Re: [Freesurfer] Help: when will the next version of FreeSurfer become available?

[fsbuild]

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We have no current reports about security issues with the FS release. 
 An address using the string fsbuild will email you directly so you can 
respond to only that address if you would like to report an issue. Please 
check you spam folder. PLEASE DO NOT POST AND/OR DISCUSS SECURITY ISSUES 
ON THE PUBLIC FREESURFER LIST.
- R.
On Jun 11, 2024, at 16:03, Tran, Kevin (NIH/NIMH) [E] 
kevint...@mail.nih.gov 
wrote:External Email - Use 
CautionHi,We have been 
pressured by our IT Security team to address some of the vulnerabilities (e.g., 
OpenSSL) they found in FreeSurfer 7.4.1.I am wondering if you could share 
with us when would the next version of FreeSurfer become 
available?Thanks,--Kevin TranData 
ScientistThe National Institutes of HealthNIMH, Laboratory of Brain and 
Cognition10 Center Drive, Room 4C215Bethesda MD 
20892-1366kevint...@mail.nih.govWork:(301)435-4936 
Cell:(301)755-3715___Freesurfer 
mailing 
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Re: [Freesurfer] Help with Recon-all Errors

[Silvia De Francesco]

External Email - Use Caution

unsubscribe 


From: "Perumalla, Sucika"  
To: "freesurfer"  
Sent: Wednesday, February 21, 2024 4:30:39 PM 
Subject: [Freesurfer] Help with Recon-all Errors 

Questa è la prima volta che ricevi un'email da questo mittente. Assicurati che 
sia qualcuno di cui ti fidi. 


Hello FreeSurfer Support, 



My name is Sucika Perumalla and I hope you can please help me with 
troubleshooting recon-all. I’m getting multiple frames errors when trying to 
run recon-all with my dicoms even after extracting the multiple frames. I was 
wondering if you can please help resolve this issue. Please refer to the 
attachment with my recon-all log. 



Thanks 


_ 

Sucika Perumalla 

Clinical Research Assistant I 

Department of Neurology, Division of Movement Disorders 

Brigham and Women’s Hospital 

60 Fenwood Road, Boston, MA 02115 

[ mailto:sperumal...@bwh.harvard.edu | sperumal...@bwh.harvard.edu ] | 
508-414-2601 




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Re: [Freesurfer] Help Download FreeSurfer Windows VM

[fsbuild]

External Email - Use Caution

We don’t expect things to work reliably with 8G total RAM for the machine. 
The host machine itself will always consume some memory when running its 
OS, probably up to a few Gig, leaving even less than 8G to be used for 
running the VM with freesurfer.
The Virtualbox VM is no longer available because the security/login credentials 
were compromised on this list.
Since you are on Windows, you could try using the windows OS built in Windows 
Subsystem for Linux (WSL). We have some notes about setting that up at,
https://secure-web.cisco.com/15CztkRxVJ7Ddir4MS_9Arksy0DkD_t2mgoGcHYmhJKK5Lsyhn9OQQF2n11zmSLeqbeGjffl8JiKJspStS5BIEqDeW4hwjubpORcz_WfM_QelzOOGCbo0-yxIrw5CRp9OTe6G_opwaoTix1AU6qWdzQ84fN4r922b3CXNohHY0nfJE_R1L5EMyO6V8j9OBROkgqBF4F3YCyusFxnCekqZ6zfNabw_pTnvaJDgwZR0JLlJ5nw84ZNy4DAJEMie-rQ8TdAxUT8Hafmh1q3BlprlvLyJxQ9QWTHDvp0ztYKxEOP5KBlgWyaJl3eak96w5YgK1ETj64k1_2sTQtEOkUs3sQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
But you would still likely run into the same issues consistent with having less 
than 8G of RAM to run Ubuntu Linux in WSL (instead of VirtualBox) + running 
freesurfer.
- R.
On Feb 6, 2024, at 08:54, lioudadraca...@gmail.com 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. 
But I have few problems.First, I do not have the access to the compressed VM 
Image file (FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible to 
have an access to that ?Second, I've seen that it also requires a login 
password for the "Developer" account. Is it possible to also have the password 
?Finally, I have a 8Go RAM, even if a 16Go is recommended, will it be able to 
run Freesurfer ?Thank you for your help.Best 
regards,Liouda___Freesurfer mailing 
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Re: [Freesurfer] Help with transform matrix for SEEG

[Douglas N. Greve]

Have you seen this page 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ?


On 12/10/2023 8:55 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I've just started using Freesurfer this week and I'm quite confused 
about coordinate systems.
Specifically, I have SEEG electrode locations that have been digitized 
in MRI RAS space, and I'm trying to apply a transform matrix so that 
these electrodes will be registered with the same brain that I 
performed recon-all on using Freesurfer, so that I can do further 
analysis in MNE python.


I understand that voxel space to MRI RAS space transform matrix is 
stored in vox2ras and the transform for voxel space to Freesurfer's 
surface RAS is in vox2ras_tkr of T1.mgz in my subject folder. Since 
the electrodes are in MRI RAS space, I am applying a transform matrix 
that is a matrix product of inverse(vox2ras) and vox2ras_tkr. However, 
this doesn't work out in real life, and I end up with electrodes half 
way outside the head.


Am I using the correct matrices? Also, T1.affine appears similar to 
vox2ras but very slightly different. Just hoping that there would be 
an easier way..

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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Re: [Freesurfer] Help (Freeview fails to launch)

[Kiyotaka Nemoto]

External Email - Use Caution

Dear R,

Thank you for the information. The deb package is useful so I agree with
you. Only one point is that using deb cannot handle installing two
different versions. Do you have any recommendation managing two (or more)
different versions using deb package?

Best regards,

Kiyotaka


On Sat, Dec 30, 2023 at 1:21 PM fsbuild  wrote:

> External Email - Use Caution
>
>
> Depending upon the state of a machine, there is no guarantee a list of
> "required" packages will encompass everything that needs to be
> installed/updated, or that a manual install will work.  So we neither
> recommend or support manual/piecemal installs, e.g., via the list below,
> instead of using the built-in linux package management tools.
>
> - R.
>
> On Dec 29, 2023, at 22:32, Kiyotaka Nemoto  wrote:
>
> External Email - Use Caution
>
> Dear Akira,
>
> I agree with R that installing FreeSurfer using the deb is preferred, but
> if you want to stick to tar.gz,
> below is the list of the packages to be installed when you install
> FreeSurfer using the deb package.
> So if you install these packages, you would be able to run freeview.
>
> Hope this helps,
>
> Kiyotaka
>
> sudo apt install -y language-pack-en binutils libx11-dev gettext x11-apps \
>   perl make csh tcsh bash file bc gzip tar \
>   xorg xorg-dev xserver-xorg-video-intel libncurses5 libbsd0 libc6 libc6 \
>   libcom-err2 libcrypt1 libdrm2 libegl1 libexpat1 libffi7 libfontconfig1 \
>   libfreetype6 libgcc-s1 libgl1 libglib2.0-0 libglu1-mesa libglvnd0
> libglx0 \
>   libgomp1 libgssapi-krb5-2 libice6 libjpeg62 libk5crypto3 libkeyutils1 \
>   libkrb5-3 libkrb5support0 libpcre3 libpng16-16 libquadmath0 libsm6 \
>   libstdc++6 libuuid1 libwayland-client0 libwayland-cursor0 libx11-6 \
>   libx11-xcb1 libxau6 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \
>   libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 \
>   libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 \
>   libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 \
>   libxkbcommon-x11-0 libxkbcommon0 libxmu6 libxrender1 libxss1 libxt6
> zlib1g
>
> On Fri, Dec 29, 2023 at 12:14 PM fsbuild  wrote:
>
>> External Email - Use Caution
>>
>>
>> That message could be the result of missing system libraries which the
>> Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify,
>> download and install for you.  You can download the package via the link 
>> *MailScanner
>> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
>> to be*
>> https://secure-web.cisco.com/1J9_Z0HLKDYWwXrGPXi_fqFTQLygJlwVaU-141E5zzDhAkkw1xXapN0nnVgWhTS6XGCgfkc5ueirEA_jvddWCTdYAfUcAH7SxCSaFAzawZC4lvbC8y_9NKqsjhD5ZFMrWt7X3muEEOwu9TlGI9rdd8dbC5nuG2Ghq2KLE70SI4ZxUWWmXSVkXCZyhhXZq5f4wFQyAvLrAHPX0lR7gws9mQ_Q3UYrjc-3musq7AJqT7K0xWCpNBXEO5jRyNhN_5IQyFWAx8la8y0nyTkV52oB8n6sf4nY9sqgm_KaTMe8Mr5-hIcABk8sdULBQpIZmVLKy5JEVPha5YlG51rCIN7H38g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
>> 
>>  and
>> the install can be done with,
>>
>> … cd to your Downloads to wherever the .deb file is …
>>
>> $ sudo apt install  ./freesurfer_ubuntu22-7.4.1_amd64.deb
>>
>> If the install succeeds, freesurfer will be under
>> /usr/local/freesurfer/7.4.1 which is the path to use for the environment
>> variable FREESURFER_HOME,
>>
>> $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
>>
>> If they are not already set in your environment, you should also set,
>>
>> $ export XDG_RUNTIME_DIR=$HOME/.xdg
>>
>> $ export DISPLAY=:0
>>
>> - R.
>>
>> On Dec 27, 2023, at 23:17, Akira Kita  wrote:
>>
>> External Email - Use Caution
>>
>> I have installed FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar
>> archive freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.
>>
>> Freeview fails to launch with the following error message:
>>
>> This application failed to start because no Qt platform plugin could be
>> initialized. Reinstalling the application may fix this problem.
>> Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, 
>> offscreen,
>> vnc, wayland-egl, wayland, webgl,
>>
>> How can I solve this?
>>
>>
>> Akira
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> 

Re: [Freesurfer] Help (Freeview fails to launch)

[fsbuild]

External Email - Use Caution

Depending upon the state of a machine, there is no guarantee a list of 
"required" packages will encompass everything that needs to be 
installed/updated, or that a manual install will work.So we neither 
recommend or support manual/piecemal installs, e.g., via the list below, 
instead of using the built-in linux package management tools.

- R.

On Dec 29, 2023, at 22:32, Kiyotaka Nemoto kiyot...@nemotos.net 
wrote:External Email - Use 
CautionDear Akira,I agree with 
R that installing FreeSurfer using the deb is preferred, but ifyou want 
to stick to tar.gz,below is the list of the packages to be installed when you 
install FreeSurfer using the deb package.So if you install these packages, you 
would be able to run freeview.Hope this helps,Kiyotakasudo apt install -y 
language-pack-en binutils libx11-dev gettext x11-apps \ perl make csh 
tcsh bash file bc gzip tar \ xorg xorg-dev xserver-xorg-video-intel 
libncurses5 libbsd0 libc6 libc6 \ libcom-err2 libcrypt1 libdrm2 libegl1 
libexpat1 libffi7 libfontconfig1 \ libfreetype6 libgcc-s1 libgl1 
libglib2.0-0 libglu1-mesa libglvnd0 libglx0 \ libgomp1 libgssapi-krb5-2 
libice6 libjpeg62 libk5crypto3 libkeyutils1 \ libkrb5-3 libkrb5support0 
libpcre3 libpng16-16 libquadmath0 libsm6 \ libstdc++6 libuuid1 
libwayland-client0 libwayland-cursor0 libx11-6 \ libx11-xcb1 libxau6 
libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \ libxcb-randr0 
libxcb-render-util0 libxcb-render0 libxcb-shape0 \ libxcb-shm0 
libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 \ 
libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 \ 
libxkbcommon-x11-0 libxkbcommon0 libxmu6 libxrender1 libxss1 libxt6 
zlib1gOn Fri, Dec 29, 2023 at 12:14 PM fsbuild 
fsbu...@contbay.com 
wrote:External Email - Use 
CautionThat message could 
be the result of missing system libraries which the Ubuntu 22 FS 7.4.1 .deb 
package will try to automatically identify, download and install for you. 
You can download the package via the linkMailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deband
 the install can be done with,… cd to your Downloads to wherever the .deb file 
is …$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.debIf the 
install succeeds, freesurfer will be under /usr/local/freesurfer/7.4.1 which is 
the path to use for the environment variable FREESURFER_HOME,$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.4.1If they are not already set in your 
environment, you should also set,$export XDG_RUNTIME_DIR=$HOME/.xdg$ 
export DISPLAY=:0- R.On Dec 27, 2023, at 23:17, Akira Kita 
jorrydep9...@gmail.com 
wrote:External Email - Use 
CautionI have installed 
FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tararchive 
freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.Freeview fails to launch with the 
following error message:This application failed to start because no Qt platform 
plugin could beinitialized. Reinstalling the application may fix this 
problem.Available platform plugins are: eglfs, linuxfb, minimal, 
minimalegl,offscreen, vnc, wayland-egl, wayland, webgl,How can I solve 
this?　　　Akira___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
fraud attempt from "secure-web..cisco.com" claiming to 
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Kiyotaka 
Nemoto, M.D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of 
Clinical Medicine, Institute of MedicineUniversity of Tsukuba1-1-1 Tennodai 
Tsukuba, Ibaraki 305-8575, 
JapanE-mail:kiyotaka@nemotos.net___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Help (Freeview fails to launch)

[Kiyotaka Nemoto]

External Email - Use Caution

Dear Akira,

I agree with R that installing FreeSurfer using the deb is preferred, but
if you want to stick to tar.gz,
below is the list of the packages to be installed when you install
FreeSurfer using the deb package.
So if you install these packages, you would be able to run freeview.

Hope this helps,

Kiyotaka

sudo apt install -y language-pack-en binutils libx11-dev gettext x11-apps \
  perl make csh tcsh bash file bc gzip tar \
  xorg xorg-dev xserver-xorg-video-intel libncurses5 libbsd0 libc6 libc6 \
  libcom-err2 libcrypt1 libdrm2 libegl1 libexpat1 libffi7 libfontconfig1 \
  libfreetype6 libgcc-s1 libgl1 libglib2.0-0 libglu1-mesa libglvnd0 libglx0
\
  libgomp1 libgssapi-krb5-2 libice6 libjpeg62 libk5crypto3 libkeyutils1 \
  libkrb5-3 libkrb5support0 libpcre3 libpng16-16 libquadmath0 libsm6 \
  libstdc++6 libuuid1 libwayland-client0 libwayland-cursor0 libx11-6 \
  libx11-xcb1 libxau6 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \
  libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 \
  libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 \
  libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 \
  libxkbcommon-x11-0 libxkbcommon0 libxmu6 libxrender1 libxss1 libxt6
zlib1g

On Fri, Dec 29, 2023 at 12:14 PM fsbuild  wrote:

> External Email - Use Caution
>
>
> That message could be the result of missing system libraries which the
> Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify,
> download and install for you.  You can download the package via the link 
> *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be*
> https://secure-web.cisco.com/1mKMabUX5OEUvCDYuNLL03gy4wla33dNI6Ox8dPzZ_qBoLFWXoufcqAf2xdwBE_BLgKkXD80OQ5NgOUxywRL0N0wr63y6xGFPMuYMVhScIysNXav0Y4z28Z__cNw9SgCGUW68fdgfU8QDsRvR5NNF7vdpsshn6ACHPjYJr6JQcf2sCXJjoGxWj4hC7KyiUOhaRHIYOptZ1d1TMm10pJl2Wo80JxmbN_ExW9WtWOeJE3QcI24nX9nwDsHhamhR7k-K7nlz_WIGFKPWcZpmd9U4iSiiuAC41kYHaqh3oc15rOX9GB1n5yIcEKNHfnxbQ8Q_Pl7T-Cii52ogXtnRAF4Nnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
> 
>  and
> the install can be done with,
>
> … cd to your Downloads to wherever the .deb file is …
>
> $ sudo apt install  ./freesurfer_ubuntu22-7.4.1_amd64.deb
>
> If the install succeeds, freesurfer will be under
> /usr/local/freesurfer/7.4.1 which is the path to use for the environment
> variable FREESURFER_HOME,
>
> $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
>
> If they are not already set in your environment, you should also set,
>
> $ export XDG_RUNTIME_DIR=$HOME/.xdg
>
> $ export DISPLAY=:0
>
> - R.
>
> On Dec 27, 2023, at 23:17, Akira Kita  wrote:
>
> External Email - Use Caution
>
> I have installed FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar
> archive freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.
>
> Freeview fails to launch with the following error message:
>
> This application failed to start because no Qt platform plugin could be
> initialized. Reinstalling the application may fix this problem.
> Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, 
> offscreen,
> vnc, wayland-egl, wayland, webgl,
>
> How can I solve this?
>
>
> Akira
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1QI73ha0dZUxEGvYoEY_1bYLyCUQHOXV-uF3VAAGaEPKSzyD1nk2DxAarPrXJTqvTusR8gBzTyWOW2-kKzsxSeIadM-y30LBoFcSz5mxwl6BrxdQ6Inv507a1TZr765rV_NZR-bk698jbJ-vqcPvC4EKJ5UTWDndvRP0uBpApG-TtOsQUPPG8ZHqP6nuQ0_aya37i0g22_g_ZxtO8xo3uJ7k-zPCumS_Eh5wFjz0kMaNw8xK2i_tLxfm9uND_vZiF4BA8RBWhfWCKe3bjJxORg6txWtP7nqolZUOmiK8132YcfTy76x54nkehXXP1lKggt5vEVxPG3qW4ilDrAduriw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1QI73ha0dZUxEGvYoEY_1bYLyCUQHOXV-uF3VAAGaEPKSzyD1nk2DxAarPrXJTqvTusR8gBzTyWOW2-kKzsxSeIadM-y30LBoFcSz5mxwl6BrxdQ6Inv507a1TZr765rV_NZR-bk698jbJ-vqcPvC4EKJ5UTWDndvRP0uBpApG-TtOsQUPPG8ZHqP6nuQ0_aya37i0g22_g_ZxtO8xo3uJ7k-zPCumS_Eh5wFjz0kMaNw8xK2i_tLxfm9uND_vZiF4BA8RBWhfWCKe3bjJxORg6txWtP7nqolZUOmiK8132YcfTy76x54nkehXXP1lKggt5vEVxPG3qW4ilDrAduriw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer



-- 
Kiyotaka Nemoto, M.D., Ph.D.
Associate Professor
Department of Psychiatry
Division of 

Re: [Freesurfer] Help (Freeview fails to launch)

[fsbuild]

External Email - Use Caution

That message could be the result of missing system libraries which the 
Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, download 
and install for you. You can download the package via the 
linkhttps://secure-web.cisco.com/1t9e2mCgXLQVxO1_HRQVcGKF8xT7sodKwA6zzWD3PnvYpEYhzi545ja6T6zaKK2EKrLVHMv6-PenWRMiweIekDa0iPsOeO98ft16CafenUS7q9BCgUBIUTZ4DVfUj_bzh0uPOyWvS4HQa596zdcqA4rd_Q-K_M2WisVZhilBIGDxBi6g1no1JAF0xGe8QRbw1_MNpA42GJvTyE3Ps_fzXnMymgErLwVj6rpub0SX6CnI2T2f2hJ-5kA2_45a9Cuj-xUsFMqWPuXjSNYYpq3gSvNU9KSI_nj_yxnrBbLWqZOIW4xjT17yKPejFlXKp808Nd2U_ZOe-9oEV5ZotlsGDQw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb%26nbsp;and
 the install can be done with,
… cd to your Downloads to wherever the .deb file is …
$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb
If the install succeeds, freesurfer will be under /usr/local/freesurfer/7.4.1 
which is the path to use for the environment variable FREESURFER_HOME,
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
If they are not already set in your environment, you should also set,
$export XDG_RUNTIME_DIR=$HOME/.xdg
$ export DISPLAY=:0

- R.

On Dec 27, 2023, at 23:17, Akira Kita jorrydep9...@gmail.com 
wrote:External Email - Use 
CautionI have installed 
FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tararchive 
freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.Freeview fails to launch with the 
following error message:This application failed to start because no Qt platform 
plugin could beinitialized. Reinstalling the application may fix this 
problem.Available platform plugins are: eglfs, linuxfb, minimal, 
minimalegl,offscreen, vnc, wayland-egl, wayland, webgl,How can I solve 
this?　　　Akira___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Help

[fsbuild]

External Email - Use Caution

It
 reads like something is not right with your setup/shell environment. 
Once you have setup the freesurfer environment via, e.g.,
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetupFreesurfer.sh 
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/usr/local/freesurfer/7.4.1
FSFAST_HOME  /usr/local/freesurfer/7..4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/7.4.1/subjects
MNI_DIR
/usr/local/freesurfer/7.4.1/mni
FSL_DIR
/usr/pubsw/packages/fsl/current

- then the head or start of your PATH has on purpose been modified to contain 
paths pointing to binaries in the freesurfer tree,
$echo $PATH | tr -s ':' '\n'/usr/local/freesurfer/7.4..1/bin
/usr/local/freesurfer/7.4.1/fsfast/bin
/usr/local/freesurfer/7..4.1/tktools
/usr/local/freesurfer/7.4.1/mni/bin…. rest of output deleted …
All
 python scripts in the freesurfer distribution are automatically run 
with fspython - which in turn runs the python distribution included in 
freesurfer. Any, e.g., system, python3 otherwise found in your path 
should not be used. We do not recommend activating a conda environment,
 or other python (virtual) environment that will change PATH or set 
PYTHONPATH after setting up the freesurfer environment.
$ which fspython/usr/local/freesurfer/7.4.1/bin/fspython$ which python3
/usr/bin/python3--- not used by freesurfer$ 
echo $PYTHONPATH… no output ...

- R.
Subject:[Freesurfer] HelpDate:Wed, 22 Nov 2023 08:44:18 
-0500From:Xincen Wuxlw...@groton.orgReply-To:Freesurfer 
support 
listfreesurfer@nmr.mgh.harvard.eduTo:Freesurfer@nmr.mgh.harvard.eduExternal
 Email - Use CautionHi,I
 am using freesurfer. I have gone through with the installation and 
diagnostics and everything works fine. FOr example, using the command 
recon-all --help in terminal yields a bunch of directions. Yet, when I 
enter something like:recon-all -s bert -autorecon1an
 error pops up saying my python3 is problematic. However, I regularly 
use python3 and redownloaded it after. Please advise on the issue at 
hand.Thanks,LucasAttached Message Part.txt

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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Help running freesurfer for FEAT-preprocessed functional data?

[Douglas N. Greve]

   External Email - Use Caution

There is no way to do this. All the fsfast commands are going to expect 
things to be in the fsfast directory structure.


On 8/11/2023 12:19 PM, Noah Lee wrote:


External Email - Use Caution

Hello!

