[Freesurfer] Partnership Proposal for Freesurfer Expert Training with Universitas Indonesia

2023-07-14 Thread Pukovisa Prawiroharjo 
External Email - Use Caution

Dear Freesurfer Team,

Greetings. My name is dr. Pukovisa Prawiroharjo, Sp.S(K), PhD. I am a
lecturer and researcher at the Department of Neurology Faculty of Medicine
Universitas Indonesia (UI) in Indonesia.

I am pleased to inform you that we have been awarded a grant from the UI
Incubate program. This program is aimed at promoting growth in university
startups that focus on innovative solutions.

Our project revolves around the concept of a "Brain Analysis Consultation
Service." Our primary goal is to democratize access to predictive analytics
for neurodegenerative diseases, making such advanced techniques more
available to the general public. The business model is to build a clinic
for brain analysis using Freesurfer as a core element of our service. The
data given by the MRI will be used to analyze and predict neurodegenerative
diseases from our patients.

The service we aim to offer will allow patients to consult with us about
their Freesurfer results for our team to analyze. Through this, we hope to
give them a clearer understanding of their condition, helping predict the
trajectory of their neurodegenerative disease more accurately.

With this in mind, we would like to invite your team to conduct an expert
class on Freesurfer for us. This class will surely boost our understanding
of the software and improve the efficiency and effectiveness of our work.

We sincerely hope this proposal interests you and aligns with your mission
to further knowledge and research in neuroscience. If so, we would be
delighted to discuss this further and provide you with any more details you
may need.

Thank you for considering our proposal. We look forward to the potential of
working together for a common goal.

Best regards,

*Pukovisa Prawiroharjo, M.D., Sp.N, Subsp. NGD (K), PhD*
Neurobehavior Consultant, Neurology Specialist
Neurology Department, Faculty of Medicine, Universitas Indonesia
Chair of Bioethics Cluster IMERI UI
Chair of International Policy Div, Board of Development Med Services IDI
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[Freesurfer] (no subject)

2023-07-14 Thread Pukovisa Prawiroharjo 
External Email - Use Caution

Dear Freesurfer Team,

Greetings. My name is dr. Pukovisa Prawiroharjo, Sp.S(K), PhD. I am a
lecturer and researcher at the Department of Neurology Faculty of Medicine
Universitas Indonesia (UI) in Indonesia.

I am pleased to inform you that we have been awarded a grant from the UI
Incubate program. This program is aimed at promoting growth in university
startups that focus on innovative solutions.

Our project revolves around the concept of a "Brain Analysis Consultation
Service." Our primary goal is to democratize access to predictive analytics
for neurodegenerative diseases, making such advanced techniques more
available to the general public. The business model is to build a clinic
for brain analysis using Freesurfer as a core element of our service. The
data given by the MRI will be used to analyze and predict neurodegenerative
diseases from our patients.

The service we aim to offer will allow patients to consult with us about
their Freesurfer results for our team to analyze. Through this, we hope to
give them a clearer understanding of their condition, helping predict the
trajectory of their neurodegenerative disease more accurately.

With this in mind, we would like to invite your team to conduct an expert
class on Freesurfer for us. This class will surely boost our understanding
of the software and improve the efficiency and effectiveness of our work.

We sincerely hope this proposal interests you and aligns with your mission
to further knowledge and research in neuroscience. If so, we would be
delighted to discuss this further and provide you with any more details you
may need.

Thank you for considering our proposal. We look forward to the potential of
working together for a common goal.

Best regards,


*Pukovisa Prawiroharjo, M.D., Sp.N, Subsp. NGD (K), PhD*
Neurobehavior Consultant, Neurology Specialist
Neurology Department, Faculty of Medicine, Universitas Indonesia
Chair of Bioethics Cluster IMERI UI
Chair of International Policy Div, Board of Development Med Services IDI
___
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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] Calculate cortical thickness of a volumetric ROI

2023-07-14 Thread Carlos Alcocer 
External Email - Use Caution

Thank you for your response. If I wanted to calculate the surface area of
this cortical ROI, would i pass lh.area.pial into ? Do i still use
--accumulate flag?

Thank you,

Carlos

On Thu, Jun 15, 2023 at 5:17 PM Huang, Yujing 
wrote:

> External Email - Use Caution
>
> Hi Carlos,
>
>
>
> Your commands look correct to calculate mean cortical thickness.
>
>
>
> To calculate the total volume, pass lh.volume to –in <>, and specify
> –accumulate on the command line: *MailScanner has detected a possible
> fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1VurGVMn29VBCV4gEY-1urMHf0Tc2Q5K6l_Q9RtFkHSD4boTU7uMNAd9KSB9eY23wb5F5JkZVhaKJ0aehfz-K1kXaPch5YcDhLo5NOKxM_huiMH0dpH5Y2hnfxkP-WVuCU6m7-1MwV0y6qQNmYPwMr3GEaRVIbLjBKZY1ASWWOW-eS7P-SKIOQ4nJY7cm4rE-x8RdyQWmQZQ0GZkq8ZeS8dHvTUWQ7jhT3QK13LbHNncTYLUhxMjeydJBdlBjqGqG8bCjQ-hdGTadf6DXCo6Bn559C9L2HGyX4hX0oSp1WBQiKqRR7g5GiWpdZHJb_-ZB/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats
> 
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer
> *Sent:* Thursday, June 15, 2023 11:36 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Calculate cortical thickness of a volumetric ROI
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
> I am trying to calculate the cortical thickness of a volumetric ROI that I
> created that I have in subject space for every subject in my dataset. I was
> using *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1pXTMCre1AsCZTEIbgrEJaknmPI8CmxkcdA4Wms31XfrQ9ENPg5XK0K7sTORK5BoKjzRhCLOEl7f2o4k5zolqfiJGu4xLzdTBbsb07maqI0XVXkw4LfzMdpk3SGUrc2PWBF9e-LbCA4129qWNpBZNMpoI1267ojoE_RAylNZI1f6HwDLSSFlDZn2-fH02MtRk_Dw9qrx1HguntVrowlahx0zmqnjD8VZO4auFqCeUKkbpvZUE1opoJiGsMq0hcJpokWUHiCJB2FjGjH4k-m_qK6TsRHpfTVQ8Nce43QMsEP9uIE7hVI9G-v4inWZNV0OO/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness
> 
> as a guide.
>
> Since, I already have the volumes in subject space. I did a modified
> pipeline and only did the following for each subject:
> 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1
> --interp nearest --hemi lh --out lh.ROI5.mgh
> 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in
> lh.thickness --sum segstats-ROI5.txt
>
> Does this make sense? Also, separately, is the volume that is also
> computed in this method accurate? I noticed that the volume is always equal
> to the number of voxels, which I assume a voxel is equal to 1mm^3? However,
> when looking at aseg.stats these volumes have different values from their
> number of voxels.
>
> Thank you,
>
> Carlos
>
>
>
>
>
>
> ___
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>  <
>

Re: [Freesurfer] Can I use Freeview (tksurferfv) Tools on surface?

2023-07-14 Thread Fischl, Bruce R.,PHD 
External Email - Use Caution

Hi Andy
The zigzag comes because the lines have to connect vertices on the surface. How 
big is your rectangle? If it is pretty big I would think the zigzags would be 
relatively small (although still high-frequency since the vertices are about 
1mm apart). I don't think we have anything that will do exactly what you want, 
but coding something up to find every vertex inside a rectangle should be 
pretty easy in matlab or python

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andy Kim
Sent: Friday, July 14, 2023 8:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Can I use Freeview (tksurferfv) Tools on surface?


External Email - Use Caution
Dear FreeSurfer Developers,

Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine 
voxel draw" of ROI edit tool (MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1fXlyaExTk7SyGjd66N0GIhTs9XnixOU0mVN4qCljTWmf84reenHeQqK0xIUfcyJ0wtNJ5SBghh5Q1f1ndMOEn7O9mnXLdlaOoSoUsjh4rJ8aA_IyfHIw5MsdSqSJXMTRZMpt5Nxi9emnBjHmyl9PvlMu4yKJyS4laACkKGZf-Zt4F0B6Bs_dFWSD0ey8jLCgP3rBE2lJyfepZKoZvPORhFms5oQznMpxxGqP4_xgJs1fAfZfqh0c7uptaWfZNQ3M/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeviewGuide%2FFreeviewTools%2FRoiEdit).

On the other hand, unfortunately, it seems that it only works in 3d volume 
space.

So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make 
Closed Path". But this time, the vertices were not connected straight. The 
lines were zigzag.

Could you tell me how to draw a rectangular ROI with straight lines. 
Furthermore, if possible, could you explain how zigzag lines form?

Thank you in advance.

Kind Regards,
Andy (Junghyun) Kim
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[Freesurfer] Can I use Freeview (tksurferfv) Tools on surface?

2023-07-14 Thread Andy Kim 
External Email - Use Caution

Dear FreeSurfer Developers,

Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine 
voxel draw" of ROI edit tool 
(https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D8qAugBQR0S6zkInLYQn1Xl3TOY0oJFkbI6RPoALUmxV8oGNWxHym5WLqi_7QJGx6lX_2lR2STOnJi8s5vxdZ04_fp6b35pehxBr4-l3lWS9mctgTSjBy8AoiErcgueL8xMXgwARppZnFQsp5XATWNDB0WoToTsJF83bHPyUNGu6Y5lPXBkaByhwQCqmvt868YGR7krXkrVJxtOzaK6CXTOosaqrURervPHT_5_uQcCLb2pTXaSosaJebFrwRElEgl4lxY-KXxNejDq39JdB4yHXidLiBk2g2KtN7BJOhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeviewGuide%2FFreeviewTools%2FRoiEdit).

On the other hand, unfortunately, it seems that it only works in 3d volume 
space.

So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make 
Closed Path". But this time, the vertices were not connected straight. The 
lines were zigzag.

Could you tell me how to draw a rectangular ROI with straight lines. 
Furthermore, if possible, could you explain how zigzag lines form?

Thank you in advance.

Kind Regards,
Andy (Junghyun) Kim
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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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 .
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