[Freesurfer] mris_flatten distortions

2022-05-25 Thread Alberto Pisoni 
External Email - Use Caution

Hi all, I am trying to flatten a whole hemisphere, and i created the cut
patch following the tutorials.

see the result here.

https://secure-web.cisco.com/1xjf27LYk5Ie25CTk51Q3cPiwVe-uMjYXB4V0ViZqlanRh7HkTXKDS-1HTcTPXJCxmT3JtXYt-sqlqTYba3y3B2xlT0j5KYd9OUxIUWG4M1l2bD8eJiwJyFN7ULqtMaNqcShZD1j9pfoIDMHkPwLQXeQzBegTua5cg8XJj2IQzIAXpclV-iPlS4zJyPVcu0aZPVRHZpbR59kD4h0kNhV2r27EjnaJQnz6gwXtHebd3zAt9zul6Da9a81ExBbcVBsSEkuKIo56Bk4UAeG4zUFxUaqXh3VdUOKAuLe3rW_KxvppnVmzzBTGolW24VY3i2YqGx-T0DeBXUqluMeJ1ZOfp3e6RoAONlmXcMMUMmP40Ng/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11co39jCDmQC8VdLrN6iQp-ytWxxz40WY%2Fview%3Fusp%3Dsharing

Then I run the command

mris_flatten  

from the surf dir and it works, but when I visualize the patch it is
distorted, like if I did not cut the inflated surface.

https://secure-web.cisco.com/128ktBKDV9wlBus-Bu1XsphHIMQpHtnuoTRQ6748JzsrgK9lPn_h05GfjIBjSL-QA4cPUy-IFGDhAUETl-kUeOrwC9-ZtdJAVVuZHIDhbFmXrSVogZpjuArXlFgXwcp8YVysQrS1qnDMwIjtXsob18Ruuc-p_jXrL-hKdZXCjWieJ09HVkdLTixeRmLvq-LtP3II8nyipaXht-odxS8YqLRWQLoDV0ra6ge_Vg7HK6AfOM2XAtiAc9PykwlNBwPk9pu5NXGXpPdnAH8RH2h2IrdfshzGVdJgp1mLcOrZj-eoDf1dgP5P3xFHm_ZMuExHuYn801IRrIlJzaJGY9yqhwHiVy6LNQNwDaZqNerVElaE/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11cOYRjQqXsyPoIly3WiMPVT7vYBK5vFw%2Fview%3Fusp%3Dsharing

What am I missing?

The Freesurfer version is 7.2.0 (although I also tried with 6.0) and the
system is a OS 11.6.1 BigSur Macbook Pro with M1 chip.

Thanks

Alberto
--
Alberto Pisoni, PhD
Associate Professor
Department of Psychology
University of Milano-Bicocca
Building U6 ~ Room 3139
piazza dell'Ateneo Nuovo 1
20126, Milano, Italy
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[Freesurfer] HRF with derivatives: results

2022-05-25 Thread Laura Doll 
External Email - Use Caution

Hi everyone,

I need some help regarding the SPM-HRF with two derivatives:
Where can I find the actual function that was used for the analysis? I am 
mostly interested in the peak latency, but would also appreciate if I can check 
the other parameters of the function somewhere. 

Best,
Laura


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[Freesurfer] (no subject)

2022-05-25 Thread Alberto Pisoni 
External Email - Use Caution

Hi all, I am trying to flatten a whole hemisphere, and i created the cut
patch following the tutorials.

see the result here.

https://secure-web.cisco.com/1yFIFkAQ7JVCxQ9XtdXA16rgidANEj5tq1VECDMPQ70qTME3GzCmOicwUAGbxA6C2o7Wi3CSEc6CbpZnD8HYT4PmTEB2s6XS9wUm_x-ezA-uOA8gVSEeigJ78aBKaLBGSooyvcQlhECKU5BINgjHPUroUHqrIDnJo65v0ssXQ9aQUzkA4J1yLUACCcO3RPZxCLc1C2GCHlXWpzQHzzJem-1PM-ZqxVqavqmplqG8zBJ2uv40DdyWpE6rlAed26gF5jTIX4o-sOSUqLxS8F7MhzLq8C6Zfo3s82W6O0odNz0Fihdpsrm-osNYT5uwaBqxZcL3W3onfaA2SDrIuZ9jgZModLjVDBr5A3hlDiuKKN1g/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11co39jCDmQC8VdLrN6iQp-ytWxxz40WY%2Fview%3Fusp%3Dsharing

Then I run the command

mris_flatten  

from the surf dir and it works, but when I visualize the patch it is
distorted, like if I did not cut the inflated surface.

