Re: [Freesurfer] FSFAST: wrong brain mask in preproc

2023-04-27 Thread Elmira Hassanzadeh 
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Thank you for clarifying.

Elmira

On Wed, Apr 26, 2023 at 6:44 PM Douglas N. Greve 
wrote:

> External Email - Use Caution
>
> Yes, this is the expected behavior, ie, it should cover only subcortical
> GM regions. It is expected that cortical regions will be handled with the
> surface based analysis. You can recombine the results at the end with
> vlrmerge.
>
> On 4/26/2023 12:22 PM, Elmira Hassanzadeh wrote:
>
> External Email - Use Caution
> Hi everyone,
>
> We preprocessed resting-state data with preproc-sess. In the output, I
> noticed although *fmcpr.nii* covers the whole brain,*
> fmcpr.sm6.mni305.2mm.nii* is only covering brain stem+cerebellum
> (screenshots attached).
>
> Any clue what went wrong? This is an example of the command we ran for one
> of our subjects(R19):
>
> *preproc-sess -surface R19 lhrh -s R19 -fwhm 6 -fsd rest -mni305 -per-run*
>
> Thanks,
> Elmira
>
>
>
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[Freesurfer] FSFAST: multiple resting state runs

2023-04-26 Thread Elmira Hassanzadeh 
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Hi,

How do we analyze multiple resting state runs for a subject at once?

- do we need certain folder structure/naming?
- do we do concatenation?

Thanks,
Elmira
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[Freesurfer] Mac OS 13 Ventura

2023-03-06 Thread Elmira Hassanzadeh 
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Hi everyone,

Could someone please direct me to the workaround instructions on installing
Freesurfer on Mac M1 ultra on OS 13.0 Ventura?

Thank you,
Elmira
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Re: [Freesurfer] problem opening freeview (on MacOS Catalina)

2021-10-02 Thread Elmira Hassanzadeh 
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Thank you! It worked. FYI I've installed 7.1.

best,
Elmira

On Sat, Oct 2, 2021 at 9:37 PM fsbuild  wrote:

> Hello Elmira,
>
> You could try what’s listed in this posting to the freesurfer mailing
> list,
> https://secure-web.cisco.com/14r6HUNpUdecs2uurR0aVhufM6oEIRKkatZhBvFY94EHiSZYqp8rG1482Iq2VG9TDvSgmhdPI1A3mb6jQ5iMrH4uesSDg5ZyAdavkcIWS4iw_mJ6JmfVPiaHSEEk1mBQhrEF6FvzA9N-8dUWNEyV3E1CP0p19IoLSnhCxwBWBeZfU3-E-s0N8IfW0BXprbyISf28zfCY4kRCp4NOk5UOU3rRsYIcKp1sHhvGsMBIN3xDeaZcbGGwhmNTRm1xI_kCNSM8MkkOK79oB4mPaSoHXJg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmaillist.html,
> from last month,
> https://secure-web.cisco.com/1bN_QoWv7_mMLp3fX8AvqovcSiCmF8fy0bMu4OTkZeJVFcnwvgw3KZ4m6xPb_JHqcgxPjC3oyIIwd3d3bU51P8pFY4YhFuPJevhysEsnWaoIUjkplJZxidW7uMg2C_tdOLioNRQ_YOBrNjU_NteQirOLCWy1ronwWWN132uZaVONadSi8vXDQNePu4WTfWPOUiOyg-WVr5D4RqLYRxyzrx40bHmxcEGlajODxMUk7Fi0Gjz33pM_YvekPiEQCabN2D2EM8Z8nzfpv5tOWXvDkfw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70979.html.
> I’ve copied it below as well.
>
> I can’t see from your crash report if you installed the latest 7.2.0
> release (via the installer
> https://secure-web.cisco.com/12v10hIiR8nFLjoZsoRpIYYuNSPeaYf-J6Yf7a5CztS85LQEGLq2vO4YjNYX-PkIAP6tsL6hLUp7k3EbCXRJzavBca9iI6QU3Gi2WsXGF5EPtJJZSsaD5RnEpXhp55-DXuWUeP1-od7zbSRj8Oh3ywhkEqHWCE9023KgtIJn8cVi-Le4mCgxON90LY7hjuTNquiFe0LySRHLF1AVTWlX6XLBW9XTrmhw5PoGX4qN3aSUD3bnYC8PNldAGhAXhxOkwHcDa05jbB67iNQfFk7Aw7g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7..2.0%2Ffreesurfer-darwin-macOS-7.2.0.pkg_
> <https://secure-web.cisco.com/1PlUHT0NhEO_c102zjohFCD3-mQQoJ9N_RJes2fcWJvHJYaU0nIgfs0XckqDAC6irGQ5NnrkGqTTKNQn0khNvaK5gDEmhVPxAiZ55MY6XU00PNvrQHr4ZHHLO7r3cFRr2ejZOaTZ3hKgFXu4xf92Q9v7kkleA6dj5Tbu2K5IPS7rPzwjvtKUPL5-P7s_YUdzpWk_dVjhKth4rzL84LgvJKVJOuf9HXu8Ic-1qvi8Ns5RhtVLaHe5UQNA_CHJvVk2bIQpYUqKaoBja6zgmSYK9cg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-darwin-macOS-7.2.0.pkg_>
> ).  But if you are not running the latest release, then I would also give
> that a try.
>
> - R.
>
> On Oct 2, 2021, at 20:35, Elmira Hassanzadeh  wrote:
> Hello FreeSurfer Developers,
>
> I installed freesurfer for the first time on my system but although the
> installation went smoothly I cannot open freeview. Here is the error I
> receive on terminal (the full log at the end of this message)
>
> 9800 Segmentation fault:
> 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>
>
>
> Begin forwarded message:
>
> *Subject: **[Freesurfer] Notes on running freesurfer on MacOS (including
> M1 Macs running MacOS BigSur 11.6)*
> *Date: *September 22, 2021 at 21:15:35 EDT
> *To: *freesurfer@nmr.mgh.harvard.edu
>
> There have been various postings to the freesurfer mail list about issues
> running freesurfer on MacOS including M1 Macs.  The information below may
> help with running freesurfer (Intel) binaries on MacOS including M1 Macs
> running BigSur (MacOS 11.6).
>
> *APPLICATION SANDBOXING*
>
> The privacy and security features introduced with macOS Mojave (10.14.X)
> and subsequently expanded in MacOS Catalina (10.15.X) and BigSur (11.X)
> means that after installation, binaries and applications are by default
> “sandboxed” and not allowed access to the disk, networked volumes, etc. -
> unless they are given permission.  Permission should only need to be
> granted once, but this can be cumbersome if many binaries each need
> permission to run (compared to a single *.app application bundle).
>
> The System Preferences GUI can be used to grant disk access to an
> individual application (bundle):
>
> • Open *System Preferences*
> • Click the *Security & Privacy* tab
> • Click the *Privacy* tab
> • On the left hand side menu scroll to and select *Full Disk Access*
> • Click on the (Locked) *padlock* in the lower left hand corner and enter
> your password to unlock it
> • Click the *+ button* under the list of applications in the right hand
> side menu; navigate using the Finder to the application you want to grant
> full disk access to; select it; hit the open button
>- OR - it may just work to directly drag the application from a
> Finder window into the right hand side menu
> • Make sure the *box is checked* next to the application you added
> • Click on the *padlock* icon to lock out changes
>
> The next time you launch the application, it should have full disk access.
>
> So for example you could do the above for the freeview application
> installed by the freesurfer 7.2.0 Mac installer package as
> */Applications/freesurfer/7.2.0/Freeview.app*
>
> Since the binaries and scripts located under
> /Applications/f