I am trying to run some freesurfer commands for a pipeline. However, I 
am coming in with functional data preprocessed by FEAT (EPI correction 
and general mcflirt, etc). For reference, I'm trying to run this 
following script:


preproc-sess -s . -fwhm 5 -stc siemens -surface fsaverage lhrh 
-per-run -fsd bold -mni305 -force

fcseed-config -wm -fcname wm.dat -fsd bold -mean -cfg wm.config -force
fcseed-config -vcsf -fcname vcsf.dat -fsd bold -mean -cfg vcsf.config 
-force

fcseed-sess -s . -cfg wm.config -force
fcseed-sess -s . -cfg vcsf.config -force

I am obviously skipping the preproc-sess step, as my data has been 
preprocessed. However, I'm not too sure how to run the following steps 
with the outputs of my feat directory. If anyone could help, I would 
greatly appreciate it!


Best,

Noah Lee
he/him/his
Yale University | Saybrook '25
B.S. Neuroscience


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 .
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview Display

[Tregidgo, Henry]

External Email - Use Caution

Hi,

Thank you for your interest in our tool. Currently these three nuclei are not 
segmented by the network implementation, but they will be segmented by the 
Bayesian tool once we have integrated it into FreeSurfer.

The Pc, VM and Pt are the three smallest nuclei in our atlas, with volumes 
generally less than 2-3 mm^3. As such they often do not have the highest 
posterior probability in any voxels during Bayesian segmentation and therefore 
don't appear in the output segmentations or only in very few voxels. We 
therefore decided to remove these labels when training the network 
implementation.

To view the segmentations you can use the following command substituting the 
paths for the segmentation, V1, FA and aligned T1 volumes

freeview  :colormap=LUT -dti  


Best wishes,
Henry


Henry Tregidgo, PhD
Research Associate

Centre for Medical Image Computing (CMIC),
University College London (UCL)



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 胡馨月 
Sent: 18 May 2023 13:15
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview 
Display


⚠ Caution: External sender


External Email - Use Caution

Dear FreeSurfer Experts,

I hope you are doing well. I have encountered an issue while using the Thalamic 
NucleiDTI module in FreeSurfer and would appreciate your guidance.

I am attempting to segment the thalamus using the module, but the Pc, VM, and 
Pt nuclei are missing in the segmentation results. Could you please advise me 
on resolving this issue?

Additionally, I would like instructions on how to display the Thalamic 
NucleiDTI module results in Freeview. Please guide me on the steps to visualize 
the results accurately in Freeview.

Thank you for your support. I look forward to your response.

Best regards,

Xinyue Hu West China Hospital of Sichuan University
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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
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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] Help with script with 7.2 on an HPC

[Huang, Yujing]

Hi Lisa,

You can find information about those scripts here 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

Executing the corresponding script with the flag -help should provide some 
information too.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Taylor, Lisa
Sent: Monday, February 6, 2023 6:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Help with script with 7.2 on an HPC


External Email - Use Caution
Hi there,

I am trying to update my scripts on our university's HPC but am running into an 
issue. I am not too savvy when it comes to this, so I apologize. My guess is I 
will have to run my old 6.0 script but without the -hippocampal-subfields-T1 
argument in the new 7.2 script that I copied over, but then run the 
'segmentHA_T1.sh' separately? Is there a way to incorporate this script in the 
7.2 script I currently have? Thank you for any help/insight you can give.

Error I get when trying to run my updated 7.2 script:


 $cat slurm-19565158.out



ERROR: the hippocampal subfield module is now in separate scripts:

  segmentHA_T1.sh

  segmentHA_T2.sh

  segmentHA_T1_long.sh

1 of 2 of the scripts used to run freesurfer on the HPC3:


cat freesurfer_template_7.2.sub

#!/bin/bash

#SBATCH --job-name=fs_reconall_subid

#SBATCH -A account

#SBATCH -p user

#SBATCH --nodes=1

#SBATCH --ntasks=1

#SBATCH --cpus-per-task=2

#SBATCH --error=slurm-reconall_subid.err

#SBATCH --mem-per-cpu=18gb



module load freesurfer/7.2.0

xport SUBJECTS_DIR=imagedir

source $FREESURFER_HOME/SetUpFreeSurfer.sh



# run freesurfer

srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all 
-hippocampal-subfields-T1 -brainstem-structures -qcache


2 of 2 of the script used to run freesurfer on the HPC3:


cat 7.2_freesurfer_prep_single_subj.sh

#!/bin/sh



# usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge] 
[freesurfer_subj_folder]

# [queue] = free | standard

# [account_to_charge] = ltaylor2

# [freesurfer_subj_folder] = This is the subject directory created by 
freesurfer for processing

#



if [[ $# -lt 3 ]] ; then

  echo 'Usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge] 
[freesurfer_subj_folder]'

  echo '[queue] = free | standard'

  echo '[account_to_charge] = ltaylor2'

  echo 'PLEASE ONLY USE THE FREE QUEUE UNLESS OTHERWISE INSTRUCTED'a

  echo '[freesurfer_subj_folder] = This is the subject directory created by 
freesurfer for processing'

  exit 0

fi



subids=$3

imagedir=`echo $PWD`



echo $subids



if [ -d freesurfer_sub ]; then

echo directory freesurfer_sub exists ...;

else

  mkdir freesurfer_sub;

fi





for subid in ${subids}; do

sed -e s/subid/${subid}/g -e s/user/${1}/g -e s/account/${2}/g -e 
s#imagedir#${imagedir}#g freesurfer_template_7.2.sub > 
freesurfer_sub/fs_${subid}.sub



cd freesurfer_sub

echo sbatch fs_${subid}.sub

   sbatch fs_${subid}.sub

cd ..

done


Thank you!

Lisa

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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] Help: Aparcstats and asegstats not working

[vittal korann]

External Email - Use Caution

Thanks, Yujing!

Happy new year!

I’m wondering what the first line is in your /usr/local/freesurfer/bin/
asegstats2table
/usr/bin/env python

python asegstats2table –subjects … --tablefile …
python /usr/local/freesurfer/bin/asegstats2table –subjects … --tablefile …
- this worked for me.

Your suggestion worked for me, thanks!

With regards
Vittal



On Mon, Jan 2, 2023 at 3:51 PM Huang, Yujing 
wrote:

> Hi Vittal,
>
>
>
> Happy new year!
>
>
>
> I’m wondering what the first line is in your
> /usr/local/freesurfer/bin/asegstats2table. Can you check it by doing ‘head
> /usr/local/freesurfer/bin/asegstats2table’ at the prompt?
>
>
>
> Can you also try the following?
>
> 1. alias python=python2  (as suggested in previous email)
>
> 2. python asegstats2table –subjects … --tablefile …
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
>
>
> *From:* vittal korann 
> *Sent:* Friday, December 30, 2022 3:56 PM
> *To:* Huang, Yujing 
> *Cc:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working
>
>
>
> *External Email - Use Caution*
>
> Thanks, Yujing, for your quick response.
>
>
>
> I tried your suggestion as well but the same error keeps appearing.
>
>
>
> $ asegstats2table --subjects Met001_1 Met002_1 Met003_1 Met005_1 Met006_1
> Met007_1 Met008_1 Met009_1 Met012_1 Met013_1 Met015_1 Met016_1 Met017_1
> Met018_1 Met019_1 Met020_1 Met021_1 Met022_1 Met023_1 Met024_1 Met025_1
> Met026_1 Met029_1 Met030_1 Met031_1 Met033_1 Met034_1 TOPIRA004_1
> TOPIRA005_1 TOPIRA012_1 TOPIRA013_1 TOPIRA019_1 TOPIRA021_1 TOPIRA022_1
> TOPIRA024_1 TOPIRA025_1 TOPIRA026_1 TOPIRA027_1 TOPIRA029_1 TOPIRA030_1
> TOPIRA032_1 Tao101_1 Tao103_1 Tao104_1 Tao105_1 Tao106_1 Tao107_1 Tao108_1
> Tao111_1 Tao112_1 Tao113_1 Tao115_1 Tao117_1 Tao118_1 Tao120_1 Tao121_1
> Tao124_1 Tao126_1 Tao127_1 C001_1 C002_1 C003_1 C004_1 C005_1 C006_1 C007_1
> C008_1 C009_1 C010_1 C011_1 C012_1 C013_1 C014_1 C015_1 C016_1 C017_1
> C018_1 C019_1 C020_1 C021_1 C023_1 C024_1 --hemi lh --meas. area
> --tablefile Area_aseg_stats txt
>
>
>
> File "/usr/local/freesurfer/bin/asegstats2table", line 195
> print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
>   ^
> SyntaxError: invalid syntax
>
>
>
> I do not know where I am going wrong with this.
>
> Any suggestion would be appreciated.
>
>
>
> Thanks,
>
> Vittal
>
>
>
>
>
>
>
> On Fri, Dec 30, 2022 at 12:33 PM Huang, Yujing 
> wrote:
>
> Hi Vittal,
>
>
>
> I can only repro your error by running ‘python asegstats2table …’.  And
> the alias solution works for me.
>
>
>
> Running ‘asegstats2table’ directly doesn’t give me any errors, and it
> doesn’t need the alias setting.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *fsbuild
> *Sent:* Friday, December 30, 2022 12:29 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* vittalkor...@gmail.com
> *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working
>
>
>
> *External Email - Use Caution*
>
>
> SyntaxError: Missing parentheses in call to 'print'. Did you mean
> print('ERROR: atleast 1 subject must be provided')?
>
> It does not look like you are running a python 2.X.  That may be because
> only python3 is installed by default.
>
>
>
> $ which python
> $ which python2
> $ which python3
> /bin/python3
>
>
>
> … if you need to install python2, you can do it with ...
>
>
>
> $ sudo apt update
>
> $ sudo apt install python2
>
>
>
> $ which python2
>
> /bin/python2
>
> $ python2 --version
> Python 2.7.18
>
>
>
> One way or another you need “python” to report it is a 2.X version *after*
> you set FREESURFER_HOME and source the freesurfer setup script.  To force
> “python” to run as “python2” you can try using an alias,
>
>
>
> $ alias python=python2
>
> $ python --version
> Python 2.7.18
>
> Similarly, if you needed python to run as python3 you could reset the
> alias to use =python3 instead.
>
>
>
> For the error,
>
>  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
>
> I would check the subjects you are listing as argument can be found as
> directories under what SUBJECTS_DIR is currently set to.
>
>
>
> - R.
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-

Re: [Freesurfer] Help: Aparcstats and asegstats not working

[Huang, Yujing]

Hi Vittal,

Happy new year!

I’m wondering what the first line is in your 
/usr/local/freesurfer/bin/asegstats2table. Can you check it by doing ‘head 
/usr/local/freesurfer/bin/asegstats2table’ at the prompt?

Can you also try the following?
1. alias python=python2  (as suggested in previous email)
2. python asegstats2table –subjects … --tablefile …

Best,

Yujing



From: vittal korann 
Sent: Friday, December 30, 2022 3:56 PM
To: Huang, Yujing 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] Help: Aparcstats and asegstats not working


External Email - Use Caution
Thanks, Yujing, for your quick response.

I tried your suggestion as well but the same error keeps appearing.

$ asegstats2table --subjects Met001_1 Met002_1 Met003_1 Met005_1 Met006_1 
Met007_1 Met008_1 Met009_1 Met012_1 Met013_1 Met015_1 Met016_1 Met017_1 
Met018_1 Met019_1 Met020_1 Met021_1 Met022_1 Met023_1 Met024_1 Met025_1 
Met026_1 Met029_1 Met030_1 Met031_1 Met033_1 Met034_1 TOPIRA004_1 TOPIRA005_1 
TOPIRA012_1 TOPIRA013_1 TOPIRA019_1 TOPIRA021_1 TOPIRA022_1 TOPIRA024_1 
TOPIRA025_1 TOPIRA026_1 TOPIRA027_1 TOPIRA029_1 TOPIRA030_1 TOPIRA032_1 
Tao101_1 Tao103_1 Tao104_1 Tao105_1 Tao106_1 Tao107_1 Tao108_1 Tao111_1 
Tao112_1 Tao113_1 Tao115_1 Tao117_1 Tao118_1 Tao120_1 Tao121_1 Tao124_1 
Tao126_1 Tao127_1 C001_1 C002_1 C003_1 C004_1 C005_1 C006_1 C007_1 C008_1 
C009_1 C010_1 C011_1 C012_1 C013_1 C014_1 C015_1 C016_1 C017_1 C018_1 C019_1 
C020_1 C021_1 C023_1 C024_1 --hemi lh --meas. area --tablefile Area_aseg_stats 
txt

File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax

I do not know where I am going wrong with this.
Any suggestion would be appreciated.

Thanks,
Vittal



On Fri, Dec 30, 2022 at 12:33 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Vittal,

I can only repro your error by running ‘python asegstats2table …’.  And the 
alias solution works for me.

Running ‘asegstats2table’ directly doesn’t give me any errors, and it doesn’t 
need the alias setting.

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 fsbuild
Sent: Friday, December 30, 2022 12:29 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: vittalkor...@gmail.com<mailto:vittalkor...@gmail.com>
Subject: Re: [Freesurfer] Help: Aparcstats and asegstats not working


External Email - Use Caution

SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: 
atleast 1 subject must be provided')?
It does not look like you are running a python 2.X.  That may be because only 
python3 is installed by default.

$ which python
$ which python2
$ which python3
/bin/python3

… if you need to install python2, you can do it with ...

$ sudo apt update
$ sudo apt install python2

$ which python2
/bin/python2
$ python2 --version
Python 2.7.18

One way or another you need “python” to report it is a 2.X version *after* you 
set FREESURFER_HOME and source the freesurfer setup script.  To force “python” 
to run as “python2” you can try using an alias,

$ alias python=python2
$ python --version
Python 2.7.18
Similarly, if you needed python to run as python3 you could reset the alias to 
use =python3 instead.

For the error,
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
I would check the subjects you are listing as argument can be found as 
directories under what SUBJECTS_DIR is currently set to.

- R.

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://secure-web.cisco.com/1_2BAmFE3qXv20f0ybxnN-fpsohRoOoShMxWrzjXK9S8cPNIBCYqeBbQGLqgIZ-bS3q3YXsz0yZ_PMmmrgEFH_EO4_tt6fJDXrTPAcZdKwkwdrahEUhvwBc4VPmXx1axB0sUzZgCPbDJAYvqG7Q0WYmO8u4v80Tofdemy_pdkpMpHE1elT_5uGjKF89ma5bOalsMMsKKRwD3rN6TLvd1XgaVSpJOPUAXv1ZrSDJSrcBMWP1D4DM3incUVVYwuN5coRm9CbizTb_RmmbsKji8LMAR2U21qLrSeiMvX0DmNda5ZgFhWSvgqNdRjnuKRHjms/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
 .
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
co

Re: [Freesurfer] Help: Aparcstats and asegstats not working

[vittal korann]

External Email - Use Caution

Thanks, Yujing, for your quick response.

I tried your suggestion as well but the same error keeps appearing.

$ asegstats2table --subjects Met001_1 Met002_1 Met003_1 Met005_1 Met006_1
Met007_1 Met008_1 Met009_1 Met012_1 Met013_1 Met015_1 Met016_1 Met017_1
Met018_1 Met019_1 Met020_1 Met021_1 Met022_1 Met023_1 Met024_1 Met025_1
Met026_1 Met029_1 Met030_1 Met031_1 Met033_1 Met034_1 TOPIRA004_1
TOPIRA005_1 TOPIRA012_1 TOPIRA013_1 TOPIRA019_1 TOPIRA021_1 TOPIRA022_1
TOPIRA024_1 TOPIRA025_1 TOPIRA026_1 TOPIRA027_1 TOPIRA029_1 TOPIRA030_1
TOPIRA032_1 Tao101_1 Tao103_1 Tao104_1 Tao105_1 Tao106_1 Tao107_1 Tao108_1
Tao111_1 Tao112_1 Tao113_1 Tao115_1 Tao117_1 Tao118_1 Tao120_1 Tao121_1
Tao124_1 Tao126_1 Tao127_1 C001_1 C002_1 C003_1 C004_1 C005_1 C006_1 C007_1
C008_1 C009_1 C010_1 C011_1 C012_1 C013_1 C014_1 C015_1 C016_1 C017_1
C018_1 C019_1 C020_1 C021_1 C023_1 C024_1 --hemi lh --meas area --tablefile
Area_aseg_stats.txt

File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax

I do not know where I am going wrong with this.
Any suggestion would be appreciated.

Thanks,
Vittal




On Fri, Dec 30, 2022 at 12:33 PM Huang, Yujing 
wrote:

> Hi Vittal,
>
>
>
> I can only repro your error by running ‘python asegstats2table …’.  And
> the alias solution works for me.
>
>
>
> Running ‘asegstats2table’ directly doesn’t give me any errors, and it
> doesn’t need the alias setting.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *fsbuild
> *Sent:* Friday, December 30, 2022 12:29 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* vittalkor...@gmail.com
> *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working
>
>
>
> *External Email - Use Caution*
>
>
> SyntaxError: Missing parentheses in call to 'print'. Did you mean
> print('ERROR: atleast 1 subject must be provided')?
>
> It does not look like you are running a python 2.X.  That may be because
> only python3 is installed by default.
>
>
>
> $ which python
> $ which python2
> $ which python3
> /bin/python3
>
>
>
> … if you need to install python2, you can do it with ...
>
>
>
> $ sudo apt update
>
> $ sudo apt install python2
>
>
>
> $ which python2
>
> /bin/python2
>
> $ python2 --version
> Python 2.7.18
>
>
>
> One way or another you need “python” to report it is a 2.X version *after*
> you set FREESURFER_HOME and source the freesurfer setup script.  To force
> “python” to run as “python2” you can try using an alias,
>
>
>
> $ alias python=python2
>
> $ python --version
> Python 2.7.18
>
> Similarly, if you needed python to run as python3 you could reset the
> alias to use =python3 instead.
>
>
>
> For the error,
>
>  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
>
> I would check the subjects you are listing as argument can be found as
> directories under what SUBJECTS_DIR is currently set to.
>
>
>
> - R.
>
>
>
> 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://secure-web.cisco.com/19vFAN3khDcvlUskxyhTYI6to-kX38th4pWvDUDnbBWQJ7FR_Ep8Xnq9k97hDZPseTitshpBRLvKMKZEobxZt1MoBl0B_A74appwj9SV8yp995CiBEoy3gKgzdO4GqYX3mRCtT7mPAktjR1Yoe_EAcrqTCFGqKgWzzcWA3tCTAQKZyu7nNnS6ELaWG1BlWXnv9bC8piZd3_myQE9taMNPcDIdlE48cTRZsgSOgyVOMplWZqZ25xi7qIBYE05Q-7DJGaWUzyy69qXcYHJdYpgORxyVKK1UuIXkuYgiMfkRdafxDN-5SMTjA5VLuMnDqxFS/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  .
>
___
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Help: Aparcstats and asegstats not working

[vittal korann]

External Email - Use Caution

Thanks, for your quick response.

I installed python2 and did set the default version to python 2.7.18 via
aliasing.
But I am getting the same old errors again. The same terminal responses
were listed below.
The subjects that are used for aseg/aparc are listed in the folder SUBJECTS
under freesurfer

$ asegstats2table --subjects Met001_1 Met002_1 --hemi lh --meas area
--tablefile Area_aseg_stats.txt
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?

$which python2
/usr/bin/python2

$ python --version
Python 2.7.18

$ export FREESURFER_HOME=/usr/local/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl

$ sh aseg_stats_extraction.sh

  File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?
  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?

I also attached the shell script file that I created for thickness and area
extraction from the list of subjects.
Is this because something is wrong in the bash_profile/bashrc file? I don't
know I am just guessing.

Any help would be appreciated!

Thanks,
Vittal



On Fri, Dec 30, 2022 at 12:29 AM fsbuild  wrote:

>
> SyntaxError: Missing parentheses in call to 'print'. Did you mean
> print('ERROR: atleast 1 subject must be provided')?
>
> It does not look like you are running a python 2.X.  That may be because
> only python3 is installed by default.
>
> $ which python
> $ which python2
> $ which python3
> /bin/python3
>
> … if you need to install python2, you can do it with ...
>
> $ sudo apt update
> $ sudo apt install python2
>
> $ which python2
> /bin/python2
> $ python2 --version
> Python 2.7.18
>
> One way or another you need “python” to report it is a 2.X version *after*
> you set FREESURFER_HOME and source the freesurfer setup script.  To force
> “python” to run as “python2” you can try using an alias,
>
> $ alias python=python2
> $ python --version
> Python 2.7.18
>
> Similarly, if you needed python to run as python3 you could reset the
> alias to use =python3 instead.
>
> For the error,
>
>  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
>
> I would check the subjects you are listing as argument can be found as
> directories under what SUBJECTS_DIR is currently set to.
>
> - R.
>
>
___
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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] Help: Aparcstats and asegstats not working

[Huang, Yujing]

Hi Vittal,

I can only repro your error by running ‘python asegstats2table …’.  And the 
alias solution works for me.

Running ‘asegstats2table’ directly doesn’t give me any errors, and it doesn’t 
need the alias setting.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of fsbuild
Sent: Friday, December 30, 2022 12:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: vittalkor...@gmail.com
Subject: Re: [Freesurfer] Help: Aparcstats and asegstats not working


External Email - Use Caution

SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: 
atleast 1 subject must be provided')?
It does not look like you are running a python 2.X.  That may be because only 
python3 is installed by default.

$ which python
$ which python2
$ which python3
/bin/python3

… if you need to install python2, you can do it with ...

$ sudo apt update
$ sudo apt install python2

$ which python2
/bin/python2
$ python2 --version
Python 2.7.18

One way or another you need “python” to report it is a 2.X version *after* you 
set FREESURFER_HOME and source the freesurfer setup script.  To force “python” 
to run as “python2” you can try using an alias,

$ alias python=python2
$ python --version
Python 2.7.18
Similarly, if you needed python to run as python3 you could reset the alias to 
use =python3 instead.

For the error,
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
I would check the subjects you are listing as argument can be found as 
directories under what SUBJECTS_DIR is currently set to.

- R.

___
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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] Help: Aparcstats and asegstats not working

[fsbuild]

External Email - Use Caution

SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: 
atleast 1 subject must be provided')?It does not look like you are running a 
python 2.X. That may be because only python3 is installed by default.
$ which python
$ which python2
$ which python3
/bin/python3

… if you need to install python2, you can do it with ...
$sudo apt update$ sudo apt install python2
$ which python2/bin/python2$python2 --version
Python 2.7.18

One way or another you need “python” to report it is a 2.X version *after* you 
set FREESURFER_HOME and source the freesurfer setup script. To force 
“python” to run as “python2” you can try using an alias,
$alias python=python2$python --version
Python 2.7.18

Similarly, if you needed python to run as python3 you could reset the alias to 
use =python3 instead.
For the error, 
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’I 
would check the subjects you are listing as argument can be found as 
directories under what SUBJECTS_DIR is currently set to.
- R.