https://secure-web.cisco.com/1tWLYU7SKnF0l2rwCeoMbCKMijBrdYwXtLipGGQBhN40aO4MC7f0YrynZNfrwOcpOh-A5EWlDhvqZeVJYIhLOAqN0FJbX3sWQzsWE-Nnpcd95dbvFVFzY9anWDQCYpXAw4NqObKHWuJ3dhSGqpuhRoU-eQZ28gSjs3l-SodUG19d8Qey8WdkQ2xsFWf_-wSIbUi2RtVhR1BlTIKQxRUUA71CdU-kVshUPRTJfyREkovpKvO0-ukHS2puAYXzic3yAN_wPTzFpPobHuG35war0MK-k80SyrEmCxxLx-yUlYrg8J4NySWvfQ_m1Zal_uEpnUq891M9JWDF-7n_pmt7ZyjEy08bidVlW86n5NJlBANY/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11cOYRjQqXsyPoIly3WiMPVT7vYBK5vFw%2Fview%3Fusp%3Dsharing

What am I missing?

The Freesurfer version is 7.2.0 (although I also tried with 6.0) and the
system is a OS 11.6.1 BigSur Macbook Pro with M1 chip.

Thanks

Alberto
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Re: [Freesurfer] mris_flatten distortions

2022-05-25 Thread Fischl, Bruce 
Hi Alberto

Usually that means that you missed some cuts and there are still attachments.  
Occasionally it is due to a local minimum. You can try changing the distance 
preservation matrix to be bigger with longer range distances. Something like 
-distances 20 20 (out to 20 neighbors and 20 at each distance) or even largely. 
The defaults were set a long time ago when there was much less ram available. 
You can also try -dilate 1 to dilate the cuts by 1 vertex, although then you 
lose more of the surface

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Alberto Pisoni
Sent: Wednesday, May 25, 2022 5:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_flatten distortions


External Email - Use Caution
Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch 
following the tutorials.

see the result here.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://drive.google.com/file/d/11co39jCDmQC8VdLrN6iQp-ytWxxz40WY/view?usp=sharing

Then I run the command

mris_flatten  

from the surf dir and it works, but when I visualize the patch it is distorted, 
like if I did not cut the inflated surface.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://drive.google.com/file/d/11cOYRjQqXsyPoIly3WiMPVT7vYBK5vFw/view?usp=sharing

What am I missing?

The Freesurfer version is 7.2.0 (although I also tried with 6.0) and the system 
is a OS 11.6.1 BigSur Macbook Pro with M1 chip.

Thanks

Alberto
--
Alberto Pisoni, PhD
Associate Professor
Department of Psychology
University of Milano-Bicocca
Building U6 ~ Room 3139
piazza dell'Ateneo Nuovo 1
20126, Milano, Italy

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[Freesurfer] Starting a new project

2022-05-25 Thread Raffaele Di Natale 
External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to develop new functions in the tool for my research
activity and I wish to know if there is a guide about to start this
kind of activity.


1) freesurfer-linux-ubuntu20_x86_64-7-dev.tar.gz


Raffaele Di Natale, PhD
Contract Researcher
DIEEI, University of Catania
+39 095738 2385 (Edificio 13)
+39 095738 7903 (OpenLab
)
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 .
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Re: [Freesurfer] Starting a new project

2022-05-25 Thread Wighton, Paul 
Hi Raffaele,

There is some info here:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide

For more details on compiling FreeSurfer from source, you can refer to this 
neurodocker template:
https://github.com/ReproNim/neurodocker/blob/12d0f21e119ad595ccf2487b4edc788a6e032dc3/neurodocker/templates/freesurfer.yaml#L260

Which documents exact versions of gcc, cmake, python etc. and is part of this 
pull request:
https://github.com/ReproNim/neurodocker/pull/445

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Raffaele Di Natale 

Sent: Wednesday, May 25, 2022 10:33 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Starting a new project


External Email - Use Caution

Hello FreeSurfer Developers,


I'm attempting to develop new functions in the tool for my research activity 
and I wish to know if there is a guide about to start this kind of activity.


1) freesurfer-linux-ubuntu20_x86_64-7-dev.tar.gz


Raffaele Di Natale, PhD
Contract Researcher
DIEEI, University of Catania
+39 095738 2385 (Edificio 13)
+39 095738 7903 
(OpenLab)
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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 
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[Freesurfer] ubuntu vm

2022-05-25 Thread Sodoma, Matthew 
External Email - Use Caution

Hello,

I was looking to receive the passcode to unzip the virtual box file below:


Freesurfer 7.2.0 release in Ubuntu 18.04.06: 
FS_7_2_0_Ubuntu_18_04_06.ova.7z

Matt
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this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] mris_flatten distortions

2022-05-25 Thread Alberto Pisoni 
External Email - Use Caution

Thanks that worked perfectly.

Now that I have my flat patch how can I import it in matlab for some
additional plotting?

