg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201201%2Fe8603f45%2Fattachment-0002.obj
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fig.1 skullstrip error after recon-all.png
Type: application/octet-stream
Size: 45526 bytes
Desc: not available
Url :
http://secure-web.cisco.com/1q-rKUt7oCl8SURwLDABTHJ-uCdwRQGlGrgV_c97r67acv1fxf_XrS-a_wNteeOaEyfFapfp88i9w0Kzy52ulLVjffcMXfO92qU58d3th3EwpIqKdkpdyjvkKy4GOpx_DeBjxOujFfyeIP1mzJTUcephJhql5Jz7UCLqdaAptwIrOrVcLwUR0KnqkUi7vYtFU5TGzKk7FCu7Xl0JYJgY5wTO16kwQ8ME4FrnR2WI6-YTFnZdNKFRleIHtNH0dfCasy33ix0NUZdSWBP8Zc13PSg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201201%2Fe8603f45%2Fattachment-0003.obj
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1z9iluK8C-0HIf0UFksBm0ZUhHli5Vc4eifBra2dUWisaOTx6GJWpI7L5vFYKrsOJvFTSsH3wh5e2ljfhrTbUnCD9E6DNV2w_ova8xc-qUpitfYGbPxqwyBzYiI5Cz4OOYLwy6Tn3zlOEbEE_01HdnQ2ZMF0dKBwCUMpc6F6wZEq6uH7euBNXmrZbEODJMFfVfAwAgT1yVVEjb_UcIEBGYe4PIzgoEuVqn82hCDhuwi3GMcEaemBH5i6A_F-1voHfrCKufDqdyFkS0FFr8ejbLg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
End of Freesurfer Digest, Vol 201, Issue 45
*******************************************_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