___
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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] Help: Vertex Properties

[Douglas N. Greve]

The coords are in the surface structure, which you can get by running 
mris_convert lh.white lh.white.asc (asc will be an ascii file)  or by 
loading into matlab with read_surf.m
The surface area is computed for white (?h.area) and pial 
(?h.pial.area). These can be converted to mgz or nifti (mri_convert 
lh.area lh.area.{mgz,nii.gz }) or read into matlab with read_curv.m
The other stuff (angles, edge lengths, dist matrix), you will have to do 
yourself but you can get it on a vertex-wise basis with something like

 mris_info --vx 1000 $SUBJECTS_DIR/fsm011/surf/lh.white
vertexno 1000
xyz  -12.5783 -89.7512 33.0777  # the coords
nxyz -0.9930  0.0542  0.1049  # the normal at this vertex
vertex_area 0.668113   # area
neighbors 6
nbr 0    994 0.6636 0.3354  1524 0.2240
nbr 1    669 0.8749 0.9553  1525 0.3357
nbr 2    677 0.8132 0.6240  1538 0.3472
nbr 3   1006 1.0009 1.0769  2226 0.2301
nbr 4   1408 0.9042 0.8405  2227 0.4085
nbr 5   1419 0.9977 1.0954  2238 0.4587

NbrInfo: nbrno, nbrvno, nbrdist, nbrarea, faceno, facearea

On 11/8/2022 3:43 AM, Sarah Lavelle wrote:


External Email - Use Caution

Hi,

I’m wondering if there’s a way to get the properties of individual 
vertices such as:


1)Coordinates
2)Surface area
3)angles
4) Side lengths
5) distance matrix from other vertices

And can you get these properties for individual surfaces/ 
transformations (eg. On the spherical map or flatmap) ?


On the FreeSurfer application or else through matlab?

Any help would be greatly appreciated,
Thanks,

Sarah

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___
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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] help

[Fischl, Bruce R.,PHD]

Hi Sarah

Sorry, I’m not sure we have much to add. We don’t flatten much any longer, and 
the cuts are kind of ad hoc – the one around the medial wall to get rid of 
non-cortical stuff, then the radial ones from there to remove particularly the 
curvature from the 3 poles. Mostly we just follow what Anders and Marty started 
doing way back when
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sarah Lavelle
Sent: Tuesday, October 25, 2022 5:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] help


External Email - Use Caution
Dear freesurfer,

Are there any additional resources on how to make cuts? I have found this 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Flattening
 but it isn't enough for the project I am doing. I want to flatten the whole 
surface but I may need to change where I am cutting from patient to patient. 
How do you know how big the hole should be? and how many relaxation cuts should 
you make? How long should they be? If you have any more guidance on how to cut 
to minimise distortion, please let me know!

Also when I perform the mris_flatten function using my patch, my terminal gives 
me a % near the end saying "41% total metric distortion". Can you confirm that 
this value is the total metric distortion from an inflated surface to a flatmap 
surface using my chosen patch?

Many thanks,
Sarah Lavelle
Trinity College Dublin
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Re: [Freesurfer] Help with group analysis

[Douglas N. Greve]

you should be able to generalize two groups/one covariate and/or four 
groups one covariate. don't use gender as a continuous covariate. Make 
sure to normalize your covariates


On 9/26/2022 10:30 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi,
TKS for helping me!
I looked at the examples of the FSGD files, but I believe that my data 
doesn't fit. I've three groups/three factors at three levels (LR=1, 
HR=2, MDD=3) and 6 covariates (gender, age and global brain measure).

I don't know if I was clear in my explanation.


Em seg., 26 de set. de 2022 às 00:06, Douglas N. Greve 
 escreveu:


look at the fsgd examples to see if any fit your situation. Note
that the input needs to be something like
Input    310211    LR 1    15,5    2,678785 645292,6651    152275,2
ie, "LR" instead of "1", etc
using commas (,) instead of points (.) may cause problems

On 9/25/2022 1:10 PM, fernanda rohrsetzer wrote:


External Email - Use Caution

I'm sorry!

attached the FSGD file.

Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve
 escreveu:

no fsgd file was attached. Also, have you looked at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


?

On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi Freesufer's,
I need to run a group analysis but I don't know how to do
it, the error always appears (print below). There are 3
groups ( risk_group) that I would like to insert as a class
(LR = level 1, HR = level 2 and MDD = level 3) and I would
like to control for sex, age and total brain measure.
Please, if anyone can help me understand what I'm doing
wrong, I'd really appreciate it.
The FSG file is attached
Thank you.


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The information in this e-mail is intended only for the
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Re: [Freesurfer] Help with group analysis

[fernanda rohrsetzer]

External Email - Use Caution

Hi,
TKS for helping me!
I looked at the examples of the FSGD files, but I believe that my data
doesn't fit. I've three groups/three factors at three levels (LR=1, HR=2,
MDD=3) and 6 covariates (gender, age and global brain measure).
I don't know if I was clear in my explanation.


Em seg., 26 de set. de 2022 às 00:06, Douglas N. Greve <
dgr...@mgh.harvard.edu> escreveu:

> look at the fsgd examples to see if any fit your situation. Note that the
> input needs to be something like
> Input310211LR 115,52,678785645292,6651152275,2
> ie, "LR" instead of "1", etc
> using commas (,) instead of points (.) may cause problems
>
> On 9/25/2022 1:10 PM, fernanda rohrsetzer wrote:
>
> External Email - Use Caution
> I'm sorry!
>
> attached the FSGD file.
>
> Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve <
> dgr...@mgh.harvard.edu> escreveu:
>
>> no fsgd file was attached. Also, have you looked at *MailScanner has
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
>> be* 
>> https://secure-web.cisco.com/1VZjXbFdR2bL-sDVykjA7yRWxHMulxkgtad-yajUBDe5kxieFMAZ3HrhOcJQ4Ylb1ECXqqD14Lr9cjrEixwE2JCoBKSfNEtjioChe3vBXqkfEL-BOCTBrlP4XhJ4OhtlV6lxe1h64ortfnkYeb9ydTazv-Bz0apkHf-geM4IX1QIbECTmFuo-sU9ChDHxeZOr3bavd-NbpqcBSivkroG4ZtVPrx2WFyH2ctoBT2G2QPldZjyfifB1eqJRAi7WuGVlTZrRmIvjoe5zZPwQ8Md6R0-7mmWSDgc0GTtsjqg_FEIYlW7pA1kGgmm3gdxtLHWR1a35UMPhyRJ2tK0Y0Bn4fg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>> 
>> ?
>>
>> On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:
>>
>> External Email - Use Caution
>> Hi Freesufer's,
>> I need to run a group analysis but I don't know how to do it, the error
>> always appears (print below). There are 3 groups ( risk_group) that I would
>> like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3)
>> and I would like to control for sex, age and total brain measure. Please,
>> if anyone can help me understand what I'm doing wrong, I'd really
>> appreciate it.
>> The FSG file is attached
>> Thank you.
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1RH_rBab9niiaia8Ck5Hx5E6-yCgZbfEFO7mLl9_xQgPrQQY9dmGd8eTpzDELCl6-z2aQSlhmH4zanLRMiSe-kDfyuGQZsAFkY3obB6Bvb7pa_KPv-TCM7cs3y6a4FIj7TRu4ezFUI9dII028iiGPGgEkIGIQmptIr2JvcSrCy1rCKkV4OG65oJL4Hcvshr-YgzB8ae6WoGhTzszODkoXHbw8s9vrKUoRzgwmbfQ4F-yEBTPvGWt7Rm8aGVq6p19pLRlyjmgNhUCsHg2_WDqadKxIX-Orqk0-z4LRv9wnCbUR2gfiOUgqljyPkhNhBZQng2bWu-f6vYTWuC6itNjMnw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> 
>>
>>
>> ___
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>> 
>> 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

Re: [Freesurfer] Help with group analysis

[Douglas N. Greve]

look at the fsgd examples to see if any fit your situation. Note that 
the input needs to be something like

Input    310211    LR 1    15,5    2,678785    645292,6651 152275,2
ie, "LR" instead of "1", etc
using commas (,) instead of points (.) may cause problems

On 9/25/2022 1:10 PM, fernanda rohrsetzer wrote:


External Email - Use Caution

I'm sorry!

attached the FSGD file.

Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve 
 escreveu:


no fsgd file was attached. Also, have you looked at *MailScanner
has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


?

On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi Freesufer's,
I need to run a group analysis but I don't know how to do it, the
error always appears (print below). There are 3 groups (
risk_group) that I would like to insert as a class (LR = level 1,
HR = level 2 and MDD = level 3) and I would like to control for
sex, age and total brain measure. Please, if anyone can help me
understand what I'm doing wrong, I'd really appreciate it.
The FSG file is attached
Thank you.


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>
.


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Re: [Freesurfer] Help with group analysis

[fernanda rohrsetzer]

External Email - Use Caution

I'm sorry!

attached the FSGD file.

Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve <
dgr...@mgh.harvard.edu> escreveu:

> no fsgd file was attached. Also, have you looked at
> https://secure-web.cisco.com/1xDB2MdU7IttZMHh8Wcpy-H4rASI2uqj9-MUHGYt5B5AJhCMmszuKV-viLm47WoU7jm403uKh8mLzeA5xcxQoHZQvsbwcGRWH_ptuX-KXJvDiLaUftl-V1VX6CaHAJNGvDardNN7ga4LKaOP2jpFCH5OG_MBWK71pE00hp5FfRsl5tvuqGeGgetChB4DtXaaEVBwBotJ0slybBFLiZSpKXjmQdl23gdAdN5B0aCJoCDC6yWZKkKkeyzIjf6Ami-wCFlRhMjMz90U_NRs0kpqyZIYvJyQ7a_cWmtIXnsRvMhGLkoGgd9tnwE_xwF_aMu_IkvPfBIn6udwK6L9TVjH0sg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>  ?
>
> On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:
>
> External Email - Use Caution
> Hi Freesufer's,
> I need to run a group analysis but I don't know how to do it, the error
> always appears (print below). There are 3 groups ( risk_group) that I would
> like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3)
> and I would like to control for sex, age and total brain measure. Please,
> if anyone can help me understand what I'm doing wrong, I'd really
> appreciate it.
> The FSG file is attached
> Thank you.
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1IeS-YL57fzD75MFwwJjA4Sd-7EvX1tlEDghimEHC83PSTZvOaTC6uMGX0MeKlQyTBAimu2DAS98JjAF8rUFAl4eqOG6dAf7DEn9gcnJBQHi7SP8IEjsZrRwbLwfrSOrB4YuKj5JI2j33_LzbO1F75s57wSnEOwgZfit1pTGvtxmDV7iW1wC3FgMxsbk2pZv4Spl1fejTSoTqEdq3IbqUp0br17fLku3me34G20-zVPj6aWecGr4KglnFxOwqfw_g7hoiai7AAwAjveXLBWwL2KQV9IzCL6pLWYPBKbkp_yGV4zQXb15sB4G3WqfLw0smntAbzCh6ZUgoaNxkgrmbiA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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://secure-web.cisco.com/1lcJ8l8iGsr8svtwqrjcj_YgzO3i4H8osHsQ5MG8o0gSMDmRRUaO02v2siHGL8OJH267EE9rpCJqbHmHeNA2dwDDSYVshI1edCUdw4LQVNdg79MFK7K-hG_m9DSFxk8k4hygrTLezzCgQmakGharcc-FhM6ResORxNNnrX1i0o-P7hJlCk6yBnFeO8G_Om_p-WARUc7EI69ecntT_HF1Pf8o6onpEAWphxwHOeUOjmNjisaQQcB7SwSbhbkp2fZShDqx3TNXAiJUDQyKAaksfscnnb9bpS2-pKhxR1i-NnFejBc0Plkhqxk8X6yb23Fkwd8ftpb22qjX5Eg7_tBHnRg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1lcJ8l8iGsr8svtwqrjcj_YgzO3i4H8osHsQ5MG8o0gSMDmRRUaO02v2siHGL8OJH267EE9rpCJqbHmHeNA2dwDDSYVshI1edCUdw4LQVNdg79MFK7K-hG_m9DSFxk8k4hygrTLezzCgQmakGharcc-FhM6ResORxNNnrX1i0o-P7hJlCk6yBnFeO8G_Om_p-WARUc7EI69ecntT_HF1Pf8o6onpEAWphxwHOeUOjmNjisaQQcB7SwSbhbkp2fZShDqx3TNXAiJUDQyKAaksfscnnb9bpS2-pKhxR1i-NnFejBc0Plkhqxk8X6yb23Fkwd8ftpb22qjX5Eg7_tBHnRg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


w0_group.fsgd 
Description: Binary data
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Re: [Freesurfer] Help with group analysis

[Douglas N. Greve]

no fsgd file was attached. Also, have you looked at 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ?


On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi Freesufer's,
I need to run a group analysis but I don't know how to do it, the 
error always appears (print below). There are 3 groups ( risk_group) 
that I would like to insert as a class (LR = level 1, HR = level 2 and 
MDD = level 3) and I would like to control for sex, age and total 
brain measure. Please, if anyone can help me understand what I'm doing 
wrong, I'd really appreciate it.

The FSG file is attached
Thank you.


___
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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 
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 .
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Re: [Freesurfer] Help - segmentHA_T1_long.sh "list of time points not found"

[Iglesias Gonzalez, Juan E.,PHD]

Dear Kimi,

When you process the scans longitudinally with FreeSurfer, the file base-tps 
should be created in the subject directory of the template. Isn’t this the case?

Cheers,

/Eugenio

Juan Eugenio Iglesias
http://www.jeiglesias.com





On 19 Sep 2022, at 01:02, Raikkonen Kimi 
mailto:akdaus2...@gmail.com>> wrote:


External Email - Use Caution

Dear FreeSurfer,

Hi, I was trying to run longitudinal analysis of the hippocampus and amygdala 
segmentation pipeline after running the main FreeSurfer longitudinal pipeline.

I ran
segmentHA_T1_long.sh 101_MRI1.long.101_template
segmentHA_T1_long.sh 101_MRI2.long.101_template
segmentHA_T1_long.sh 101_MRI3.long.101_template   etc.

but I got the following error message:
List of time points:
   /study/101_MRI1.long.101_template/base-tps
does not exist




I think I’ve headed the wrong direction, I was wondering how to do the list of 
time points for a subject.
Thanks so much for your help in advance.

Best regards,
Alex
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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
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 .
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] help troubleshooting lta_convert error

[fsbuild]

External Email - Use Caution

Hello Megan,
The errors you list below usually result from running a version of Freesurfer 
that does not match the operating system you are using, i.e., it looks like you 
are trying to run the version built for Ubuntu linux,
7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b)
… on a CentOS6 system,
Description:  CentOS release 6.7 (Final)
If you have admin privileges on your system, then I would try installing the 
Freesurfer 7.2.0 CentOS6 rpm file on your CentOS6 system, which you can 
download from, 
https://secure-web.cisco.com/1_TrIriXqcfLg6YdYhz-fK97TtRKLaLawhDUmlefqUI_U6mlXmgpjgQk2UXhcwN2NC7TyNy3ieN31qh3FbGtBDSxQ1szMQN7SfmRdFpj7ysB-LpBCtwl5TH7fK4H1H001TDw7DTL2tjz6TTW50f3rwGbs89zFyTAUMfG9E7Gc856Bf8UyftY4htNXC9nvupCoIvaUkjIAeDGtT0Ir_jWBFyzc2ZLLYenGRXDhi1gsEWFCJe7BBe9s42X7KXD71wg5xI_R5f5PnfclBoppYxU9ESHu67HB5DFcg8Fl9ITpQIvU0pANCNzWJSxdGgdm6gY7rbTtZ3b1vG8l46LcvdpnQw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-CentOS6-7.2.0-1.x86_64.rpm
If you do not have admin privs to install the RPM, then you can download and 
expand the tar archive 
from,https://secure-web.cisco.com/1Fhw7EkvdlF04-nFWgMtF44HHWjdGMGEq_-VbJMp12jSu5l2WVbX1_vPjRjQTHB2HY5XwvKzKrLkqZVDPnu_aJXqAcH0GwbhGwRxc1fwpALyZH5Mo4Pc7OpAEk8vQzQOEn6ZdiCjVukVLIoDshJKKcWVg5XB_OBhrYeUXu5OH8cBun2eM_YCigbRGHmwOzS76XnfEX4I3SQKk39JIii0PMjB5zGP0EQEDLtcyOv8Z8WUSPSmsNqls6-NXgCQekj_OMiXrloh2sjr-QTp5XjW_513WvVyJbJ2rjpPE3-9b0A2nGAH4Lk5xK6hxN4JjCM4qAusRy4Kr8BJ-6o8PlsOeHw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-linux-centos6_x86_64-7.2.0.tar.gz
The Freesurfer 7.2.0 distributions available for each operating system are 
currently listed on this 
page,https://secure-web.cisco.com/1Sbf8V045U7e_z5ui8AhyYxoVSIwU0U2mshLiNckTmoysYXiKZ_gXc_vmjX3G-CwmBxGanNK5RoXJ1vwteBU0PTf6LQwTjPCtf6X0MW2rHHcd28Ml4EV6kuZ-8P_24Jy5ppQz4PfGFp1umeUIKtSQAxseIrw50CEtcUQpGMb7HhD1pS7FK0xb_1g-hQbOppeif-4fNt284anghqS_kmzO1fLoNtQh817_Qk4_asTfdz9vXnMhwOK84aO9NQ3tUJsLjUQo3pqVTme4YmmKcO3mX6qBa9Mx0ipQl_oaSL9cKV2N1BKgIncltx7pdb9JhfC2-BcTgPi5dTeLfloC00K0ag/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads

- R.
On Jul 1, 2022, at 13:32, Megan Schendel mschen...@mrn.org 
wrote:External Email - Use 
CautionHi all,I had a working 
distribution on an old system a few weeks ago, but now I'm getting an 
error. Can anyone offer any troubleshooting ideas?I am working on a 
shared server with a freesurfer distribution that I own.Here is some system 
info:[mschendel@earth scripts]$ lsb_release -aLSB Version:  
:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarchDistributor
 ID: CentOSDescription:  CentOS release 6.7 (Final)Release:  
  6.7Codename:FinalOn the command line, 
the error looks like this:lta_convert: /lib64/libm.so.6: version `GLIBC_2.27' 
not found (required by lta_convert)lta_convert: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by lta_convert)lta_convert: 
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by 
lta_convert)lta_convert: /lib64/libc.so.6: version `GLIBC_2.14' not found 
(required by lta_convert)The recon-all.log file contains the following:Fri Jul 
1 11:08:24 MDT 2022cd 
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87124539setenv
 SUBJECTS_DIR 
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer//bin/recon-all
 -all -i 
/export/research/archive/human/dicom/prisma/dquinn/navigate_20673//M87124539/Study20210623at161830/mprage_5e_32ch_RMS_0003/SerieMR-0003-0001-1.dcm
 -s 
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis//M87124539
 -openmp 8subjid M87124539setenv SUBJECTS_DIR 
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysisFREESURFER_HOME
 
/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer/Actual
 FREESURFER_HOME 
/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurferbuild-stamp.txt:
 
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bLinuxearth.mind.unm.edu2.6.32-573.26.1.el6.x86_64
 #1 SMP Wed May 4 00:57:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linuxcputime 
  unlimitedfilesize   unlimiteddatasize  
 unlimitedstacksize  10240 kbytescoredumpsize 0 
kbytesmemoryuse  unlimitedvmemoryuse  unlimiteddescriptors 
1024memorylocked 64 kbytesmaxproc   
unlimitedprogram versions 
used7.2.0 (freesurfer-linux-ubuntu18_x86_64-7..2.0-20210721-aa8f76b)ERROR: 
Executable 'lta_convert -all-info failed! Is it missing from the 
distribution?'MEG TechnicianPronouns: she/herThe Mind Research Network1101 Yale 
Blvd. NEAlbuquerque, New Mexico 
87106___Freesurfer mailing 

Re: [Freesurfer] help - unzip Ubuntu ova password

[fsbuild]

External Email - Use Caution

Sending the info to your email shortly.
- R.On Apr 27, 2022, at 15:31, Dan Lerner d...@findsurgicalsciences.com 
wrote:External Email - Use 
CautionHi,Setting up the Ubuntu 
vm provided by FreeSurfer. I'm emailing for the password as per the 
instructions.Thanks,Dan___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
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] [Help needed] recon-all log error

[Douglas N. Greve]

you did not point out the lines that worry you. At the end, it says 
"finished without error", which means that you should not visually check 
your results.


On 2/9/2022 6:28 PM, HYE JUNG YOUN wrote:


External Email - Use Caution

Good day,

I hope this email finds you well.

I’d love your assistance with understanding my recon-all.log as I am 
trying to figure out if the reconstruction I’ve done is done properly 
without an error.


But I am seeing a few lines that worries me (please see attached log)

I look forward to hearing from you at your earliest convenience.

Thank you in advance.

Best wishes,

H. Youn

Asan Medical Center

88, Olympic-ro 43-Gil, Songpa-gu, Seoul 05505, Korea


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Help

[Douglas N. Greve]

There is an automatic topology fixer in the stream. While sometimes it 
fixes an topo error properly, it does not always do so, so you will need 
to see whether it has fixed is or not. It is the white surface that is 
in error, which is created from the wm.mgz (or filled.mgz), so you will 
need to fix one of those volumes.


On 12/14/2021 5:26 AM, Nilab Nasrullah wrote:


External Email - Use Caution

I am using freesurfer 7.1.This particular subject's segmentation 
didn't include the cerebral cortex of the occipital lobe (see image 
1). Although I can see there are defects in that specific place, there 
are also defects in other places (see atttached images). I have 
followed the instructions on how to correct topological errors but 
that doesn't seem to help much since it is the grey matter that is not 
included in the segmentation.


Can you provide me with some instructions on how to fix these defects?

Thanks,
Nilab

*From:* Douglas N. Greve 
*Sent:* 11 December 2021 00:24
*To:* Nilab Nasrullah ; 
freesurfer@nmr.mgh.harvard.edu 

*Subject:* Re: [Freesurfer] Help
The data look pretty noisy in those images. My guess is that the WM is 
not getting segmented properly in that temporal area or there is an 
incorrectly fixed topology error. Try looking at the wm.mgz (or the 
filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz 
to see where the defects are.


On 11/29/2021 9:41 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Sure. See attached.

//Nilab

*From:* Douglas N. Greve  
<mailto:dgr...@mgh.harvard.edu>

*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah  
<mailto:nilab.nasrul...@stud.ki.se>; freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] Help
Can you send them in plain, unzipped format?

On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:


External Email - Use Caution

I am attaching a few screenshots of the segmented brain as 
zip-files. Hopefully, you can see the results. If not, let me know 
so I can send it to you in a different format.


Thanks,
Nilab

*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:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] Help
Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. 
Often, some parts of the temporal lobe and the cortex of the 
occipital lobe are not included. In some cases, the cortex of the 
frontal lobe is also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, 
used the gcut command and edited manually after autorecon1 but in 
the end, the results don't vary significantly compared to running 
recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] Help

[Douglas N. Greve]

The data look pretty noisy in those images. My guess is that the WM is 
not getting segmented properly in that temporal area or there is an 
incorrectly fixed topology error. Try looking at the wm.mgz (or the 
filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz to 
see where the defects are.