Also, I read the wiki but I am not sure if and how I can import an atlas
and create the annotation for the vertexes with that atlas.

Thanks

A

Il giorno mer 25 mag 2022 alle ore 16:19 Fischl, Bruce <
bfis...@mgh.harvard.edu> ha scritto:

> Hi Alberto
>
>
>
> Usually that means that you missed some cuts and there are still
> attachments.  Occasionally it is due to a local minimum. You can try
> changing the distance preservation matrix to be bigger with longer range
> distances. Something like -distances 20 20 (out to 20 neighbors and 20 at
> each distance) or even largely. The defaults were set a long time ago when
> there was much less ram available. You can also try -dilate 1 to dilate the
> cuts by 1 vertex, although then you lose more of the surface
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Pisoni
> *Sent:* Wednesday, May 25, 2022 5:28 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] mris_flatten distortions
>
>
>
> *External Email - Use Caution*
>
> Hi all, I am trying to flatten a whole hemisphere, and i created the cut
> patch following the tutorials.
>
>
>
> see the result here.
>
>
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1N9EKkJRI3SMjA-28IiUHnC68ClmCdOeSDkGVpd1mOdlYui8d2Pe6fOTfMesKmlq51aH-wHR35xEELFYb0MRhof4ENjauzJ9o3SrXyKA3ba0MHhkVDMnqtvX_yPNVNXN4dZUdwiU0-0LhhLEewzubfwW0Cf16QbyXFSZHgIEnvW1cgDopucZZvVPoZhVyhhYIur3YetpvN2e4evqeQOULyDmGbSIU8dgnyAVZquS8R0RgMy-l4DfN2uqKGCiOhv7yBXSVYfVOft9KpGv9c-vZH87YnoGGgz11UZEIq7N6ftM3-LGnyPa7ZEcABJ1uoBWlolcQ3TzJ9ESQn8WZHWhcTBOCZh1gCVManvwdkLHJX70/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11co39jCDmQC8VdLrN6iQp-ytWxxz40WY%2Fview%3Fusp%3Dsharing
> 
>
>
>
> Then I run the command
>
>
>
> mris_flatten  
>
>
>
> from the surf dir and it works, but when I visualize the patch it is
> distorted, like if I did not cut the inflated surface.
>
>
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1HW92OlrvEK6mHN3vcjNmWf4fsHDczdr9nCDLh1gFGMfvq8yqfgnebX3f7IgsN0FkQTUJTXV5661gbea7hbMszlOXzb2FTayrAb6wkWxGlbxM3XwbQJi-Qw8VWyND-nZUIa3CmSvceSj00OzxP6QyLkKjeva70teRHKB5BStF5lRihnhg1o7F6kzDmSoFw7V7JRK12DHrkfvxR3u2V6SJLT0XMhMTCg8VUlKHZ0j-xn05PzvZhAZgfOzWHZpBuZsqtHq5DRRp1_v69C1ZdGoTtYWVbIDepJBe2II3lUZm1Z-kEft2mUPnyzopbgaRJvISZUtw1Cah0MoS6k0CryTIwMzB9ZqFP72JmfAs96VVlyM/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11cOYRjQqXsyPoIly3WiMPVT7vYBK5vFw%2Fview%3Fusp%3Dsharing
> 
>
>
>
> What am I missing?
>
>
>
> The Freesurfer version is 7.2.0 (although I also tried with 6.0) and the
> system is a OS 11.6.1 BigSur Macbook Pro with M1 chip.
>
>
>
> Thanks
>
>
>
> Alberto
>
> --
>
> Alberto Pisoni, PhD
>
> Associate Professor
>
> Department of Psychology
>
> University of Milano-Bicocca
>
> Building U6 ~ Room 3139
>
> piazza dell'Ateneo Nuovo 1
>
> 20126, Milano, Italy
>
>
> ___
> Freesurfer mailing list
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> https://secure-web.cisco.com/1r93O2oOGeOsEyNn0wnGrGwVoVfMWacJgyZ1Bj0cs1wPKeBqv6P_vN3YwxO2oH_3wrsuphQm_ea5Nf69yaFMUvTN0OyuUb2Hkl16tBekl8wPP18_V6TEhcsQ9yersMO68iqUWd0ad9QvuEgWx-ZMcZzyh5TzjSY_nlM5dfHbJwqFoqdomrbpctgNUrSdDVdSAeuZfrmiDfo4UeLxWJdvJN_22yORsfvYI-yTGCFgRPsO2MAL0TQvlB4ZlGFkSjCjhR2I9KPoFZKYBkYHAn4kFQdCV1E30ZD7lUvQT4Apfe2P26zoc7ewyKbbDMNNzNJ5VusZyATZMIRnSXG2JipQrzLA7Yb44jEglEo5OPx_l7FU/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 co