date:20220915

[Freesurfer] Virtual Machine password request

2022-09-15 Thread Dakota Graham

External Email - Use Caution

Dear Admins,

I've installed VirtualBox and am now at the stage of extracting the
7zip Ubuntu image that includes freesurfer. Could you please send the
password for extracting this encrypted file?

Thanks,
Dakota
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Re: [Freesurfer] White matter normalization

2022-09-15 Thread James Brown

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Hi Dr Greeve,
I ran recon-all using the flag -flair. I couldn't find any command in
recon-all.log that normalizes the flair images. It seems just normalization
to the T1.
I would like to inquire about the flag sigma in the command "mri_normalize"
the default is 8. when it is recommended to increase this value? and how
much can weincrease it?

I'm not sure of the order. You can run recon-all passing in the flair with
-flair flair.mgz. At some point in the process it will apply a
normalization to the flair (it will not necessarily be the same
normalization that is applied to the t1)




On Mon, Sep 12, 2022 at 4:01 PM James Brown  wrote:

> Dear Freesurfer experts,
> In order to normalize white matter intensity of T1 images and correct for
> bias field. I do the following steps:
> mri_convert T1.nii.gz T1.mgz
> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
> mri_convert T1_norm.mgz T1_norm.nii.gz
>
> I would like to apply bias field correction on FLAIR images then
> normalize white matter intensity.
> I tried N4biasfieldcorrection from ANTS but it didn't work as expected.
> Reviewing documents about N4biasfieldcorrection I realize that the
> algorithm has been developed to correct bias field correction in T1.
>
> Are the steps above valid for FLAIR images or it can only be applied on T1
> images. We appreciate any feedback about the proper way to correct FLAIR
> images for bias field and normalize white matter intensity.
>
> Thank you
> JamesB
>
>
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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] Freesurfer: fs_install_mcr: Unzip command not found

2022-09-15 Thread Wighton, Paul

One more note:

The command:
export SUBJECTS_DIR=/home/ylee6/ADIPA_data

May or may not work, depending on the type of shell environment you are using.  
If it doesn't work, you can try:
setenv SUBJECTS_DIR /home/ylee6/ADIPA_data

To set the environment variable

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally located in the path /home/ylee6/ADIPA_data/26/scripts), 
in which at the end of the log you can see that the recon-all is completed 
successfully.

Secondly, with the output from the 'env' command you can see it described as 
such below:

SHELL=/bin/bash
WSL_DISTRO_NAME=Ubuntu
OS=Linux
MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
FREESURFER=/usr/local/freesurfer/7.3.2
MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
FS_OVERRIDE=0
NAME=LAPTOP-63HA9ANS
PWD=/home/ylee6/ADIPA_data/26/mri
LOGNAME=ylee6
FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
MOTD_SHOWN=update-motd
HOME=/home/ylee6
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/8_interop
MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
WAYLAND_DISPLAY=wayland-0
FMRI_ANALYSIS_DIR=/usr/local/freesurfer/7.3.2/fsfast
MNI_DIR=/usr/local/freesurfer/7.3.2/mni
PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
MNI_PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
FREESURFER_HOME=/usr/local/freesurfer/7.3.2
LESSCLOSE=/usr/bin/lesspipe %s %s
LOCAL_DIR=/usr/local/freesurfer/7.3.2/local
TERM=xterm-256color
FIX_VERTEX_AREA=
LESSOPEN=| /usr/bin/lesspipe %s
USER=ylee6
DISPLAY=172.25.144.1:0
SHLVL=1
SUBJECTS_DIR=/usr/local/freesurfer/7.3.2/subjects
XDG

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

2022-09-15 Thread Wighton, Paul

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally located in the path /home/ylee6/ADIPA_data/26/scripts), 
in which at the end of the log you can see that the recon-all is completed 
successfully.

Secondly, with the output from the 'env' command you can see it described as 
such below:

SHELL=/bin/bash
WSL_DISTRO_NAME=Ubuntu
OS=Linux
MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
FREESURFER=/usr/local/freesurfer/7.3.2
MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
FS_OVERRIDE=0
NAME=LAPTOP-63HA9ANS
PWD=/home/ylee6/ADIPA_data/26/mri
LOGNAME=ylee6
FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
MOTD_SHOWN=update-motd
HOME=/home/ylee6
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/8_interop
MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
WAYLAND_DISPLAY=wayland-0
FMRI_ANALYSIS_DIR=/usr/local/freesurfer/7.3.2/fsfast
MNI_DIR=/usr/local/freesurfer/7.3.2/mni
PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
MNI_PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
FREESURFER_HOME=/usr/local/freesurfer/7.3.2
LESSCLOSE=/usr/bin/lesspipe %s %s
LOCAL_DIR=/usr/local/freesurfer/7.3.2/local
TERM=xterm-256color
FIX_VERTEX_AREA=
LESSOPEN=| /usr/bin/lesspipe %s
USER=ylee6
DISPLAY=172.25.144.1:0
SHLVL=1
SUBJECTS_DIR=/usr/local/freesurfer/7.3.2/subjects
XDG_RUNTIME_DIR=/home/ylee6/.xdg
FS_LICENSE=/home/ylee6/license.txt
WSLENV=
XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop
PATH=/usr/local/freesurfer/7.3.2/bin:/usr/local/freesurfer/7.3.2/fsfast/bin:/usr/local/freesurfer/7.3.2/tktools:/usr/local/freesurfer/7.3.2/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System3

[Freesurfer] Virtual Machine password request

Re: [Freesurfer] White matter normalization

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

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