On 11/29/2021 9:41 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Sure. See attached.

//Nilab

*From:* Douglas N. Greve 
*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah ; 
freesurfer@nmr.mgh.harvard.edu 

*Subject:* Re: [Freesurfer] Help
Can you send them in plain, unzipped format?

On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:


External Email - Use Caution

I am attaching a few screenshots of the segmented brain as zip-files. 
Hopefully, you can see the results. If not, let me know so I can send 
it to you in a different format.


Thanks,
Nilab

*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:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] Help
Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. Often, 
some parts of the temporal lobe and the cortex of the occipital lobe 
are not included. In some cases, the cortex of the frontal lobe is 
also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, 
used the gcut command and edited manually after autorecon1 but in 
the end, the results don't vary significantly compared to running 
recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] Help

[Douglas N. Greve]

Can you send them in plain, unzipped format?

On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:


External Email - Use Caution

I am attaching a few screenshots of the segmented brain as zip-files. 
Hopefully, you can see the results. If not, let me know so I can send 
it to you in a different format.


Thanks,
Nilab

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


*Sent:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Help
Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. Often, 
some parts of the temporal lobe and the cortex of the occipital lobe 
are not included. In some cases, the cortex of the frontal lobe is 
also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, 
used the gcut command and edited manually after autorecon1 but in the 
end, the results don't vary significantly compared to running 
recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] Help

[Douglas N. Greve]

Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. Often, 
some parts of the temporal lobe and the cortex of the occipital lobe 
are not included. In some cases, the cortex of the frontal lobe is 
also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, used 
the gcut command and edited manually after autorecon1 but in the end, 
the results don't vary significantly compared to running recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] Help

[Fischl, Bruce]

Hi Nilab

Can you send us an example? Usually you can fix this using expert options to 
constrain the range of intensities that white matter is allowed to take

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nilab Nasrullah
Sent: Thursday, November 18, 2021 8:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: gr...@nmr.mgh.harvard.edu
Subject: [Freesurfer] Help


External Email - Use Caution
Hi,

I am editing about 120 subjects for a research project. In some 
reconstructions, the grey matter boundary is not recognised, thus Freesurfer 
classifies it as white matter. I have tried to remove additional pial surface 
in the area and it gets a bit better. I have also tried to erase the wm that is 
classified as gm but the results don't change. Using control points is useless 
since the white matter is classified correct. Is there any way I can edit the 
subject to get better boundaries for the grey matter?

Thank you for your help in advance.

//Nilab Nasrullah





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Re: [Freesurfer] Help segmenting all subjects in a folder

[Douglas N. Greve]

That does not apply to the recon-all command, only to 
mri_segment_hypothalamus_subunits



On 7/1/2021 12:23 PM, g.ton...@libero.it wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

Thank you for your work !
I successfully set up Freesurfer and ran a test on my computer, and I 
am now attempting to run recon-all on all subjects in a folder 
("/home/users/s/saccaro/Groupe_0" in the example script below). I run 
the analysis on a HPC (SLURM system).


I found that, concerning the recon-all command, "If no name is given 
after --s, the code will be run on ALL subjects in $SUBJECTS_DIR 
." 
but I do not find information on how this could work also for the 
previous step, mri_convert: is there a way to submit a job to segment 
all subjects in the folder "Groupe_0", and not just S001 (in the 
example below)? All folders are structured as follows: 
/S@@@/scans/struct/@@.nii .


I am new to Freesurfer and I apologize if my question is naive but I 
cannot find a solution in any of the online resources.


Thank you very much for your time!
Best,

Giorgio

*- Script, without SBATCH settings (I join the full version):*

module load FreeSurfer/6.0.0-centos6_x86_64
source /home/users/s/saccaro/SetUpFreeSurfer.sh
FSDIR="/home/users/s/saccaro/Groupe_0"

mksubjdris ${FSDIR}/S001;

mri_convert -i 
${FSDIR}/S001/scans/struct/s44891-153636-1-00192-1.nii -o 
${FSDIR}/S001/scans/struct/s44891-153636-1-00192-1.mgz


recon-all -all -s S001

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Re: [Freesurfer] Help with LGI pipeline output - Freeview

[Douglas N. Greve]

First, try using tksurferfv (this is the freeview version of tksurfer; 
tksurfer is obsolete)
Second, you'll have to tell us more than "it did not work" (eg, send the 
terminal output or some other description)


On 6/21/2021 3:03 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


External Email - Use Caution

Dear FreeSurfer experts,

Hope that everyone is well and having a great Monday.

I am having some trouble opening the outputs for the LGI pipeline via 
Freeview - could someone please help me with this?


I tried using + editing the code available on the website *tksurfer 
my_subject_id lh inflated -overlay lh.pial_lgi*; however it did not work.


Thank you so much,
Alex

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Re: [Freesurfer] 'help: aparcstats2table'

[Nolan, Jackson]

Hello again,

Thank you for sending the screenshot and additional information.

It looks like your directory structure is correct. It also looks like you are 
correct about the python version causing your error.

That utility is written in Python 2.7, and it appears that your environment is 
sourcing some version of Python 3. (You can confirm this by running the command 
'python --version' in your terminal).

You need to check that you have a version of Python2.7 installed, and then add 
that to your path.

To check that you have a version of Python2.7: run the command 'which python2'. 
If a version of Python2.7 is installed, the path to it will be printed in the 
terminal. If no version of is found, you will need to install one.

To source that python version (add it to your path): run 'export 
PATH="":$PATH'

Best,

Jackson



From: Zeynep Boz 
Sent: Friday, June 4, 2021 2:00 PM
To: Nolan, Jackson 
Subject: Re: 'help: aparcstats2table'


External Email - Use Caution

Dear Jackson,

I run these commands "FreesurferWork on my computer" in the directory 
containing that subject. My subject is H1_deneme in named directory 
FreesurferWork
According to the comments I read, I think this error may be related to the 
phyton version, but of course you know better.
Attached I am sending you a screenshot of the terminal and the folders with the 
file directories.

Thank you for your support
I wish you good work


Dr. Zeynep YÜKSEL
Ondokuz Mayis University
Vocational School of Health Services,
Medical İmaging
55139, Atakum, Samsun, Turkey
Tel: +903623121919 Ext:5261


Kimden: "Nolan, Jackson" 
Kime: "freesurfer" , "zeynep boz" 

Gönderilenler: 2 Haziran Çarşamba 2021 23:20:11
Konu: Re: 'help: aparcstats2table'

Hello Dr. Zeynep,

Are you running those commands in the directory containing that subject? The 
script needs the file path to the subject, and absolute paths tend to work 
better than relative paths.

If you have specified these are still getting those errors, please send your 
full terminal output with the command run and all error messages.

Best,
Jackson

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zeynep Boz 

Sent: Saturday, May 29, 2021 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] 'help: aparcstats2table'


External Email - Use Caution

Hello,
I am using Ubuntu 18.05 version and Freesurfer6 version.
I've completed all the recon-all parts without any problems, but I'm having 
trouble with the "aparcstats2table" part.
The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness 
--tablefile lh.thicknes.xlsx" gives the following error:
   File "/usr/local/freesurfer/bin/aparcstats2table", line 156
 print 'ERROR: atleast 1 subject must be provided'
   On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas 
volume --stats = aseg.stats --table = segstats.txt" gives the following error:
   File "/usr/local/freesurfer/bin/asegstats2table", line 195
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
Thank you in advance for your support



Dr.Zeynep YÜKSEL
Ondokuz Mayis University
Vocational School of Health Services,
Medical İmaging
55139, Atakum, Samsun, Turkey
Tel: +903623121919 Ext:5261

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addressed. If you believe this e-mail was sent to you in error and the e-mail 
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Re: [Freesurfer] 'help: aparcstats2table'

[Nolan, Jackson]

Hello Dr. Zeynep,

Are you running those commands in the directory containing that subject? The 
script needs the file path to the subject, and absolute paths tend to work 
better than relative paths.

If you have specified these are still getting those errors, please send your 
full terminal output with the command run and all error messages.

Best,
Jackson

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zeynep Boz 

Sent: Saturday, May 29, 2021 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] 'help: aparcstats2table'


External Email - Use Caution

Hello,
I am using Ubuntu 18.05 version and Freesurfer6 version.
I've completed all the recon-all parts without any problems, but I'm having 
trouble with the "aparcstats2table" part.
The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness 
--tablefile lh.thicknes.xlsx" gives the following error:
   File "/usr/local/freesurfer/bin/aparcstats2table", line 156
 print 'ERROR: atleast 1 subject must be provided'
   On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas 
volume --stats = aseg.stats --table = segstats.txt" gives the following error:
   File "/usr/local/freesurfer/bin/asegstats2table", line 195
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
Thank you in advance for your support



Dr.Zeynep YÜKSEL
Ondokuz Mayis University
Vocational School of Health Services,
Medical İmaging
55139, Atakum, Samsun, Turkey
Tel: +903623121919 Ext:5261

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Re: [Freesurfer] help Optseq2 study design

[Douglas N. Greve]

On 5/17/2021 10:16 AM, Ellen JOOS wrote:

External Email - Use Caution
Dear Freesurfer team,

I am currently preparing my first fMRI study and used OptSeq2 for 
creating the trial sequence. Since I am not experienced with the study 
design in MRI (I mainly conducted EEG studies so far), I would like to 
have your professional opinion on my design choices and use of your 
program.


The parameters of my study are the following:

I will conduct a multiband fMRI study with an event-related design 
that will have a TR of 0.5s. I will present 10 different types of 
trials that will have a length of 2.5s each, but that will be shown 
with different amounts of repetitions across the experiment. Within 
the 2.5s trial time, I included a fixed time period of 1.3s to respond.


As indicated in your recommendations, I added time to the overall 
presentation time for the "NULL events" that corresponds to the time 
needed for one of my trial types (as if I would have another trial 
type). You can find the output of OptSeq attached.


My questions are the following:

1) Did I use the program correctly by having a fixed response time 
window within the trial duration estimation?

Yes


2) Is the use of the NULL events (as can be seen in the attached file) 
correct and sufficient to introduce varying amounts of time between 
the individual trials such that the hemodynamic response can be 
captured appropriately?
This is a tricky question because you end up not having many nulls 
relative to your task, so they might look a little like odd balls (eg, 
at one point there are 7 task trials between nulls). This is more of a 
question for you and whether you think the psychology is affected by the 
nulls. I would probably double the null time.


3) In the summary of the OptSeq results, I found an efficiency value 
of 0.009 and a VRFAvg of 6.24. I saw in your recommendations that the 
VRFAvg should be 20-40. Is the result of my calcuation too bad to have 
an efficient recording that allows analyzing the data in an 
event-related manner?
Are you planning to use an FIR or are you going to assume a shape to the 
HRF? Probably the latter; if so, then those values are not meaningful.


4) In the actual experiment I will present the attached sequence 
twice. I have now the options to either present two different 
sequences (e.g. the two most efficient sequences produced by OptSeq) 
or to repeat the most efficient sequence twice. Do you have a 
recommendation? And further, might using the same sequence across 
participants result in a general ordering effect that might bias my 
results?
I would use two different sequences and then randomize the order across 
subjects.



I am very much looking forward to your response and already thank you 
for your advice and help!


Kind regards,

Ellen Joos


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Re: [Freesurfer] help with SAMSEG

[Hoopes, Andrew]

The atlases used by samseg are very different from freesurfer GCAs, and the 
samseg-template creation is not an easily-accessible utility at the moment. 
Feel free to look through the GEMS code in the FS repository, but it might be 
some time before we have an easy-to-use samseg atlas building tool in 
freesurfer.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alberto Del Cerro Leon 

Date: Wednesday, May 5, 2021 at 11:11 AM
To: Freesurfer support list 
Subject: [Freesurfer] help with SAMSEG

External Email - Use Caution
Hello Freesurfer team, my group is interested in using the SAMSEG tool to 
evaluate white matter lesions in MCI patients. We would like to use a 
personalized atlas for the measure. We suppose that we need to use the flag 
--atlas but we don`t know if we need a generic atlas or we need an atlas at 
each subject' spaces.

Thanks in advance for your help.
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Re: [Freesurfer] Help

[Douglas N. Greve]

We don't have a lobar segmentation. You can get whole cerebellum (GM and 
WM) from our standard analysis (recon-all) or using samseg.

On 3/5/2021 3:27 PM, Murray Howerth wrote:
>  External Email - Use Caution
>
> I am new to this platform and would like some direction as how to obtain 
> adjusted cerebellar volumes, specifically lobular cerebellum structure.
> With thanks,
> M
>
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Re: [Freesurfer] help with labels

[Douglas N. Greve]

You can manully edit the annotation or you can manually edit the AAL 
segmentation to fill in the holes


On 1/28/2021 6:09 AM, Alberto Del Cerro Leon wrote:


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I found the vertex for the holes but how can i modify them or how can 
I solve them?


El mié, 27 ene 2021 a las 16:36, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:


Look at the surface superimposed on the volume along with the AAL
segmentation to make sure that it intersects the segmentation at
all vertices. You can find the vertex numbers for the holes, and
then go specifically to that vertex

On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:


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Hello Freesurfer team, I did an AAL atlas on the surface using
mri_vol2surf, however when I look at this overlay there are many
holes in the labels with vertices that don't belong to any label.
Could u help me with this problem?

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Re: [Freesurfer] help with labels

[Alberto Del Cerro Leon]

External Email - Use Caution

I found the vertex for the holes but how can i modify them or how can I
solve them?

El mié, 27 ene 2021 a las 16:36, Douglas N. Greve ()
escribió:

> Look at the surface superimposed on the volume along with the AAL
> segmentation to make sure that it intersects the segmentation at all
> vertices. You can find the vertex numbers for the holes, and then go
> specifically to that vertex
>
> On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Freesurfer team, I did an AAL atlas on the surface using
> mri_vol2surf, however when I look at this overlay there are many holes in
> the labels with vertices that don't belong to any label. Could u help me
> with this problem?
>
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>
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Re: [Freesurfer] help with labels

[Douglas N. Greve]

Look at the surface superimposed on the volume along with the AAL 
segmentation to make sure that it intersects the segmentation at all 
vertices. You can find the vertex numbers for the holes, and then go 
specifically to that vertex


On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Hello Freesurfer team, I did an AAL atlas on the surface using 
mri_vol2surf, however when I look at this overlay there are many holes 
in the labels with vertices that don't belong to any label. Could u 
help me with this problem?


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Re: [Freesurfer] Help with mergecontrasts-sess function

[Douglas N. Greve]

They way you have specified your contrast is a conjunction of individual 
contrasts, ie, cA>cAc AND cB>cBc. If that what you want? Originally, you 
were just asking about  the interaction

On 1/26/2021 5:17 AM, Paula Maldonado wrote:
>  External Email - Use Caution
>
> Thanks for your reply,
> However I have now a doubt regarding one aspect that I had not noticed before.
>
> What I wanted to do is to perform the contrast 
> (condA>condAcontrol)>(condB>condBcontrol) with the order of my condition 
> being condA, condAcontrol, condB, condBcontrol
>
> You said that to do so I should use -a 1 -c 2 -c 3 -a 4, but I don’t 
> understand why condition 3 is -c and condition 4 is -a.
> To my understanding a is assigning a positive weight to my predictors, while 
> c is assigning a negative one.
> So if I run  -a 1 -c 2 -c 3 -a 4, am I not testing the contrast 
> (condA>condAcontrol)>(condBcontrol>condB) ?
>
> In addition, if now I want to obtain: 
> (condA>condB)>(condAcontrol>condBcontrol)
> should I run mkcontrast-sess -analysis analysis -contrast contrastname -a 1 
> -c 3 -c 2 -a 4, or -a 1 -c 3 -a 2 -c 4?
>
>
> Thanks,
>
>
> Paula
>
>
>> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>>  ha scritto:
>>
>> You would just run mkcontrast-sess, eg, if your four conditions are
>> ordered condA, condAcontrol, condB, condBcont, then
>> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
>> -a 4
>> If you want it reversed, then just reverse the a's and c's
>>
>> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>>>  External Email - Use Caution
>>>
>>> Dear experts,
>>> I am running an fMRI experiment in which I have four conditions: two main 
>>> conditions (condition A and condition B) and two respective control 
>>> conditions (condition Acontrol and condition Bcontrol).
>>> I would like to create a map showing significantly greater activity for 
>>> condition A relative to condition B, after subtracting out the activity for 
>>> the respective control conditions. In other words, I would like to perform 
>>> the following contrast:
>>> (condition A - condition A control) - (condition B - condition B control)
>>> Then I would like to have a map that shows the reverse contrast 
>>> too:(condition B - condition B control) - (condition A - condition A 
>>> control).
>>>
>>> How do I do that?To obtain the first map: (condition A - condition A 
>>> control) - (condition B - condition B control) I have tried with the 
>>> mergecontrasts-sess function with the -conjunction flag and the OR option 
>>> as detailed below:
>>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
>>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
>>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>>>
>>> where Contrast1= (condition A - condition A control) and Contrast2= 
>>> (condition B - condition B control)
>>> however the map I get is exactly the same as (condition A - condition A 
>>> control), as if subtracting out Contrast 2 had no impact on the map.
>>>
>>> Thanks,
>>>
>>> Paula
>>>
>>>
>>>
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Re: [Freesurfer] Help with mergecontrasts-sess function

[Paula Maldonado]

External Email - Use Caution

Thanks for your reply, 
However I have now a doubt regarding one aspect that I had not noticed before.

What I wanted to do is to perform the contrast 
(condA>condAcontrol)>(condB>condBcontrol) with the order of my condition being 
condA, condAcontrol, condB, condBcontrol

You said that to do so I should use -a 1 -c 2 -c 3 -a 4, but I don’t understand 
why condition 3 is -c and condition 4 is -a.
To my understanding a is assigning a positive weight to my predictors, while c 
is assigning a negative one.
So if I run  -a 1 -c 2 -c 3 -a 4, am I not testing the contrast 
(condA>condAcontrol)>(condBcontrol>condB) ?

In addition, if now I want to obtain: (condA>condB)>(condAcontrol>condBcontrol) 
should I run mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 
3 -c 2 -a 4, or -a 1 -c 3 -a 2 -c 4?


Thanks, 


Paula


> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>  ha scritto:
> 
> You would just run mkcontrast-sess, eg, if your four conditions are 
> ordered condA, condAcontrol, condB, condBcont, then
> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
> -a 4
> If you want it reversed, then just reverse the a's and c's
> 
> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Dear experts,
>> I am running an fMRI experiment in which I have four conditions: two main 
>> conditions (condition A and condition B) and two respective control 
>> conditions (condition Acontrol and condition Bcontrol).
>> I would like to create a map showing significantly greater activity for 
>> condition A relative to condition B, after subtracting out the activity for 
>> the respective control conditions. In other words, I would like to perform 
>> the following contrast:
>> (condition A - condition A control) - (condition B - condition B control)
>> Then I would like to have a map that shows the reverse contrast 
>> too:(condition B - condition B control) - (condition A - condition A 
>> control).
>> 
>> How do I do that?To obtain the first map: (condition A - condition A 
>> control) - (condition B - condition B control) I have tried with the 
>> mergecontrasts-sess function with the -conjunction flag and the OR option as 
>> detailed below:
>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>> 
>> where Contrast1= (condition A - condition A control) and Contrast2= 
>> (condition B - condition B control)
>> however the map I get is exactly the same as (condition A - condition A 
>> control), as if subtracting out Contrast 2 had no impact on the map.
>> 
>> Thanks,
>> 
>> Paula
>> 
>> 
>> 
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Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

[Greve, Douglas N.,Ph.D.]

If you want a cluster table, then you will have to run mri_surfcluster on the 
output of the conjunction. Run it with --help and write back if you need more 
info

On 11/21/2020 10:03 AM, Paula Maldonado wrote:

External Email - Use Caution

Dear Douglas,

Could you please tell me where can I find the cluster table?

Thank you,
Best regards,

Paula

Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

There is not a summary table, it is just a map. Do you want a cluster table?

On 11/10/2020 11:26 AM, Paula Maldonado wrote:

External Email - Use Caution

Thanks for your reply, that worked. Can you please tell me where I can find a 
summary table of the activated regions resulting from the conjunction analysis?

Best regards,

Paula




Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

You would just run mkcontrast-sess, eg, if your four conditions are
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:
External Email - Use Caution

Dear experts,
I am running an fMRI experiment in which I have four conditions: two main 
conditions (condition A and condition B) and two respective control conditions 
(condition Acontrol and condition Bcontrol).
I would like to create a map showing significantly greater activity for 
condition A relative to condition B, after subtracting out the activity for the 
respective control conditions. In other words, I would like to perform the 
following contrast:
(condition A - condition A control) - (condition B - condition B control)
Then I would like to have a map that shows the reverse contrast too:(condition 
B - condition B control) - (condition A - condition A control).

How do I do that?To obtain the first map: (condition A - condition A control) - 
(condition B - condition B control) I have tried with the mergecontrasts-sess 
function with the -conjunction flag and the OR option as detailed below:
mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
-contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh

where Contrast1= (condition A - condition A control) and Contrast2= (condition 
B - condition B control)
however the map I get is exactly the same as (condition A - condition A 
control), as if subtracting out Contrast 2 had no impact on the map.

Thanks,

Paula



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Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

[Paula Maldonado]

External Email - Use Caution

Dear Douglas, 

Could you please tell me where can I find the cluster table?

Thank you, 
Best regards, 

Paula

> Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve 
>  ha scritto:
> 
> There is not a summary table, it is just a map. Do you want a cluster table?
> 
> On 11/10/2020 11:26 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Thanks for your reply, that worked. Can you please tell me where I can find 
>> a summary table of the activated regions resulting from the conjunction 
>> analysis?
>> 
>> Best regards,
>> 
>> Paula
>> 
>> 
>> 
>> 
>>> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> You would just run mkcontrast-sess, eg, if your four conditions are 
>>> ordered condA, condAcontrol, condB, condBcont, then
>>> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
>>> -a 4
>>> If you want it reversed, then just reverse the a's and c's
>>> 
>>> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
 External Email - Use Caution
 
 Dear experts,
 I am running an fMRI experiment in which I have four conditions: two main 
 conditions (condition A and condition B) and two respective control 
 conditions (condition Acontrol and condition Bcontrol).
 I would like to create a map showing significantly greater activity for 
 condition A relative to condition B, after subtracting out the activity 
 for the respective control conditions. In other words, I would like to 
 perform the following contrast:
 (condition A - condition A control) - (condition B - condition B control)
 Then I would like to have a map that shows the reverse contrast 
 too:(condition B - condition B control) - (condition A - condition A 
 control).
 
 How do I do that?To obtain the first map: (condition A - condition A 
 control) - (condition B - condition B control) I have tried with the 
 mergecontrasts-sess function with the -conjunction flag and the OR option 
 as detailed below:
 mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
 analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
 -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
 
 where Contrast1= (condition A - condition A control) and Contrast2= 
 (condition B - condition B control)
 however the map I get is exactly the same as (condition A - condition A 
 control), as if subtracting out Contrast 2 had no impact on the map.
 
 Thanks,
 
 Paula
 
 
 
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Re: [Freesurfer] Help with MRI labels {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

I want to obtain gray matter, withe matter volume, thickness and curvature
based on AAL segmentation.

El jue., 12 nov. 2020 15:27, Douglas N. Greve 
escribió:

> So you want the AAL atlas on the surface? If so, then run recon-all on the
> AAL anatomical T1w volume template, then use mri_vol2surf to sample the
> labels on the surface, then use this surface segmentation or extract labels
> (mri_cor2label with --surf option) or convert to an annotation
> (mris_seg2annot)
>
>
> On 11/11/2020 11:32 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Good afternoon, my name is Alberto del Cerro and I am a PhD student in the
> cognitive and computational neuroscience laboratory (LNCyC) at the
> biomedical technology center (CTB) of the Polytechnic University of Madrid
> (UPM). I am currently extracting the structural data from the T1 images of
> my project and I would like to extract the volume, thickness and curvature
> data in the regions of interest where I obtained results in
> electrophysiology (MEG). The point is that for this data I used the AAL
> atlas and I would like to use these regions to obtain structural data in
> FreeSurfer. Researching on the internet I have read that this is possible
> with the mri_label2vol command but I would like to know how I can proceed
> to obtain this data. Can you guide me in this process?
>
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Re: [Freesurfer] Help with MRI labels

[Douglas N. Greve]

So you want the AAL atlas on the surface? If so, then run recon-all on 
the AAL anatomical T1w volume template, then use mri_vol2surf to sample 
the labels on the surface, then use this surface segmentation or extract 
labels (mri_cor2label with --surf option) or convert to an annotation 
(mris_seg2annot)



On 11/11/2020 11:32 AM, Alberto Del Cerro Leon wrote:


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Good afternoon, my name is Alberto del Cerro and I am a PhD student in 
the cognitive and computational neuroscience laboratory (LNCyC) at the 
biomedical technology center (CTB) of the Polytechnic University of 
Madrid (UPM). I am currently extracting the structural data from the 
T1 images of my project and I would like to extract the volume, 
thickness and curvature data in the regions of interest where I 
obtained results in electrophysiology (MEG). The point is that for 
this data I used the AAL atlas and I would like to use these regions 
to obtain structural data in FreeSurfer. Researching on the internet I 
have read that this is possible with the mri_label2vol command but I 
would like to know how I can proceed to obtain this data. Can you 
guide me in this process?


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Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

[Paula Maldonado]

External Email - Use Caution

Yes, please,

Best regards, 

Paula

> Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve 
>  ha scritto:
> 
> There is not a summary table, it is just a map. Do you want a cluster table?
> 
> On 11/10/2020 11:26 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Thanks for your reply, that worked. Can you please tell me where I can find 
>> a summary table of the activated regions resulting from the conjunction 
>> analysis?
>> 
>> Best regards,
>> 
>> Paula
>> 
>> 
>> 
>> 
>>> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> You would just run mkcontrast-sess, eg, if your four conditions are 
>>> ordered condA, condAcontrol, condB, condBcont, then
>>> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
>>> -a 4
>>> If you want it reversed, then just reverse the a's and c's
>>> 
>>> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
 External Email - Use Caution
 
 Dear experts,
 I am running an fMRI experiment in which I have four conditions: two main 
 conditions (condition A and condition B) and two respective control 
 conditions (condition Acontrol and condition Bcontrol).
 I would like to create a map showing significantly greater activity for 
 condition A relative to condition B, after subtracting out the activity 
 for the respective control conditions. In other words, I would like to 
 perform the following contrast:
 (condition A - condition A control) - (condition B - condition B control)
 Then I would like to have a map that shows the reverse contrast 
 too:(condition B - condition B control) - (condition A - condition A 
 control).
 
 How do I do that?To obtain the first map: (condition A - condition A 
 control) - (condition B - condition B control) I have tried with the 
 mergecontrasts-sess function with the -conjunction flag and the OR option 
 as detailed below:
 mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
 analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
 -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
 
 where Contrast1= (condition A - condition A control) and Contrast2= 
 (condition B - condition B control)
 however the map I get is exactly the same as (condition A - condition A 
 control), as if subtracting out Contrast 2 had no impact on the map.
 
 Thanks,
 
 Paula
 
 
 
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Re: [Freesurfer] Help with mergecontrasts-sess function

[Douglas N. Greve]

There is not a summary table, it is just a map. Do you want a cluster table?

On 11/10/2020 11:26 AM, Paula Maldonado wrote:


External Email - Use Caution

Thanks for your reply, that worked. Can you please tell me where I can 
find a summary table of the activated regions resulting from the 
conjunction analysis?


Best regards,

Paula




Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:


You would just run mkcontrast-sess, eg, if your four conditions are
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:

External Email - Use Caution

Dear experts,
I am running an fMRI experiment in which I have four conditions: two 
main conditions (condition A and condition B) and two respective 
control conditions (condition Acontrol and condition Bcontrol).
I would like to create a map showing significantly greater activity 
for condition A relative to condition B, after subtracting out the 
activity for the respective control conditions. In other words, I 
would like to perform the following contrast:
(condition A - condition A control) - (condition B - condition B 
control)
Then I would like to have a map that shows the reverse contrast 
too:(condition B - condition B control) - (condition A - condition A 
control).


How do I do that?To obtain the first map: (condition A - condition A 
control) - (condition B - condition B control) I have tried with the 
mergecontrasts-sess function with the -conjunction flag and the OR 
option as detailed below:
mergecontrasts-sess -mergedcontrast conjres -conjunction or 
-analysis analysisname -map sig -space sph -isxavg fixed -contrast 
Contrast1 2 pos 0 -contrast Contrast 2 pos 0 -s 
sessionsfMRI/Sub01/bold -hemi lh


where Contrast1= (condition A - condition A control) and Contrast2= 
(condition B - condition B control)
however the map I get is exactly the same as (condition A - 
condition A control), as if subtracting out Contrast 2 had no impact 
on the map.


Thanks,

Paula



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Re: [Freesurfer] Help with mergecontrasts-sess function

[Paula Maldonado]

External Email - Use Caution

Thanks for your reply, that worked. Can you please tell me where I can find a 
summary table of the activated regions resulting from the conjunction analysis?

Best regards,

Paula




> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>  ha scritto:
> 
> You would just run mkcontrast-sess, eg, if your four conditions are 
> ordered condA, condAcontrol, condB, condBcont, then
> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
> -a 4
> If you want it reversed, then just reverse the a's and c's
> 
> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Dear experts,
>> I am running an fMRI experiment in which I have four conditions: two main 
>> conditions (condition A and condition B) and two respective control 
>> conditions (condition Acontrol and condition Bcontrol).
>> I would like to create a map showing significantly greater activity for 
>> condition A relative to condition B, after subtracting out the activity for 
>> the respective control conditions. In other words, I would like to perform 
>> the following contrast:
>> (condition A - condition A control) - (condition B - condition B control)
>> Then I would like to have a map that shows the reverse contrast 
>> too:(condition B - condition B control) - (condition A - condition A 
>> control).
>> 
>> How do I do that?To obtain the first map: (condition A - condition A 
>> control) - (condition B - condition B control) I have tried with the 
>> mergecontrasts-sess function with the -conjunction flag and the OR option as 
>> detailed below:
>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>> 
>> where Contrast1= (condition A - condition A control) and Contrast2= 
>> (condition B - condition B control)
>> however the map I get is exactly the same as (condition A - condition A 
>> control), as if subtracting out Contrast 2 had no impact on the map.
>> 
>> Thanks,
>> 
>> Paula
>> 
>> 
>> 
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Re: [Freesurfer] Help with mergecontrasts-sess function

[Douglas N. Greve]

You would just run mkcontrast-sess, eg, if your four conditions are 
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>  External Email - Use Caution
>
> Dear experts,
> I am running an fMRI experiment in which I have four conditions: two main 
> conditions (condition A and condition B) and two respective control 
> conditions (condition Acontrol and condition Bcontrol).
> I would like to create a map showing significantly greater activity for 
> condition A relative to condition B, after subtracting out the activity for 
> the respective control conditions. In other words, I would like to perform 
> the following contrast:
> (condition A - condition A control) - (condition B - condition B control)
> Then I would like to have a map that shows the reverse contrast 
> too:(condition B - condition B control) - (condition A - condition A control).
>
> How do I do that?To obtain the first map: (condition A - condition A control) 
> - (condition B - condition B control) I have tried with the 
> mergecontrasts-sess function with the -conjunction flag and the OR option as 
> detailed below:
> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>
> where Contrast1= (condition A - condition A control) and Contrast2= 
> (condition B - condition B control)
> however the map I get is exactly the same as (condition A - condition A 
> control), as if subtracting out Contrast 2 had no impact on the map.
>
> Thanks,
>
> Paula
>
>
>
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Re: [Freesurfer] Help to create flattened images of a whole hemisphere

[Wang, Ruopeng]

Hi Ornaith,

Regarding your freeview question - you can use shift + Ctrl + left button to 
select vertex for filling uncut area. But I just found out there is a glitch on 
macOS that prevent that from working. A workaround is to uncheck the Cut 
button, which will quit Cut mode and return to normal viewing mode, then just 
left mouse button to move the 3D cursor to the vertex you want, then check Cut 
button again and finish filling uncut area. I’ll fix this issue asap. May also 
drop the shift + ctrl requirement to make the whole process more intuitive.

Best,
Ruopeng

On Oct 23, 2020, at 5:03 AM, Ornaith O Reilly 
mailto:oreil...@tcd.ie>> wrote:


External Email - Use Caution

Hello Freesurfer developers,

I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting 
to get a flattened patch of an entire hemisphere.  Below is a page outlining 
how to use mris_flatten to achieve this:

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch

I am just trying to achieve this with the tutorial data to start with.

1. First problem is that when I run the command 'tksurferfv bert lh inflated'; 
I am getting the error outlined below:

Ornaiths-MacBook-Air-3:subjects ornaithoreilly$ tksurferfv bert lh inflated
freeview -f 
/Applications/freesurfer/7.1.1/subjects/bert/surf/lh.inflated:curvature=/Applications/freesurfer/7.1.1/subjects/bert/surf/lh.curv
 -viewport 3d
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary 
operator expected
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near 
`FS_ALLOW_VGLRUN'
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v 
FS_ALLOW_VGLRUN ]]; then'
Ornaiths-MacBook-Air-3:subjects ornaithoreilly$


2.  I realised that I could create a patch using freeview instead of tksurfer.  
However I attempted to follow the instructions on the page above to do this and 
ran into some problems.  Image 2 shows an example of the patch that I created 
but when I attempt to press the Press Fill Uncut Area button  (I tried this 
many times and got the same result) a pop up appeared saying "please move 
cursor to a valid vertex".

3.  However one time I did succeed in making a patch (I don't know what I did 
differently this time?) - see image 4 attached.  I saved it as 
lh.full.patch.3d. When I tried to run the command mris_flatten :
mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d

I got the output:
Ornaiths-MacBook-Air-3:surf ornaithoreilly$ mris_flatten -w 10 lh.full.patch.3d 
lh.full.flat.patch.3d
using write iterations = 10
reading new surface format patch lh.full.patch.3d with 125717 vertices (94.1% 
of total)
reading original vertex positions...
minimizing metric distortion induced by projection...
MRISunfold() max_passes = 1 ---
tol=2.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=2, l_nlarea=1.000, 
l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.00
nfields 0
scale 0.00
desired_rms_height -1.00
momentum 0.90
nbhd_size 7
max_nbrs 12
niterations 40
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0


/Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:9034
 Error opening parms.fp using filename lh.full.flat.patch.3d.out mode w

The version of Freesurfer and the platform that I'm using is outlined below:
1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: macOS High Sierra 10.13.6 (17G7024)

If anyone could shed some light on any of these errors or suggest an 
alternative method it would be greatly appreciated.

Thanks a lot.

Kind Regards
Ornaith O'Reilly
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Re: [Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables

[Douglas N. Greve]

With 6 classes and 3 variables, you will have 24 regression coefficients 
and so 24 items in your contrast matrix (so good, so far). The order will be

1. MaleMaxT-Offset
2. MaleKahn-Offset
3.
4.
5.
6.
7. MaleMaxT-AgeSlope
8
9
10
11
12
13 MaleMaxT-HRSD_Reduction-Slope
14 MaleKahn-HRSD_Reduction-Slope
15
16
17
18 FemaleNone-HRSD_Reduction-Slope
19 MaleMaxT-SessionNumber-Slope
20
...

So all the HRSD_Reduction-Slopevariables are in items 13-18, so you set 
them all to 1 and let the others be 0, which is what you have.


Bottom line: you have done it correctly.

On 10/13/2020 7:52 PM, Paul Dhami wrote:


External Email - Use Caution

Dear Freesurfer community,

I am having trouble with my contrast matrix, and would greatly 
appreciate any help with this.


I have 2 categorical variables, sex (2 levels) and training type (3 
levels).


I also have three (continuous) variables: Age, percentage reduction in 
depression scores, and number of sessions.


I would like to assess the correlation between cortical thickness and 
% reduction in depression scores, while accounting for the effects of 
sex, training type, age, and number of sessions as nuisance variables.


Below is 1) my command line, 2) the FSGD fiile, and 3) the design matrix

1.

mri_glmfit.bin --y MDD-lh-thickness.mgh --fsgd 
Reduction_Correlation.fsgd.txt --C 
ME_ReductionCorrelation_Contrast.txt --fwhm 20 --surf fsaverage lh 
--glmdir /Users/prabhjotdhami/Desktop/CorticalThickness/Data/myGLM



2.


GroupDescriptorFile 1
Title MDD_correlation
Class MaleMaxT
Class MaleKahn
Class MaleNone
Class FemaleMaxT
Class FemaleKahn
Class FemaleNone
Variables Age HRSD_Reduction SessionNumber
Input yct-001 FemaleMaxT 24 62.5 20
Input yct-002 MaleKahn 18 70 20
Input yct-004 MaleMaxT 21 50 20
Input yct-005 MaleMaxT 24 25 20
Input yct-006 FemaleKahn 24 65.2173913 20
Input yct-012 FemaleKahn 17 71.42857143 20
Input yct-013 MaleMaxT 22 53.84615385 20
Input yct-014 FemaleMaxT 19 63.63636364 20
Input yct-015 FemaleMaxT 16 80.95238095 20
Input yct-016 FemaleKahn 24 65.2173913 20
Input yct-017 FemaleKahn 22 55 20
Input yct-018 FemaleMaxT 18 82.60869565 20
Input yct-019 MaleKahn 16 85 20
Input yct-020 FemaleMaxT 22 85 20
Input yct-021 MaleMaxT 24 81.81818182 20
Input yct-022 FemaleKahn 21 70.8333 20
Input yct-023 FemaleMaxT 20 52 20
Input yct-024 MaleKahn 16 73.68421053 20
Input yct-025 MaleKahn 21 23.80952381 20
Input yct-026 FemaleMaxT 20 78.26086957 20
Input yct-027 FemaleMaxT 17 20 20
Input yct-030 FemaleMaxT 19 52 20
Input yd-p002 MaleNone 20 54.54545455 10
Input yd-p006 FemaleNone 23 30 10
Input yd-p008 MaleNone 22 44 10
Input yd-p010 FemaleNone 16 50 10
Input yd-p014 FemaleNone 22 3.846153846 10
Input yd-p015 MaleNone 19 10 10
Input yd-p022 FemaleNone 24 37.03703704 10
Input yd-p026 FemaleNone 21 47.61904762 10
Input yd-p027 MaleNone 23 31.57894737 10
Input yd-p032 FemaleNone 21 75 10
Input yd-p033 MaleNone 24 22. 10
Input yd-p034 FemaleNone 22 25 10
Input yd-p035 MaleNone 24 30.43478261 10
Input yd-p047 MaleNone 16 78.26086957 10
Input yd-p048 MaleNone 17 20 10
Input yd-p051 FemaleNone 18 45 10
Input yd-p052 FemaleNone 20 47.82608696 10


3.

0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0


Any help would be greatly appreciated.


Thank you,

Paul



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Re: [Freesurfer] Help!

[Yendiki, Anastasia]

What version of FSL are you using? It seems to be an incompatibility between 
the version of FSL and version of python that you have:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;73e3d6df.1604

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Samar Fouda 

Sent: Friday, October 16, 2020 6:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Help!


External Email - Use Caution

Hi Anastasia,

Thank you so much for responding, please find the log attached!

On Fri, Oct 16, 2020 at 3:24 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Samar - Can you please attach your trac-all.log file and your configuration 
file? It's hard to guess what's going on just from the line where the error 
occurs without seeing everything that came before it.

Thanks!
Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Samar Fouda mailto:samarsfo...@gmail.com>>
Sent: Friday, October 16, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Help!


External Email - Use Caution

Hi! I am trying to run tracula- TRAC-All and I get this error message, i 
assumed it is because that bvals and bvecs needed to be predetermined but it 
seems like that is not the case and i am still getting the same error:

Transform file should be eddy_correct/eddy log file or .mat file

What do you think the problem is?

Thanks so much for your help.
--

--

Samar Fouda

Post Doctoral Associate

Emerge Research Program

National Center for PTSD, Clinical Neuroscience Division

Yale School of Medicine

samar.fo...@yale.edu<mailto:samar.fo...@yale.edu>

+1203285-7568

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--

--

Samar Fouda

Post Doctoral Associate

Emerge Research Program

National Center for PTSD, Clinical Neuroscience Division

Yale School of Medicine

samar.fo...@yale.edu<mailto:samar.fo...@yale.edu>

+1203285-7568
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Re: [Freesurfer] Help!

[Samar Fouda]

External Email - Use Caution

Hi Anastasia,

Thank you so much for responding, please find the log attached!

On Fri, Oct 16, 2020 at 3:24 PM Yendiki, Anastasia 
wrote:

> Hi Samar - Can you please attach your trac-all.log file and your
> configuration file? It's hard to guess what's going on just from the line
> where the error occurs without seeing everything that came before it.
>
> Thanks!
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Samar Fouda <
> samarsfo...@gmail.com>
> *Sent:* Friday, October 16, 2020 10:00 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] Help!
>
>
> External Email - Use Caution
>
> Hi! I am trying to run tracula- TRAC-All and I get this error message, i
> assumed it is because that bvals and bvecs needed to be predetermined but
> it seems like that is not the case and i am still getting the same error:
>
> Transform file should be eddy_correct/eddy log file or .mat file
>
> What do you think the problem is?
>
> Thanks so much for your help.
> --
>
> *--*
>
> *Samar Fouda*
>
> *Post Doctoral Associate*
>
> *Emerge Research Program*
>
> *National Center for PTSD, Clinical Neuroscience Division*
>
> *Yale School of Medicine*
>
> *samar.fo...@yale.edu *
>
> *+1203285-7568*
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

*--*

*Samar Fouda*

*Post Doctoral Associate*

*Emerge Research Program*

*National Center for PTSD, Clinical Neuroscience Division*

*Yale School of Medicine*

*samar.fo...@yale.edu *

*+1203285-7568*


trac-all.log
Description: Binary data
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Help!

[Yendiki, Anastasia]

Hi Samar - Can you please attach your trac-all.log file and your configuration 
file? It's hard to guess what's going on just from the line where the error 
occurs without seeing everything that came before it.

Thanks!
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Samar Fouda 

Sent: Friday, October 16, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Help!


External Email - Use Caution

Hi! I am trying to run tracula- TRAC-All and I get this error message, i 
assumed it is because that bvals and bvecs needed to be predetermined but it 
seems like that is not the case and i am still getting the same error:

Transform file should be eddy_correct/eddy log file or .mat file

What do you think the problem is?

Thanks so much for your help.
--

--

Samar Fouda

Post Doctoral Associate

Emerge Research Program

National Center for PTSD, Clinical Neuroscience Division

Yale School of Medicine

samar.fo...@yale.edu

+1203285-7568
___
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Re: [Freesurfer] Help with LGI

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear Tim,

1) Here is the output after I type matlab:
- Matlab does open, and the following appears on terminal:
shell-init: error retrieving current directory: getcwd: cannot access
parent directories: No such file or directory
pwd: error retrieving current directory: getcwd: cannot access parent
directories: No such file or directory
pwd: error retrieving current directory: getcwd: cannot access parent
directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent
directories: No such file or directory
GVA encoder info: AMD performance mode : 2
GVA encoder info: deleteSCDMetalContext : texture cache hits: 0, misses: 0

2) and /Applications/MATLAB_R2020a/bin/matlab:
/Applications/MATLAB_R2020a/bin/matlab: No such file or directory

Please let me know if you need more information.

Thank you,
Alex


On Wed, Aug 5, 2020 at 3:42 AM Tim Schäfer  wrote:

> External Email - Use Caution
>
> Looks like something is wrong with the Matlab installation. It would be
> good to know:
>
> 1) What happens if you type 'matlab' in your shell?
> 2) What happens if you type '/Applications/MATLAB_R2020a/bin/matlab' in
> your shell?
>
> Best,
>
> Tim
>
> > On August 4, 2020 at 8:31 PM "Lab of Autism and Developmental
> Neuroscience, Lab of Autism and Developmental Neuroscience" <
> l...@email.gwu.edu> wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> > Just wanted to follow up my last email - does anyone know what might be
> > wrong with my code?
> >
> > Thank you and stay safe,
> > Alex
> >
> > On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental
> > Neuroscience, Lab of Autism and Developmental Neuroscience <
> > l...@email.gwu.edu> wrote:
> >
> > > Dear Douglas,
> > >
> > > Yes, now matlab is correctly set to my freesurfer path, but the
> following
> > > error occurs when I run localGI (please see below). Any ideas what
> might be
> > > wrong? Maybe there are some issues with the matlab version or image
> > > processing toolbox that I'm using?
> > >
> > > iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4
> -localGI
> > > Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> > > Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> > > INFO: SUBJECTS_DIR is /Applications/BAP_complete
> > > Actual FREESURFER_HOME /Applications/freesurfer
> > > -rw-rw-r--  1 ajobsaid  982768932  956144 Jun 30 09:20
> > > /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log
> > > Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul  5
> > > 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
> > > /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms
> > > /Applications/BAP_complete/nih00024_epoch11_4
> > > /Applications/BAP_complete/nih00024_epoch11_4
> > > #@# white curv lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
> > >Update not needed
> > > #@# white area lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
> > >Update not needed
> > > #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
> > >Update not needed
> > > #@# pial area lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
> > >Update not needed
> > > #@# thickness lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> > > ../surf/lh.thickness
> > >Update not needed
> > > #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> > > ../surf/lh.thickness
> > >Update not needed
> > > #@# white curv rh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
> > >Update not needed
> > > #@# white area rh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
> > >Update not needed
> > > #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
> > >Update not needed
> > > #@# pial area rh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > 

Re: [Freesurfer] Help with LGI

[Tim Schäfer]

External Email - Use Caution

Looks like something is wrong with the Matlab installation. It would be good to 
know:

1) What happens if you type 'matlab' in your shell?
2) What happens if you type '/Applications/MATLAB_R2020a/bin/matlab' in your 
shell?

Best,

Tim

> On August 4, 2020 at 8:31 PM "Lab of Autism and Developmental Neuroscience, 
> Lab of Autism and Developmental Neuroscience"  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Freesurfer experts,
> 
> Just wanted to follow up my last email - does anyone know what might be
> wrong with my code?
> 
> Thank you and stay safe,
> Alex
> 
> On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental
> Neuroscience, Lab of Autism and Developmental Neuroscience <
> l...@email.gwu.edu> wrote:
> 
> > Dear Douglas,
> >
> > Yes, now matlab is correctly set to my freesurfer path, but the following
> > error occurs when I run localGI (please see below). Any ideas what might be
> > wrong? Maybe there are some issues with the matlab version or image
> > processing toolbox that I'm using?
> >
> > iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 -localGI
> > Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> > Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> > INFO: SUBJECTS_DIR is /Applications/BAP_complete
> > Actual FREESURFER_HOME /Applications/freesurfer
> > -rw-rw-r--  1 ajobsaid  982768932  956144 Jun 30 09:20
> > /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log
> > Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul  5
> > 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
> > /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms
> > /Applications/BAP_complete/nih00024_epoch11_4
> > /Applications/BAP_complete/nih00024_epoch11_4
> > #@# white curv lh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
> >Update not needed
> > #@# white area lh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
> >Update not needed
> > #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
> >Update not needed
> > #@# pial area lh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
> >Update not needed
> > #@# thickness lh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> > ../surf/lh.thickness
> >Update not needed
> > #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> > ../surf/lh.thickness
> >Update not needed
> > #@# white curv rh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
> >Update not needed
> > #@# white area rh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
> >Update not needed
> > #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
> >Update not needed
> > #@# pial area rh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
> >Update not needed
> > #@# thickness rh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> > ../surf/rh.thickness
> >Update not needed
> > #@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020
> > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> > ../surf/rh.thickness
> >Update not needed
> > /Applications/BAP_complete/nih00024_epoch11_4/surf
> > #
> > #@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020
> > \n mris_compute_lgi --i lh.pial \n
> > =
> > rm -Rf
> > /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
> > =
> > =
> > mkdir -p
> > /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
> > =
> > =
> > mris_fill -c -r 1 lh.pial
> > 

Re: [Freesurfer] Help with LGI

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear Freesurfer experts,

Just wanted to follow up my last email - does anyone know what might be
wrong with my code?

Thank you and stay safe,
Alex

On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental
Neuroscience, Lab of Autism and Developmental Neuroscience <
l...@email.gwu.edu> wrote:

> Dear Douglas,
>
> Yes, now matlab is correctly set to my freesurfer path, but the following
> error occurs when I run localGI (please see below). Any ideas what might be
> wrong? Maybe there are some issues with the matlab version or image
> processing toolbox that I'm using?
>
> iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 -localGI
> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> INFO: SUBJECTS_DIR is /Applications/BAP_complete
> Actual FREESURFER_HOME /Applications/freesurfer
> -rw-rw-r--  1 ajobsaid  982768932  956144 Jun 30 09:20
> /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log
> Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul  5
> 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
> /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms
> /Applications/BAP_complete/nih00024_epoch11_4
> /Applications/BAP_complete/nih00024_epoch11_4
> #@# white curv lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
>Update not needed
> #@# white area lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
>Update not needed
> #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
>Update not needed
> #@# pial area lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
>Update not needed
> #@# thickness lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
>Update not needed
> #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
>Update not needed
> #@# white curv rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
>Update not needed
> #@# white area rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
>Update not needed
> #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
>Update not needed
> #@# pial area rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
>Update not needed
> #@# thickness rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
>Update not needed
> #@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
>Update not needed
> /Applications/BAP_complete/nih00024_epoch11_4/surf
> #
> #@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020
> \n mris_compute_lgi --i lh.pial \n
> =
> rm -Rf
> /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mkdir -p
> /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mris_fill -c -r 1 lh.pial
> /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
> =
> reading surface from lh.pial...
> writing filled volume to
> /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
> conforming output volume
> setting resolution for intermediate calculations to 1.
> =
> make_outer_surface('/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
> exit
> =
>
>   

Re: [Freesurfer] Help with LGI

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear Douglas,

Yes, now matlab is correctly set to my freesurfer path, but the following
error occurs when I run localGI (please see below). Any ideas what might be
wrong? Maybe there are some issues with the matlab version or image
processing toolbox that I'm using?

iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 -localGI
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Applications/BAP_complete
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r--  1 ajobsaid  982768932  956144 Jun 30 09:20
/Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log
Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul  5
00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
/Applications/BAP_complete/nih00024_epoch11_4/mri/transforms
/Applications/BAP_complete/nih00024_epoch11_4
/Applications/BAP_complete/nih00024_epoch11_4
#@# white curv lh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
../surf/rh.thickness
   Update not needed
#@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020
cd /Applications/BAP_complete/nih00024_epoch11_4/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
../surf/rh.thickness
   Update not needed
/Applications/BAP_complete/nih00024_epoch11_4/surf
#
#@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020
\n mris_compute_lgi --i lh.pial \n
=
rm -Rf
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
make_outer_surface('/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=

< M A T L A B (R) >
  Copyright 1984-2020 The MathWorks, Inc.
  R2020a Update 3 (9.8.0.1396136) 64-bit (maci64)
May 27, 2020

Warning: Name is nonexistent or not a directory:
/Applications/MATLAB_R2020a/bin
Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a
Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020
Warning: Name is nonexistent or not a directory:

Re: [Freesurfer] Help with LGI

[Douglas N. Greve]

If you type matlab at the command line, does matlab start?

On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


External Email - Use Caution

Dear Freesurfer experts,

I have added Matlab my path and either the same error (please see my 
first email) occurs, or recon-all -s (ID) -localGI command is said to 
'not exist'. Any other ideas on how to properly solve this problem? 
Thank you and hope everyone is safe!


On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental 
Neuroscience, Lab of Autism and Developmental Neuroscience 
mailto:l...@email.gwu.edu>> wrote:


Dear Douglas,

So to accomplish this, should I do the following through matlab?

The following code has to be in matlab’s startup.m file:

1
2
3
4
5
6
7
8
9

%FreeSurfer-%
fshome=getenv('FREESURFER_HOME');
fsmatlab=sprintf('%s/matlab',fshome);
if(exist(fsmatlab)==7)
path(path,fsmatlab);
end
clearfshome fsmatlab;
%-%

Also, if you are getting “ERROR: Matlab is required to run
mris_compute_lgi!”, it means your have to add the Matlab path to
Freesurfer`s $PATH variable for it to run.

To do this automatically when starting FS, just edit the .tcshrc
file (assuming you run FS from TCSH) adding the location of your
Matlab’s bin folder:

1

setenv PATH"/Applications/MATLAB_R2014a.app/bin":"$PATH"


Thanks,
Alex






On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

You need to have matlab in your path so that when you type
"matlab" it starts matlab

On 7/9/2020 4:58 PM, Lab of Autism and Developmental
Neuroscience, Lab of Autism and Developmental Neuroscience wrote:


External Email - Use Caution

Dear Freesurfer experts,

I'm needing some simple help running LGI. After downloading
MATLAB + Image processing toolbox and double checking if the
?h.pial file is located in the SUBJECT_DIR, the recon-all -s
(subject_ID) -localGI command still doesn't work. The output
says that I still didn't install matlab onto my computer, so
maybe it has something to do with setting
$FREESURFER_HOME/matlab in your matlab path setup in your
~/matlab/starup.m script, but I'm unsure how to do this.
Please see the output below:

Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2
-localGI
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Applications/ace_complete
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r--  1 ajobsaid  982768932  959822 Jul  9 10:50
/Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log
Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0:
Tue Aug 20 16:57:14 PDT 2019;
root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
/Applications/ace_complete/HAR30003_srs2_2/mri/transforms
/Applications/ace_complete/HAR30003_srs2_2
/Applications/ace_complete/HAR30003_srs2_2
#@# white curv lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --curv-map ../surf/lh.white 2 10
../surf/lh.curv
   Update not needed
#@# white area lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10
../surf/lh.curv.pial
   Update not needed
#@# pial area lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --area-map ../surf/lh.pial
../surf/lh.area.pial
   Update not needed
#@# thickness lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --thickness ../surf/lh.white
../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --thickness ../surf/lh.white
../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# white curv rh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --curv-map ../surf/rh.white 2 10
../surf/rh.curv
   Update 

Re: [Freesurfer] Help with LGI

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear Freesurfer experts,

I have added Matlab my path and either the same error (please see my first
email) occurs, or recon-all -s (ID) -localGI command is said to 'not
exist'. Any other ideas on how to properly solve this problem? Thank you
and hope everyone is safe!

On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental
Neuroscience, Lab of Autism and Developmental Neuroscience <
l...@email.gwu.edu> wrote:

> Dear Douglas,
>
> So to accomplish this, should I do the following through matlab?
>
> The following code has to be in matlab’s startup.m file:
> 1
> 2
> 3
> 4
> 5
> 6
> 7
> 8
> 9
> % FreeSurfer -%
>
> fshome = getenv('FREESURFER_HOME');
> fsmatlab = sprintf('%s/matlab',fshome);
> if (exist(fsmatlab) == 7)
> path(path,fsmatlab);
> end
> clear fshome fsmatlab;
> %-%
>
> Also, if you are getting “ERROR: Matlab is required to run
> mris_compute_lgi!”, it means your have to add the Matlab path to
> Freesurfer`s $PATH variable for it to run.
>
> To do this automatically when starting FS, just edit the .tcshrc file
> (assuming you run FS from TCSH) adding the location of your Matlab’s bin
> folder:
> 1
> setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
>
>
> Thanks,
> Alex
>
>
>
>
>
>
> On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve 
> wrote:
>
>> You need to have matlab in your path so that when you type "matlab" it
>> starts matlab
>>
>> On 7/9/2020 4:58 PM, Lab of Autism and Developmental Neuroscience, Lab of
>> Autism and Developmental Neuroscience wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer experts,
>>
>> I'm needing some simple help running LGI. After downloading MATLAB +
>> Image processing toolbox and double checking if the ?h.pial file is located
>> in the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still
>> doesn't work. The output says that I still didn't install matlab onto my
>> computer, so maybe it has something to do with setting
>> $FREESURFER_HOME/matlab in your matlab path setup in your ~/matlab/starup.m
>> script, but I'm unsure how to do this. Please see the output below:
>>
>> Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI
>> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
>> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
>> INFO: SUBJECTS_DIR is /Applications/ace_complete
>> Actual FREESURFER_HOME /Applications/freesurfer
>> -rw-rw-r--  1 ajobsaid  982768932  959822 Jul  9 10:50
>> /Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log
>> Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20
>> 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
>> /Applications/ace_complete/HAR30003_srs2_2/mri/transforms
>> /Applications/ace_complete/HAR30003_srs2_2
>> /Applications/ace_complete/HAR30003_srs2_2
>> #@# white curv lh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
>>Update not needed
>> #@# white area lh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
>>Update not needed
>> #@# pial curv lh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
>>Update not needed
>> #@# pial area lh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
>>Update not needed
>> #@# thickness lh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
>> ../surf/lh.thickness
>>Update not needed
>> #@# area and vertex vol lh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
>> ../surf/lh.thickness
>>Update not needed
>> #@# white curv rh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
>>Update not needed
>> #@# white area rh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
>>Update not needed
>> #@# pial curv rh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
>>Update not needed
>> #@# pial area rh Thu Jul  9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
>>Update not needed
>> #@# 

Re: [Freesurfer] Help with LGI

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear Douglas,

So to accomplish this, should I do the following through matlab?

The following code has to be in matlab’s startup.m file:
1
2
3
4
5
6
7
8
9
% FreeSurfer -%

fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
%-%

Also, if you are getting “ERROR: Matlab is required to run
mris_compute_lgi!”, it means your have to add the Matlab path to
Freesurfer`s $PATH variable for it to run.

To do this automatically when starting FS, just edit the .tcshrc file
(assuming you run FS from TCSH) adding the location of your Matlab’s bin
folder:
1
setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"


Thanks,
Alex






On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve 
wrote:

> You need to have matlab in your path so that when you type "matlab" it
> starts matlab
>
> On 7/9/2020 4:58 PM, Lab of Autism and Developmental Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I'm needing some simple help running LGI. After downloading MATLAB + Image
> processing toolbox and double checking if the ?h.pial file is located in
> the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still
> doesn't work. The output says that I still didn't install matlab onto my
> computer, so maybe it has something to do with setting
> $FREESURFER_HOME/matlab in your matlab path setup in your ~/matlab/starup.m
> script, but I'm unsure how to do this. Please see the output below:
>
> Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI
> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> INFO: SUBJECTS_DIR is /Applications/ace_complete
> Actual FREESURFER_HOME /Applications/freesurfer
> -rw-rw-r--  1 ajobsaid  982768932  959822 Jul  9 10:50
> /Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log
> Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20
> 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
> /Applications/ace_complete/HAR30003_srs2_2/mri/transforms
> /Applications/ace_complete/HAR30003_srs2_2
> /Applications/ace_complete/HAR30003_srs2_2
> #@# white curv lh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
>Update not needed
> #@# white area lh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
>Update not needed
> #@# pial curv lh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
>Update not needed
> #@# pial area lh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
>Update not needed
> #@# thickness lh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
>Update not needed
> #@# area and vertex vol lh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
>Update not needed
> #@# white curv rh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
>Update not needed
> #@# white area rh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
>Update not needed
> #@# pial curv rh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
>Update not needed
> #@# pial area rh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
>Update not needed
> #@# thickness rh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
>Update not needed
> #@# area and vertex vol rh Thu Jul  9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
>Update not needed
> /Applications/ace_complete/HAR30003_srs2_2/surf
> #
> #@# Local Gyrification Index lh Thu 

Re: [Freesurfer] Help with LGI

[Douglas N. Greve]

You need to have matlab in your path so that when you type "matlab" it 
starts matlab


On 7/9/2020 4:58 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


External Email - Use Caution

Dear Freesurfer experts,

I'm needing some simple help running LGI. After downloading MATLAB + 
Image processing toolbox and double checking if the ?h.pial file is 
located in the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI 
command still doesn't work. The output says that I still didn't 
install matlab onto my computer, so maybe it has something to do with 
setting $FREESURFER_HOME/matlab in your matlab path setup in your 
~/matlab/starup.m script, but I'm unsure how to do this. Please see 
the output below:


Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Applications/ace_complete
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r--  1 ajobsaid  982768932  959822 Jul  9 10:50 
/Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log
Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 
16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
/Applications/ace_complete/HAR30003_srs2_2/mri/transforms 
/Applications/ace_complete/HAR30003_srs2_2

/Applications/ace_complete/HAR30003_srs2_2
#@# white curv lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness

   Update not needed
#@# area and vertex vol lh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness

   Update not needed
#@# white curv rh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness

   Update not needed
#@# area and vertex vol rh Thu Jul  9 12:58:04 PDT 2020
cd /Applications/ace_complete/HAR30003_srs2_2/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness

   Update not needed
/Applications/ace_complete/HAR30003_srs2_2/surf
#
#@# Local Gyrification Index lh Thu Jul  9 12:58:04 PDT 2020
\n mris_compute_lgi --i lh.pial \n
ERROR: Matlab is required to run mris_compute_lgi!
Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 
16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64


recon-all -s HAR30003_srs2_2 exited with ERRORS at Thu Jul  9 12:58:04 
PDT 2020


Thanks,
Alex


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Re: [Freesurfer] help

[Douglas N. Greve]

It  is not created by the tutorial.
You will need to create a symlink to fsaverage with
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage


On 2/18/2020 8:00 AM, Parks, Sean wrote:


Hello,

I am working through the tutorial fro FSFAST, and am up to the 
Preprocessing step. I followed the instructions as indicated and was 
not receiving errors up until the following command:


preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh 
-mni305 -fwhm 5 -per-run


With this command I receive the error after the code runs for a while:

MRISread(/home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg): 
could not open file

Reading target registration
/home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg
No such file or directory
ERROR: could not read 
/home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg


Checking the fsaverage/surf folder I do not see lh.sphere.reg or 
rh.sphere.reg. In the fsaverage/surf folder of my freesurfer home 
subjects, lh.sphere.reg and rh.sphere.reg are present.


My question is: is rh.sphere.reg and lh.sphere.reg something that is 
created during the tutorial (ie is something wrong with my freesurfer 
installation that it cannot create these files), or are they simply 
missing from the tutorial subjects folder?


I downloaded the tutorial package this week, and am using ubuntu 16.04 
and freesurfer version 6.


Any help would be greatly appreciated. Thank you.​​


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Re: [Freesurfer] help: fs-fast group level analysis per run

[Rami Hamati]

External Email - Use Caution

Thanks Dr. Greve.

We've made our script available on github for anyone who may be interested!

https://github.com/MolecularImagingLab/fMRI_scripts

-- 
Rami Hamati, MSc.
Royal's Institute of Mental Health Research
Molecular Imaging Laboratory (MIL)
1145 Carling Ave, Ottawa, ON K1Z 7K4

rami.ham...@theroyal.ca
rhama...@uottawa.ca
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Re: [Freesurfer] help: fs-fast group level analysis per run

[Greve, Douglas N.,Ph.D.]

you can use mri_concat to concatenate all the ces.nii.gz files for a single 
subject into a single file, then run your glm


On 1/25/20 12:15 PM, Rami Hamati wrote:

External Email - Use Caution

Sorry if my question was unclear. We would like to analyze each run separately 
to observe if there is any habituation between runs of our task. Is there a way 
to concatenate each run separately?

Message: 15
Date: Fri, 24 Jan 2020 15:36:36 +
From: "Greve, Douglas N.,Ph.D." 
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] help: fs-fast group level analysis per run
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
mailto:a30ff7c6-3179-7c73-54f1-636ff15d8...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"

The run-wise functionality was added after selxavg was written as a way to help 
debug. If you want all the runs in your group analysis, why not turn off the 
run-wise flag?

On 1/22/2020 4:40 PM, Rami Hamati wrote:

External Email - Use Caution

Hello freesurfers,

I'm attempting to run second-level analysis on separate runs of a brain scan, 
that were generated by selxavg3-sess -run-wise (pr001, pr002, pr003, pr004) as 
described in selxavg3-sess --help.

But, when attempting to concatenate the data using isxconcat-sess, (as 
described here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel ) 
there is no similar -run-wise function. I've searched the list and no similar 
errors have been reported.. I am wondering if there is a command or workaround 
for this. Thank you very much!

--
Rami Hamati, MSc.
Royal's Institute of Mental Health Research
Molecular Imaging Laboratory (MIL)
1145 Carling Ave, Ottawa, ON K1Z 7K4

rami.ham...@theroyal.ca<mailto:rami.ham...@theroyal.ca><mailto:rami.ham...@theroyal.ca<mailto:rami.ham...@theroyal.ca>>
rhama...@uottawa.ca<mailto:rhama...@uottawa.ca><mailto:rhama...@uottawa.ca<mailto:rhama...@uottawa.ca>>




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Message: 16
Date: Fri, 24 Jan 2020 11:11:55 -0500
From: Graduate Imaging 
mailto:graduate.imag...@gmail.com>>
Subject: Re: [Freesurfer] FreeSurfer analyses in MatLab
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:

mailto:1xbnocapbrzgm...@mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

On Fri, Jan 24, 2020 at 10:32 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:

>
>
> On 1/22/2020 2:13 PM, Graduate Imaging wrote:
>
> External Email - Use Caution
>
>
> On Tue, Jan 21, 2020 at 10:40 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
>
>>
>>
>> On 1/17/2020 10:39 AM, Graduate Imaging wrote:
>>
>> External Email - Use Caution
>>
>>> Hello,
>>>
>>> I recently ran a vertex wise analysis on two different projects the
>>> first had three groups with three co-variates that looked at if group
>>> membership was associated with brain volume. The second project had two
>>> groups with three co-variates looking at psychiatric x BMI interaction
>>> effect on brain volume. I'm interested in running ROI analyses in matlab to
>>> ensure the same matrices were used.
>>>
>>> To run the ROI analyses I'm going to important the design matrix from
>>> the vertex wise analysis and use the fast_glmfit and fast_fratio commands
>>> as shown below:
>>> X = load('Xg.dat');
>>> C = load('C.dat');
>>> y = load('ROI.dat'); text file containing participant ROI values from
>>> the DKT atlas.
>>> [beta rvar] = fast_glmfit(y,X);
>>> [F pvalues] = fast_fratio(beta,X,rvar,C
>>>
>>> My first question is the beta values that are calculated from
>>> fast_glmfit are unstandardized is there anyway way to have it compute
>>> standardized values?
>>>
>>> I think this is how you would compute that
>>> betastddev = sqrt(rvar*diag(inv(X'*X)));
>>> betastandard = beta./betastddev;
>>>
>> When I try running this in Matlab I get

Re: [Freesurfer] help: fs-fast group level analysis per run

[Rami Hamati]

External Email - Use Caution

Sorry if my question was unclear. We would like to analyze each run
separately to observe if there is any habituation between runs of our task.
Is there a way to concatenate each run separately?


> Message: 15
> Date: Fri, 24 Jan 2020 15:36:36 +
> From: "Greve, Douglas N.,Ph.D." 
> Subject: Re: [Freesurfer] help: fs-fast group level analysis per run
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Message-ID: 
> Content-Type: text/plain; charset="utf-8"
>
> The run-wise functionality was added after selxavg was written as a way to
> help debug. If you want all the runs in your group analysis, why not turn
> off the run-wise flag?
>
> On 1/22/2020 4:40 PM, Rami Hamati wrote:
>
> External Email - Use Caution
>
> Hello freesurfers,
>
> I'm attempting to run second-level analysis on separate runs of a brain
> scan, that were generated by selxavg3-sess -run-wise (pr001, pr002, pr003,
> pr004) as described in selxavg3-sess --help.
>
> But, when attempting to concatenate the data using isxconcat-sess, (as
> described here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel
> ) there is no similar -run-wise function. I've searched the list and no
> similar errors have been reported.. I am wondering if there is a command or
> workaround for this. Thank you very much!
>
> --
> Rami Hamati, MSc.
> Royal's Institute of Mental Health Research
> Molecular Imaging Laboratory (MIL)
> 1145 Carling Ave, Ottawa, ON K1Z 7K4
>
> rami.ham...@theroyal.ca<mailto:rami.ham...@theroyal.ca>
> rhama...@uottawa.ca<mailto:rhama...@uottawa.ca>
>
>
>
>
> ___
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> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200124/aaa698dd/attachment-0001.html
>
> --
>
> Message: 16
> Date: Fri, 24 Jan 2020 11:11:55 -0500
> From: Graduate Imaging 
> Subject: Re: [Freesurfer] FreeSurfer analyses in MatLab
> To: Freesurfer support list 
> Message-ID:
>  1xbnocapbrzgm...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> On Fri, Jan 24, 2020 at 10:32 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
> >
> >
> > On 1/22/2020 2:13 PM, Graduate Imaging wrote:
> >
> > External Email - Use Caution
> >
> >
> > On Tue, Jan 21, 2020 at 10:40 AM Greve, Douglas N.,Ph.D. <
> > dgr...@mgh.harvard.edu> wrote:
> >
> >>
> >>
> >> On 1/17/2020 10:39 AM, Graduate Imaging wrote:
> >>
> >> External Email - Use Caution
> >>
> >>> Hello,
> >>>
> >>> I recently ran a vertex wise analysis on two different projects the
> >>> first had three groups with three co-variates that looked at if group
> >>> membership was associated with brain volume. The second project had two
> >>> groups with three co-variates looking at psychiatric x BMI interaction
> >>> effect on brain volume. I'm interested in running ROI analyses in
> matlab to
> >>> ensure the same matrices were used.
> >>>
> >>> To run the ROI analyses I'm going to important the design matrix from
> >>> the vertex wise analysis and use the fast_glmfit and fast_fratio
> commands
> >>> as shown below:
> >>> X = load('Xg.dat');
> >>> C = load('C.dat');
> >>> y = load('ROI.dat'); text file containing participant ROI values from
> >>> the DKT atlas.
> >>> [beta rvar] = fast_glmfit(y,X);
> >>> [F pvalues] = fast_fratio(beta,X,rvar,C
> >>>
> >>> My first question is the beta values that are calculated from
> >>> fast_glmfit are unstandardized is there anyway way to have it compute
> >>> standardized values?
> >>>
> >>> I think this is how you would compute that
> >>> betastddev = sqrt(rvar*diag(inv(X'*X)));
> >>> betastandard = beta./betastddev;
> >>>
> >> When I try running this in Matlab I get the Error using  ***  incorrect
> >> dimensions for matrix multiplication message.
> >>
> >> That means that the number of items in y (ie, number of subjects in
> >> ROI.dat) is different th

Re: [Freesurfer] help: fs-fast group level analysis per run

[Greve, Douglas N.,Ph.D.]

The run-wise functionality was added after selxavg was written as a way to help 
debug. If you want all the runs in your group analysis, why not turn off the 
run-wise flag?

On 1/22/2020 4:40 PM, Rami Hamati wrote:

External Email - Use Caution

Hello freesurfers,

I'm attempting to run second-level analysis on separate runs of a brain scan, 
that were generated by selxavg3-sess -run-wise (pr001, pr002, pr003, pr004) as 
described in selxavg3-sess --help.

But, when attempting to concatenate the data using isxconcat-sess, (as 
described here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel ) 
there is no similar -run-wise function. I've searched the list and no similar 
errors have been reported.. I am wondering if there is a command or workaround 
for this. Thank you very much!

--
Rami Hamati, MSc.
Royal's Institute of Mental Health Research
Molecular Imaging Laboratory (MIL)
1145 Carling Ave, Ottawa, ON K1Z 7K4

rami.ham...@theroyal.ca
rhama...@uottawa.ca




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Re: [Freesurfer] Help with "orig.mgz"

[Fernando Castellano]

External Email - Use Caution

Thanks you  Bruce

El jue., 7 de nov. de 2019 12:18, Bruce Fischl 
escribió:

> Hi Fernando
>
> it is a volume after resampling to 1mm isotropic, 8 bits/voxel and 256^3
>
> cheers
> Bruce
> On
> Thu, 7 Nov 2019, Fernando Castellano wrote:
>
> >
> > External Email - Use Caution
> >
> > good afternoon,
> > I am using freesurfer for my thesis in image technician.
> > I would like to know specifically what the orig.mgz file is?
> > I have read that it is step 1 of re-conall. But I don't fully understand
> >
> > thank you, best regards
> >
> >___
> Freesurfer mailing list
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Re: [Freesurfer] Help with "orig.mgz"

[Bruce Fischl]

Hi Fernando

it is a volume after resampling to 1mm isotropic, 8 bits/voxel and 256^3

cheers
Bruce
On 
Thu, 7 Nov 2019, Fernando Castellano wrote:




External Email - Use Caution

good afternoon,
I am using freesurfer for my thesis in image technician.
I would like to know specifically what the orig.mgz file is?
I have read that it is step 1 of re-conall. But I don't fully understand

thank you, best regards

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Re: [Freesurfer] help

[Bruce Fischl]

Hi Asim

can you give us a bit more information? Where does the brainmask come 
from? I believe we should detect the fact that the brainmask.mgz is 
different than the automatically created one (brainmask.auto.mgz) and use 
it instead. Note that the recon editing mode in freeview sets erased voxels 
to "1" instead of "0" so we can keep track of edits. You might want to do 
something similar in whatever stream you are using.


cheers
Bruce



On Fri, 18 Oct 2019, Asim Hassan wrote:



External Email - Use Caution

​Good afternoon,


Is there any other way to incorporate a manually edited brain mask into the
recon all process other than through the recon-mode in freeview?

Thanks!
Asim Hassan
Research Technician II
Waugh Lab
Division of Pediatric Neurology
University of Texas Southwestern Medical Center
Phone: 214-645-9259



UT Southwestern

Medical Center

The future of medicine, today.


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Re: [Freesurfer] help

[Bruce Fischl]

Hi Asim

if you edited the brainmask in recon-mode in freeview the edits will be 
detected and retained.


cheers
Bruce
On Mon, 14 Oct 2019, Asim Hassan wrote:



External Email - Use Caution

Good afternoon,


I would like to know is there a way to run recon-all on subjects in which
manual edits have been done on the brainmask.mgz files?

Or at least incorporate manually edited brainmask files into the recon-all
process?


Thanks!




Asim Hassan
Research Technician II
Division of Pediatric Neurology
University of Texas Southwestern Medical Center



UT Southwestern

Medical Center

The future of medicine, today.


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Re: [Freesurfer] help! Hippocampal subfield segmentation with FS development version

[Liwen Zhang]

External Email - Use Caution

 Dear Eugenio,
Many thanks for your prompt reply and explanation. May I ask few follow-up 
questions, please?
1) You mentioned "we rebuilt the atlas ... change the code...", would you 
please explain a little bit more about what you mean with "rebuilt"? In the FS 
dev, does the "rebuilt" mean that you use different segmentation algorithm on 
the same FS v.6.0 ex-vivo atlas template, or even the ex-vivo atlas template 
per se is already different in FS dev from that in FS v.6.0?
2) Related to 1), given the volume discrepancy between the two FS versions, 
from your perspective, would you say the current hippocampal subfield 
segmentation in FS dev is more accurate compared with FS v.6.0 algorithm? Does 
this further HBT segmentation within subfields help us understand distinct 
subfield functions along the anterior-posterior axis?
3) In our analyses in patients with atrophy, we noticed that the results 
between FS dev. and FS v.6.0 were relatively more consistent for patients with 
less severe atrophy, but inconsistent for patients with more severe atrophy. In 
your opinion, would you suggest that we use the FS dev to segment the 
hippocampus in patients with atrophy, or stay with the stable FS v.6.0 version 
at this moment, since those subfields are already small?
4) For the latest FS dev version, may I know whether you have any plans to 
further consolidate/optimize the algorithm, or it can be considered as the 
stable version?
Apologize for so many questions, but I am really interested in this method and 
find it very helpful.Greatly appreciate your help and reply in advance!
Best,Liwen

On Monday, 23 September 2019, 8:04:13 pm GMT+8, Iglesias Gonzalez, Juan E. 
 wrote:  
 
 
Dear Liwen,
 
We rebuilt the atlas and there were also minor changes in the code, so the 
volume won’t be exactly the same.
 
Having said that, if you plot 6 vs dev volumes, they should be highly 
correlated.
 
Cheers,
 
/E
 
  
 
Juan Eugenio Iglesias
 
Senior research fellow
 
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
 
http://www.jeiglesias.com 
 
 
 
  
 
From:  on behalf of Liwen Zhang 

Reply-To: Freesurfer support list 
Date: Sunday, 22 September 2019 at 10:40
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] help! Hippocampal subfield segmentation with FS 
development version
 
  
 
External Email - Use Caution
 
Hello freesurfer experts,
 
  
 
I previously applied hippocampal subfield segmentation using FS v.6.0. I am now 
trying to devide subfields into head/body where applicable using FS development 
version (latest version). However, I encountered the following 
problems/quesetions:
 
  
 
1) X represents certain subfield (volume)
 
X_head + X_body (from FS dev) ~= X (from FS v.6.0)
 
  
 
What possibly causes this volume discrepancy between FS dev and FS v.6.0? Is 
the head/body segmentation template in FS dev based on the same ex-vivo 
template as used in FS v.6.0?
 
  
 
2) Related to 1), subfield volume as obtained from FS v.6.0 generally larger 
than that from FS dev (not for all subfields though)
 
  
 
I processed T1 images with FS v.6.0 and then applied hippocampal segmentation 
with both FS v.6.0 and FS dev. 
 
  
 
Any suggestions/comments would be greatly appreicated! 
 
  
 
Thank you for your time and help in advance!
 
  
 
Best, 
 
Liwen
 
  
 
  
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Re: [Freesurfer] help! Hippocampal subfield segmentation with FS development version

[Iglesias Gonzalez, Juan E.]

Dear Liwen,
We rebuilt the atlas and there were also minor changes in the code, so the 
volume won’t be exactly the same.
Having said that, if you plot 6 vs dev volumes, they should be highly 
correlated.
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Liwen Zhang 

Reply-To: Freesurfer support list 
Date: Sunday, 22 September 2019 at 10:40
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] help! Hippocampal subfield segmentation with FS 
development version


External Email - Use Caution
Hello freesurfer experts,

I previously applied hippocampal subfield segmentation using FS v.6.0. I am now 
trying to devide subfields into head/body where applicable using FS development 
version (latest version). However, I encountered the following 
problems/quesetions:

1) X represents certain subfield (volume)
X_head + X_body (from FS dev) ~= X (from FS v.6.0)

What possibly causes this volume discrepancy between FS dev and FS v.6.0? Is 
the head/body segmentation template in FS dev based on the same ex-vivo 
template as used in FS v.6.0?

2) Related to 1), subfield volume as obtained from FS v.6.0 generally larger 
than that from FS dev (not for all subfields though)

I processed T1 images with FS v.6.0 and then applied hippocampal segmentation 
with both FS v.6.0 and FS dev.

Any suggestions/comments would be greatly appreicated!

Thank you for your time and help in advance!

Best,
Liwen


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Re: [Freesurfer] Help with using family as random effect in sibling study

[Hopkinson, Casey E]

Hi Doug, thanks for getting back to me! So since we have just one pair of 
siblings per family, this way will not work?


--


Casey Hopkinson

Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA, 02129
(p) 617.643.3215


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

Sent: Friday, August 23, 2019 10:17 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Help with using family as random effect in sibling 
study


You could create a class for each family and assign each pair to a class. But 
this will not work unless you have multiple pairs per family for each family.


On 8/23/2019 9:01 AM, Hopkinson, Casey E wrote:
Hi everyone,

Just wanted to follow up with this in case anyone may have an idea of if this 
can be done. Thanks!


--


Casey Hopkinson

Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA, 02129
(p) 617.643.3215


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Hopkinson, Casey E 
<mailto:chopkin...@mgh.harvard.edu>
Sent: Tuesday, August 20, 2019 9:47 AM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with using family as random effect in sibling 
study

Sure! We have been conducting analyses in a large sample of pairs of siblings 
to see the effect of prenatal exposures on cortical thickness. For the current 
analysis, we're looking at the effect of the exposure load (total # of 
exposures) on cortical thickness using a paired-difference model, so the 
covariant being used is the difference in exposure load between each pair. 
We're trying to figure out if it is possible to also covary for the family the 
siblings belong to (using the assigned Family ID), to see the effect of family 
on cortical thickness as well as exposure load. This was able to be done 
statistically, however we weren't sure if it could be done in Freesurfer, too.

My apologies if this is still unclear - please let me know if you have any 
further questions. Thank you!

Best,
Casey


--


Casey Hopkinson

Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA, 02129
(p) 617.643.3215


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, August 19, 2019 6:29 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with using family as random effect in sibling 
study

I'm not sure I understand. Can you elaborate?

On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
> Hello!
>
> I am trying to generate significance maps for a paired-difference
> analysis of cortical thickness using multiple pairs of siblings, and
> was wondering if there is a way to incorporate the family ID as a
> random effect/covariate in Freesurfer. Is it possible for the family
> ID for each sibling pair to be used as a categorical/discrete variable
> to then see the effect of family on cortical thickness in addition to
> the main effects we are looking at? Any guidance would be greatly
> appreciated!
>
> Best,
> Casey
>
> *--*
>
> *
> *
>
> *Casey Hopkinson*
>
> Clinical Research Coordinator
> Brain Genomics Laboratory
> Division of Psychiatric Neuroimaging
> Massachusetts General Hospital
> 149 13th Street, Charlestown, MA, 02129
> (p) 617.643.3215
>
>
> ___
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Re: [Freesurfer] Help with using family as random effect in sibling study

[Greve, Douglas N.,Ph.D.]

You could create a class for each family and assign each pair to a class. But 
this will not work unless you have multiple pairs per family for each family.


On 8/23/2019 9:01 AM, Hopkinson, Casey E wrote:
Hi everyone,

Just wanted to follow up with this in case anyone may have an idea of if this 
can be done. Thanks!


--


Casey Hopkinson

Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA, 02129
(p) 617.643.3215


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Hopkinson, Casey E 
<mailto:chopkin...@mgh.harvard.edu>
Sent: Tuesday, August 20, 2019 9:47 AM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with using family as random effect in sibling 
study

Sure! We have been conducting analyses in a large sample of pairs of siblings 
to see the effect of prenatal exposures on cortical thickness. For the current 
analysis, we're looking at the effect of the exposure load (total # of 
exposures) on cortical thickness using a paired-difference model, so the 
covariant being used is the difference in exposure load between each pair. 
We're trying to figure out if it is possible to also covary for the family the 
siblings belong to (using the assigned Family ID), to see the effect of family 
on cortical thickness as well as exposure load. This was able to be done 
statistically, however we weren't sure if it could be done in Freesurfer, too.

My apologies if this is still unclear - please let me know if you have any 
further questions. Thank you!

Best,
Casey


--


Casey Hopkinson

Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA, 02129
(p) 617.643.3215


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, August 19, 2019 6:29 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with using family as random effect in sibling 
study

I'm not sure I understand. Can you elaborate?

On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
> Hello!
>
> I am trying to generate significance maps for a paired-difference
> analysis of cortical thickness using multiple pairs of siblings, and
> was wondering if there is a way to incorporate the family ID as a
> random effect/covariate in Freesurfer. Is it possible for the family
> ID for each sibling pair to be used as a categorical/discrete variable
> to then see the effect of family on cortical thickness in addition to
> the main effects we are looking at? Any guidance would be greatly
> appreciated!
>
> Best,
> Casey
>
> *--*
>
> *
> *
>
> *Casey Hopkinson*
>
> Clinical Research Coordinator
> Brain Genomics Laboratory
> Division of Psychiatric Neuroimaging
> Massachusetts General Hospital
> 149 13th Street, Charlestown, MA, 02129
> (p) 617.643.3215
>
>
> ___
> Freesurfer mailing list
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Re: [Freesurfer] Help with using family as random effect in sibling study

[Hopkinson, Casey E]

Hi everyone,

Just wanted to follow up with this in case anyone may have an idea of if this 
can be done. Thanks!


--


Casey Hopkinson

Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA, 02129
(p) 617.643.3215


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hopkinson, Casey E 

Sent: Tuesday, August 20, 2019 9:47 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Help with using family as random effect in sibling 
study

Sure! We have been conducting analyses in a large sample of pairs of siblings 
to see the effect of prenatal exposures on cortical thickness. For the current 
analysis, we're looking at the effect of the exposure load (total # of 
exposures) on cortical thickness using a paired-difference model, so the 
covariant being used is the difference in exposure load between each pair. 
We're trying to figure out if it is possible to also covary for the family the 
siblings belong to (using the assigned Family ID), to see the effect of family 
on cortical thickness as well as exposure load. This was able to be done 
statistically, however we weren't sure if it could be done in Freesurfer, too.

My apologies if this is still unclear - please let me know if you have any 
further questions. Thank you!

Best,
Casey


--


Casey Hopkinson

Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA, 02129
(p) 617.643.3215


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

Sent: Monday, August 19, 2019 6:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Help with using family as random effect in sibling 
study

I'm not sure I understand. Can you elaborate?

On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
> Hello!
>
> I am trying to generate significance maps for a paired-difference
> analysis of cortical thickness using multiple pairs of siblings, and
> was wondering if there is a way to incorporate the family ID as a
> random effect/covariate in Freesurfer. Is it possible for the family
> ID for each sibling pair to be used as a categorical/discrete variable
> to then see the effect of family on cortical thickness in addition to
> the main effects we are looking at? Any guidance would be greatly
> appreciated!
>
> Best,
> Casey
>
> *--*
>
> *
> *
>
> *Casey Hopkinson*
>
> Clinical Research Coordinator
> Brain Genomics Laboratory
> Division of Psychiatric Neuroimaging
> Massachusetts General Hospital
> 149 13th Street, Charlestown, MA, 02129
> (p) 617.643.3215
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Help with using family as random effect in sibling study

[Hopkinson, Casey E]

Sure! We have been conducting analyses in a large sample of pairs of siblings 
to see the effect of prenatal exposures on cortical thickness. For the current 
analysis, we're looking at the effect of the exposure load (total # of 
exposures) on cortical thickness using a paired-difference model, so the 
covariant being used is the difference in exposure load between each pair. 
We're trying to figure out if it is possible to also covary for the family the 
siblings belong to (using the assigned Family ID), to see the effect of family 
on cortical thickness as well as exposure load. This was able to be done 
statistically, however we weren't sure if it could be done in Freesurfer, too.

My apologies if this is still unclear - please let me know if you have any 
further questions. Thank you!

Best,
Casey


--


Casey Hopkinson

Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Massachusetts General Hospital
149 13th Street, Charlestown, MA, 02129
(p) 617.643.3215


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

Sent: Monday, August 19, 2019 6:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Help with using family as random effect in sibling 
study

I'm not sure I understand. Can you elaborate?

On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
> Hello!
>
> I am trying to generate significance maps for a paired-difference
> analysis of cortical thickness using multiple pairs of siblings, and
> was wondering if there is a way to incorporate the family ID as a
> random effect/covariate in Freesurfer. Is it possible for the family
> ID for each sibling pair to be used as a categorical/discrete variable
> to then see the effect of family on cortical thickness in addition to
> the main effects we are looking at? Any guidance would be greatly
> appreciated!
>
> Best,
> Casey
>
> *--*
>
> *
> *
>
> *Casey Hopkinson*
>
> Clinical Research Coordinator
> Brain Genomics Laboratory
> Division of Psychiatric Neuroimaging
> Massachusetts General Hospital
> 149 13th Street, Charlestown, MA, 02129
> (p) 617.643.3215
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Help with using family as random effect in sibling study

[Greve, Douglas N.,Ph.D.]

I'm not sure I understand. Can you elaborate?

On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
> Hello!
>
> I am trying to generate significance maps for a paired-difference 
> analysis of cortical thickness using multiple pairs of siblings, and 
> was wondering if there is a way to incorporate the family ID as a 
> random effect/covariate in Freesurfer. Is it possible for the family 
> ID for each sibling pair to be used as a categorical/discrete variable 
> to then see the effect of family on cortical thickness in addition to 
> the main effects we are looking at? Any guidance would be greatly 
> appreciated!
>
> Best,
> Casey
>
> *--*
>
> *
> *
>
> *Casey Hopkinson*
>
> Clinical Research Coordinator
> Brain Genomics Laboratory
> Division of Psychiatric Neuroimaging
> Massachusetts General Hospital
> 149 13th Street, Charlestown, MA, 02129
> (p) 617.643.3215
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] help for calculating the correlation

[Greve, Douglas N.,Ph.D.]

If there is no interaction between F/R and Active, then there should not be any 
theoretical difference between the two analyses, except that FR combined will 
be slightly more powerful since it has one more degree of freedom. You should 
first use the uncombined model to look for an interaction, and then proceed 
with the combined if there is no significant interaction.

There are several other things that could also come into play. First, it looks 
like the Rs have a much higher active score than Fs. This will create some 
correlation in the uncombined model and weaken the power. Second, it looks like 
there might be more Sex=1 in the R group; this will also weaken the uncombined 
model.

One more thing: you are not modeling sex properly. You should create four 
Classes (F-Male, F-Female, R-Male, and R-Female)


On 8/19/2019 8:32 AM, tange_neuro wrote:

External Email - Use Caution
Hi all,
I am deeply confused and terribly needed some help, and I failed to find the 
answer in the Freesurfer website.
I had two patient groups F and R. To analysis the correlation between active 
time and cortical thickness, I tried two different methods A and B (A, treating 
patients in different group F and R as shown in attached figure A; B, treating 
all patients as one group FR as shown in attached figure B), and got distinctly 
different results.
So, my questions:
1、Which one is actually correct for calculating the correlation between active 
time and thickness, and what does the other one mean?
2、Does "--cache 3 abs --cwp 0.999" means that the result is only corrected with 
vertex level P < 0.001, and no cluster level correction is conducted?
I am looking forward to getting your help.
Sincerely yours,
Ge Tan







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Re: [Freesurfer] Help with MRI segstats

[Greve, Douglas N.,Ph.D.]

erkauf Graduate School of Psychology
> > Yeshiva University
> > Albert Einstein College of Medicine
> >
> >     From: freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >     <mailto:freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>     >      <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >     <mailto:freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>> On Behalf Of
> >     Greve, Douglas N.,Ph.D.
> >     Sent: Tuesday, August 6, 2019 12:56 PM
> >     To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >     <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> >     Subject: Re: [Freesurfer] Help with MRI segstats
> >
> >     Can you send command lines? Also, are you using the built-in
> >     permutation tool or trying to do something outside of FS?
> >
> >     On 8/6/19 8:40 AM, Daliah Ross wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Hi FreeSurfer experts,
> >     >
> >     > I have a couple of questions regarding mri_segstats
> tool for an
> >     > analysis on vertex-wise cortical thickness data. We are
> >     attempting to
> >     > compare maximum cluster sizes among permutations. We
> are having
> >     > trouble figuring out how to get the anatomical label
> for each
> >     cluster
> >     > using the --slabel argument. We are also wondering if the
> >     difference
> >     > between cluster sizes between mri_surfcluster and
> mri_segstats
> >     is due
> >     > to partial volumes, and if so, how to correctly use
> the --pv
> >     argument.
> >     > It suggests in the wiki page that mri/norm.mgz volume
> is usually
> >     used
> >     > but I believe we need something surface-based since we
> are using
> >     > thickness data.
> >     >
> >     > Thank you in advance for any help you can provide.
> >     >
> >     > Best,
> >     > Daliah
> >     >
> >     > *Daliah Ross* | dro...@mail.yu.edu
> <mailto:dro...@mail.yu.edu> <mailto:dro...@mail.yu.edu
> <mailto:dro...@mail.yu.edu>>
> >     <mailto:dro...@mail.yu.edu <mailto:dro...@mail.yu.edu>
> <mailto:dro...@mail.yu.edu <mailto:dro...@mail.yu.edu>>>
> >     >
> >     > Ph.D. Student, Clinical Psychology with Health
> Emphasis Ferkauf
> >     > Graduate School of Psychology Yeshiva University
> Albert Einstein
> >     > College of Medicine
> >     >
> >     > ___
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >     > https://mail
> >     > .nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu>
> >   
>  
> <http://nmr.mgh.harvard.edu>%2Fmailman%2Flistinfo%2Ffreesurferdata=02%7C0
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>  <http://40einstein.yu.edu>%7Cfde693609070412c457808d71a8f16f2%
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> >
>  
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Re: [Freesurfer] Help with MRI segstats

[Greve, Douglas N.,Ph.D.]

You should only pass one of --seg, --annot, or --slabel  to 
mri_segstats. I don't understand how you are trying to use this in the 
context of your permutation. Is this something that you are running on 
each iteration? If so, it is probably not what you want to do. Probably 
you want to run mri_surfcluster to get the cluster sizes out.

On 8/7/19 1:31 PM, Daliah Ross wrote:
>
> External Email - Use Caution
>
> This is the command line:
> mri_segstats --seg F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.mgh 
> --annot lh.aparc.annot lh parc --slabel fsaverage lh cortex --sum 
> F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.txt
>
> We are running the permutations within FS, but because our model is a 
> linear mixed model, and we didn't think that this would be compatible 
> with fspalm. So, we are running the permutations "manually" (i.e. we 
> are generating the random permutations, which in our case is just 
> switching the subject labels for the thickness data. We are then using 
> mri_surfcluster to extract the maximum cluster size per permutation 
> and will use the permutation distribution to determine our the 
> statistical significance of our results). In addition, our analyses 
> are a bit out of the ordinary in that the thickness data are an 
> independent variable in our model, for which we have a repeated 
> non-imaging measure as the outcome. Effectively, we are using the 
> thickness maps to generate vertex-wise regressors, with a fixed 
> outcome measure (fixed in the sense that it doesn't vary across the 
> brain).
>
> If you have any thoughts about how we could use fspalm in our case, 
> your advice would be most appreciated.
>
> Thanks again,
> Daliah
>
> *Daliah Ross* | dro...@mail.yu.edu <mailto:dro...@mail.yu.edu>
>
> Ph.D. Student, Clinical Psychology with Health Emphasis
> Ferkauf Graduate School of Psychology
> Yeshiva University
> Albert Einstein College of Medicine
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of
> Greve, Douglas N.,Ph.D.
> Sent: Tuesday, August 6, 2019 12:56 PM
> To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Help with MRI segstats
>
> Can you send command lines? Also, are you using the built-in
> permutation tool or trying to do something outside of FS?
>
> On 8/6/19 8:40 AM, Daliah Ross wrote:
> >
> > External Email - Use Caution
> >
> > Hi FreeSurfer experts,
> >
> > I have a couple of questions regarding mri_segstats tool for an
> > analysis on vertex-wise cortical thickness data. We are
> attempting to
> > compare maximum cluster sizes among permutations. We are having
> > trouble figuring out how to get the anatomical label for each
> cluster
> > using the --slabel argument. We are also wondering if the
> difference
> > between cluster sizes between mri_surfcluster and mri_segstats
> is due
> > to partial volumes, and if so, how to correctly use the --pv
> argument.
> > It suggests in the wiki page that mri/norm.mgz volume is usually
> used
> > but I believe we need something surface-based since we are using
> > thickness data.
> >
> > Thank you in advance for any help you can provide.
> >
> > Best,
> > Daliah
> >
> > *Daliah Ross* | dro...@mail.yu.edu <mailto:dro...@mail.yu.edu>
> <mailto:dro...@mail.yu.edu <mailto:dro...@mail.yu.edu>>
> >
> > Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf
> > Graduate School of Psychology Yeshiva University Albert Einstein
> > College of Medicine
> >
> > ___
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> > .nmr.mgh.harvard.edu
> 
> <http://nmr.mgh.harvard.edu>%2Fmailman%2Flistinfo%2Ffreesurferdata=02%7C0
> > 1%7Cmark.wagshul%40einstein.yu.edu
> <http://40einstein.yu.edu>%7Cfde693609070412c457808d71a8f16f2%
> >
> 7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637007074183066654sd
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Re: [Freesurfer] Help with MRI segstats

[Greve, Douglas N.,Ph.D.]

Can you send command lines? Also, are you using the built-in permutation 
tool or trying to do something outside of FS?

On 8/6/19 8:40 AM, Daliah Ross wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer experts,
>
> I have a couple of questions regarding mri_segstats tool for an 
> analysis on vertex-wise cortical thickness data. We are attempting to 
> compare maximum cluster sizes among permutations. We are having 
> trouble figuring out how to get the anatomical label for each cluster 
> using the --slabel argument. We are also wondering if the difference 
> between cluster sizes between mri_surfcluster and mri_segstats is due 
> to partial volumes, and if so, how to correctly use the --pv argument. 
> It suggests in the wiki page that mri/norm.mgz volume is usually used 
> but I believe we need something surface-based since we are using 
> thickness data.
>
> Thank you in advance for any help you can provide.
>
> Best,
> Daliah
>
> *Daliah Ross* | dro...@mail.yu.edu 
>
> Ph.D. Student, Clinical Psychology with Health Emphasis
> Ferkauf Graduate School of Psychology
> Yeshiva University
> Albert Einstein College of Medicine
>
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Re: [Freesurfer] Help for Hippocampal Calculation

[Greve, Douglas N.,Ph.D.]

I don't think it will take 20h, probably more like 10-12h, so that's 
only 1.5 years:). Most people who are running it that many data sets 
have access to a computational cluster (on ours it would only take a few 
weeks). Alternatively, you can try buying cloud-based computational 
power (eg, amazon web services).

On 7/30/19 4:56 PM, Jiajun Luo wrote:
>
> External Email - Use Caution
>
> Hi,
>
> Now I have T1 and T2 images (dcm files) and want to calculate the 
> hippocampal volume. I find it takes ~20h to run recon-all -all and 
> then ~40min to run -hippocampal-subfields-T1. However, I need to 
> calculate the hippocampal volume for more than 1,000 individuals 
> (which means it may take ~3 years to complete). Do you know how I can 
> improve my efficiency?
>
> Thank you!
>
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Re: [Freesurfer] Help for smoothing the pial surface

[Tim Schäfer]

External Email - Use Caution

Hello Ryan,

> On June 26, 2019 at 9:26 PM "Nillo, Ryan Michael R" 
>  wrote:
> [...]
> I want to generate a smooth pial surface similar to the one displayed on the 
> LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI 
> ) without having to run the 
> entire recon-all process.

I'm not 100% sure what you want as the output, but if it is a surface file 
(like ?h.white or pial) I think the easiest way is to follow the commands 
listed on the LGI wiki page you linked, under the section "Processing Stream" 
up to the point that you need. Most likely you can stop after step 4, when 
?h.pial-outer-smoothed has been produced. 

> Additionally, I want to map this surface to the white surface. Is there an 
> easy way to do this?

I am not sure what you mean by this. Could you explain what would be the inputs 
and the expected output files of this process? 

If you mean that the vertex indices in the meshes of the white and your 
pial-outer-smoothed surface files should match: this should be the case by 
default I guess.

Best,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Help

[Alvarado,Luis R]

External Email - Use Caution

Please disregard this last email. I was trying to make adjustments to my mail 
list settings by following these instructions from the welcome email:

You can also make such adjustments via email by sending a message to:

  
freesurfer-requ...@nmr.mgh.harvard.edu

with the word `help' in the subject or body (don't include the
quotes), and you will get back a message with instructions.



Luis R. Alvarado
Ph.D. Candidate
Department of Anatomical Sciences and Neurobiology
University of Louisville School of Medicine
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202


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Re: [Freesurfer] Help

[Greve, Douglas N.,Ph.D.]

can you be more specific?

On 4/17/19 12:20 PM, Alvarado,Luis R wrote:
>
> External Email - Use Caution
>
>
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Re: [Freesurfer] help

[Bruce Fischl]

1, 2019 at 8:44 PM
>> To: Freesurfer support list 
>> mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: [Freesurfer] Gray matter normalized intensity
>>
>>
>>External Email - Use Caution
>>
>> Dear Freesurfers
>>
>> Usually, the mean normalized intensity in aseg.stats is not considered 
>> important. However, by mistake, I put it in my analysis and found out that 
>> the mean intensity of the thalamus explains a lot the variance of my data.
>>
>> What could be the physiological meaning of higher intensity in the thalamus? 
>> Could it be associated with either increased myelinization ( more axons or 
>> synapses) or with decreased neural soma? Has anybody reported mean 
>> normalized intensity effects in subcortical structures?
>>
>>
>> Thanks
>> Dorothy
>>
>>
>> 
>> 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 --
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>>
>> --
>>
>> Message: 6
>> Date: Thu, 21 Mar 2019 21:52:59 -0400 (EDT)
>> From: Bruce Fischl 
>> Subject: Re: [Freesurfer] Gray matter normalized intensity
>> To: Freesurfer support list 
>> Message-ID:
>>  
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Dorothy
>>
>> yes, we have looked at intensity effects in the gray matter before (David
>> Salat for example has done this). It certainly reflects degree of
>> myelination as well as other things. Which volume are you looking at? The
>> norm should be ok for this
>>
>> cheers
>> Bruce
>> On Thu, 21 Mar 2019, Dorothy Sincasto
>> wrote:
>>
>>>
>>> External Email - Use Caution
>>>
>>> Dear Freesurfers
>>> Usually, the mean normalized intensity in aseg.stats is not considered 
>>> important. However, by
>>> mistake, I put it in my analysis and found out that the mean intensity of 
>>> the thalamus explains a
>>> lot the variance of my data.?
>>>
>>> What could be the physiological meaning of higher intensity in the 
>>> thalamus? Could it be associated
>>> with either increased myelinization ( more axons or synapses) or with 
>>> decreased neural soma? Has
>>> anybody reported mean normalized intensity effects in subcortical 
>>> structures?
>>>
>>>
>>> Thanks
>>> Dorothy
>>>
>>>
>>>
>>
>> --
>>
>> Message: 7
>> Date: Fri, 22 Mar 2019 11:39:42 +0800
>> From: " Lance " <363046...@qq.com>
>> Subject: [Freesurfer] help
>> To: " freesurfer " 
>> Message-ID: 
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>External Email - Use Caution
>>
>> Hi there,
>>I want to calculate the significance of grayvol between two groups, but 
>> the data i noticed in the 'lh.aparc.stats' file shew some problem.The pic 
>> below shows the grayvol of entorhinal of some subjects,but one of them 
>> appears to be 136,far more lower than the others, what's the problem? is it 
>> a normal systematic error or is there something wrong with my operation 
>> while calculating? The same situation is also found in CurvInd and FoldInd.
>>
>>
>>
>> Thank you for your help!
>> -- next part --
>> An HTML attachment was scrubbed...
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>>
>> --
>>
>> Message: 8
>> D

Re: [Freesurfer] help

[Bruce Fischl]

did you look at the entorhinal label in the aparc to see if it is 
reasonable? Then check the white and pial surfaces in that region. Sounds 
like something went wrong there


cheers
Bruce


On Fri, 22 Mar 2019, Lance wrote:



External Email - Use Caution

Hi there,
    I want to calculate the significance of grayvol between two groups, but the 
data i noticed in
the 'lh.aparc.stats' file shew some problem.The pic below shows the grayvol of 
entorhinal of some
subjects,but one of them appears to be 136,far more lower than the others, 
what's the problem? is it
a normal systematic error or is there something wrong with my operation while 
calculating? The same
situation is also found in CurvInd and FoldInd.
[IMAGE]

Thank you for your help!

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Re: [Freesurfer] Help with Reviewer Comment

[Bruce Fischl]

Hi Shane

that's a pretty tough one to answer. Certainly some developmental 
conditions (e.g. dramatic FCDs) can mess up the thickness. It really 
depends on the details.


sorry I don't have a better answer
Bruce

On Thu, 10 Jan 2019, Shane Schofield wrote:



External Email - Use Caution

Hi Freesurfer

A reviewer asked whether there are concerns about whether Freesurfer may obtain 
accurate cortical
thickness data in people with developmental conditions - the main focus in my 
study. I did a search
and could not find any validation studies in these cohorts.  Any idea? Thanks a 
lot.

Regards,
Shane

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Re: [Freesurfer] Help with Data

[Greve, Douglas N.,Ph.D.]

On 12/04/2018 02:17 PM, T and LS wrote:
>
> External Email - Use Caution
>
>
> Dear Help Desk - I have a few basic questions about freesurfer.  I am 
> retired military bomb technician working on a blast TBI initiative and 
> not a research so please bear with me.  We are looking at a long term 
> study of bomb technicians and I am curious about the following before 
> moving forward.
>
>  1. Total number of images processed by freesurver?  Is this in the
> thousands or millions?
>
Do you mean since FS was created? Probably around 100,000 by now.
>
>  1. Cohart group data is this from each organization or is there a
> central pool.  e.g. I had a 3D volumetric MRI done with DTI at
> Washington University in St Louis and am 49yrs old is this only
> from their pool or larger data base? Any idea number of images in
> that data base?
>
I'm not sure what you mean. Can you elaborate? You cannot use DTI as 
input to freesurfer. Are you talking about the Human Connectome Project 
(HCP) data from Wash U?
>
>  1. Standard Deviations, Patient Annual Volume Change and Group Annual
> Volume change; are these organizations specific or a larger data base.
>
I'mnot sure what you mean. Are you asking if we have such a data base?
>
>  1. How accurate are the volumes from a 3T MRI and is there a huge
> fluctuation if scans are done on the same exact MRI system?  e.g.
> in my scan some of the thicknesses were down to .0013mm and
> volumes down to .9mm3 = is there a lot of error in those numbers.
>
The actual values are not accurate downto that level. It is hard to say 
what the accuracy really is but probably worse than 3%.
> Thanks for any information you can provide!  It seems there will be a 
> DVBIC site open soon where our school is and I would like to be able 
> to provide some input on this.
>
> Thanks,
> Todd Sheckley
>
>
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Re: [Freesurfer] help with subjects concatenation/dimension inconsistency error

[Barletta, Valeria]

Oh yeah... That could actually be the problem!
Thank you so much!
Vale

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, November 05, 2018 4:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] help with subjects concatenation/dimension 
inconsistency error

Hi Valeria

that means there is a mismatch between the surface overlay and the surface.
Maybe you sampled:

/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh

to the surface then recreated the surfaces after editing?

cheers
Bruce


On Mon, 5 Nov 2018, Barletta, Valeria wrote:

> Dear FreeSurfers,
> I am trying to apply surface processes to concatenate my cohort, but for some 
> subjects I am getting this error:
>
> mri_surf2surf --srcsubject Ctrl034_R01_07 --srchemi rh --srcsurfreg
> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg
> --tval
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/T1/allSubj/tmp.mris_preproc.61312/Ctrl034_R01_07.18.mgh
> --sval
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh
> --noreshape --no-cortex ERROR: dimension inconsistency in source data
>   Number of surface vertices = 138446
>   Number of value vertices = 137970
> Source registration surface changed to sphere.reg
> Target registration surface changed to sphere.reg
> srcsubject = Ctrl034_R01_07
> srcval = 
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh
> srctype=
> trgsubject = fsaverage
> trgval = 
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/T1/allSubj/tmp.mris_preproc.61312/Ctrl034_R01_07.18.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= rh
> trghemi= rh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/rh.sphere.reg
> Loading source data
>
>
> And the script running stops immediately after. I already tried to relaunch 
> the-autorecon2 -autorecon3command for those subjects, since we 
> already had this kind of issue in the past, but it didn't work.
> Do you have any idea of what could be the problem?
> Thank you very much,
> Valeria
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>
>
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Re: [Freesurfer] help with subjects concatenation/dimension inconsistency error

[Bruce Fischl]

Hi Valeria

that means there is a mismatch between the surface overlay and the surface. 
Maybe you sampled:

/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh

to the surface then recreated the surfaces after editing?

cheers
Bruce


On Mon, 5 Nov 2018, Barletta, Valeria wrote:

> Dear FreeSurfers,
> I am trying to apply surface processes to concatenate my cohort, but for some 
> subjects I am getting this error:
>
> mri_surf2surf --srcsubject Ctrl034_R01_07 --srchemi rh --srcsurfreg 
> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg 
> --tval 
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/T1/allSubj/tmp.mris_preproc.61312/Ctrl034_R01_07.18.mgh
>  
> --sval 
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh
>  
> --noreshape --no-cortex ERROR: dimension inconsistency in source data
>   Number of surface vertices = 138446
>   Number of value vertices = 137970
> Source registration surface changed to sphere.reg
> Target registration surface changed to sphere.reg
> srcsubject = Ctrl034_R01_07
> srcval = 
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh
> srctype=
> trgsubject = fsaverage
> trgval = 
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/T1/allSubj/tmp.mris_preproc.61312/Ctrl034_R01_07.18.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= rh
> trghemi= rh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/rh.sphere.reg
> Loading source data
>
>
> And the script running stops immediately after. I already tried to relaunch 
> the-autorecon2 -autorecon3command for those subjects, since we 
> already had this kind of issue in the past, but it didn't work.
> Do you have any idea of what could be the problem?
> Thank you very much,
> Valeria
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>
>
>
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Re: [Freesurfer] Help with extraction of cortical thickness from ROI and creation of mask.

[Douglas Greve]

On 10/21/17 10:31 AM, Dennis M. Hedderich wrote:

Dear Freesurfer Team,

I built a GLM, did a 2 sample t-test and found significant differences 
in cortical thickness in the right middle temporal gyrus between two 
groups. Now, I would like to kindly ask for your help with two 
problems that I am facing:
1) for further correlation analyses in SPSS, I would like to extract 
cortical thickness exactly from the region of difference in the middle 
temporal gyrus of every subject. Extraction of cortical thickness of 
the whole middle temporal gyrus worked well, however there is a lot of 
noise in that information because the area of significant difference 
is a lot smaller than the MTG roi from the Desikan atlas.
If you run mri_glmfit-sim, it will create a ocn.dat file with that 
information in it. Run it with mri_glmfit-sim --help to get more info
2) to assess thalamocortical structural connectivity to that region, I 
would like to create and extract a mask in MNI space that I could use 
with fsl. Is that possible?
Run the mni152 through recon-all, then map your ROI (either label or 
annotation) from fsaverage to the mni152 with mri_surf2surf (annotation) 
or mri_label2label (label), then use mri_label2vol to create a volume in 
the mni152 space.

Thank you very much in advance for any kind of help.
Best wishes,
Dennis


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Re: [Freesurfer] Help with hippocampal subfield alignment

[Elizabeth Hall]

Hi Bruce,

I've uploaded the subject through FileDrop. Thanks for your help.

-Elizabeth

On Tue, Aug 15, 2017 at 6:00 PM, Bruce Fischl 
wrote:

> HI Elizabeth
>
> that should definitely not happen. Something must have gone pretty
> dramatically wrong. If you upload the subject I'll take a look
>
> cheers
> Bruce
>
>
> On Tue, 15 Aug 2017, Elizabeth Hall wrote:
>
> Hi Eugenio,
>> It looks like the segmentation is missing all of the left hippocampus in
>> the
>> ASEG.
>>
>> Is there a way to go in and manually correct this?
>>
>> Best,
>>
>> Elizabeth
>>
>> On Tue, Aug 15, 2017 at 12:54 PM, Iglesias Gonzalez, Eugenio
>>  wrote:
>>
>>   Dear Elizabeth,
>>
>>   This is pretty unusual. Would you mind taking a look at
>>   aseg.mgz? Does the segmentation of the (whole)  left hippocampus
>>   look fine in ASEG?
>>
>>   Cheers,
>>
>>   /Eugenio
>>
>>
>>
>>
>>
>>   From:  on behalf of
>>   Elizabeth Hall 
>>   Reply-To: Freesurfer support list
>>   
>>   Date: Tuesday, 15 August 2017 at 17:32
>>   To: "freesurfer@nmr.mgh.harvard.edu"
>>   
>>   Subject: [Freesurfer] Help with hippocampal subfield alignment
>>
>>
>>
>> Hello FreeSurfer Developers,
>>
>>
>>
>> I have run the hippocampal-subfields-T1 tag on a MP2RAGE scan for one
>> of my subjects and find that the subfield segmentation for the left
>> hemisphere only is off (pictures attached). No errors were reported in
>> the log.
>>
>>
>>
>> Is there a way to manually reset the alignment for only one
>> hemisphere? Or is there a reason why it might be failing to segment
>> that hemisphere?
>>
>>
>>
>> Thank you,
>>
>>
>>
>> Elizabeth
>>
>>
>>
>> --
>>
>> Elizabeth Hall
>>
>> ehall1...@gmail.com| +1 559 824 6695
>>
>>
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>> addressed. If you believe this e-mail was sent to you in error and the
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>> HelpLine at
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>> dispose of the e-mail.
>>
>>
>>
>>
>> --
>> Elizabeth Hall
>> ehall1...@gmail.com| +1 559 824 6695
>>
>>
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Elizabeth Hall
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Re: [Freesurfer] Help with hippocampal subfield alignment

[Bruce Fischl]

HI Elizabeth

that should definitely not happen. Something must have gone pretty 
dramatically wrong. If you upload the subject I'll take a look


cheers
Bruce

On Tue, 15 Aug 2017, Elizabeth Hall wrote:


Hi Eugenio,
It looks like the segmentation is missing all of the left hippocampus in the
ASEG. 

Is there a way to go in and manually correct this?

Best,

Elizabeth

On Tue, Aug 15, 2017 at 12:54 PM, Iglesias Gonzalez, Eugenio
 wrote:

  Dear Elizabeth,

  This is pretty unusual. Would you mind taking a look at
  aseg.mgz? Does the segmentation of the (whole)  left hippocampus
  look fine in ASEG?

  Cheers,

  /Eugenio

   

   

  From:  on behalf of
  Elizabeth Hall 
  Reply-To: Freesurfer support list
  
  Date: Tuesday, 15 August 2017 at 17:32
  To: "freesurfer@nmr.mgh.harvard.edu"
  
  Subject: [Freesurfer] Help with hippocampal subfield alignment

 

Hello FreeSurfer Developers,

 

I have run the hippocampal-subfields-T1 tag on a MP2RAGE scan for one
of my subjects and find that the subfield segmentation for the left
hemisphere only is off (pictures attached). No errors were reported in
the log. 

 

Is there a way to manually reset the alignment for only one
hemisphere? Or is there a reason why it might be failing to segment
that hemisphere?

 

Thank you,

 

Elizabeth

 

--

Elizabeth Hall

ehall1...@gmail.com| +1 559 824 6695


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--
Elizabeth Hall
ehall1...@gmail.com| +1 559 824 6695

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