Re: [Freesurfer] registration error (reCAPTCHA not checked)

2023-09-06 Thread lizhao...@sjtu.edu.cn 
External Email - Use Caution

Thanks for the quick reply. 
I have tried my mac mini (safari), windows workstation (chrome), windows server 
(edge), and ubuntu server (firefox) to get the license. 
Yet it all turned out with a captcha error. 


Best!
Lizhao Du
 
School of Biomedical Engineering, Shanghai Jiao Tong University
lizhao...@sjtu.edu.cn 
 
From: fsbuild
Date: 2023-09-07 09:04
To: freesurfer
Subject: Re: [Freesurfer] registration error (reCAPTCHA not checked)
External Email - Use Caution
 
The captcha authentication will not work if javascript is blocked from running 
in your browser.  Check that you browser preferences are not set to 
block/filter javascript in its preferences and/or by using some added browser 
extension.  I’m not aware that a firewall enabled on your machine or your ISP 
would otherwise block javascript from running.

If your current browser does not work, you could do a clean install of some 
browser you do not currently have installed on your machine (w/o changing its 
default preference settings).   Choices for chrome based browsers you might not 
already have installed could be Vivaldi or Opera.  You could search for 
"download Vivaldi" or "download Opera" and go directly to that vendors web site 
and download the installer.

- R.


On Sep 6, 2023, at 09:21, lizhao...@sjtu.edu.cn wrote:

External Email - Use Caution

Hi there, 
I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A 
license is required yet I could not get the 
license.txt from my e-mail. After filling the form from MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/registration.html, a registration 
error occured (see below).  Is there something wrong for my internet? Or what 
could I do to get the license? 
A few words from you may help me a lot. Thanks in advance.





Best!
Lizhao Du

 
School of Biomedical Engineering, Shanghai Jiao Tong University
lizhao...@sjtu.edu.cn 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1FO75jIzaXoep6Jr9JaHJXvbKjlrdF9T606BGLeD4Rrt00hguLh7GiIg2yzEbT9eaECmZCcrav5MQujpYF0ranH4yZLTBtBln-dKMud8O4ar9M4r5ZrjuvkM-ORVYT1rGm-qjN0jg8e801JOYEuFnkD-h0ge9cr4AOD3I_ZJjAJUqMzL8WPBYatP5HN4fwfVlYfrmkACudNAWjs4b69sAfT3FDnGaK3SDvo0nc7wlKXb4usVqyI_0iGLm5pybo7CQeOTQqG92NR72zZuPX5ZgbHy64ONEGZkHKR1XGPGUYbBdZ5j6L2dZmV0b18u5q61U/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] registration error (reCAPTCHA not checked)

2023-09-06 Thread fsbuild 
External Email - Use Caution

 The captcha authentication will not work if javascript is blocked from 
running in your browser.  Check that you browser preferences are not set 
to block/filter javascript in its preferences and/or by using some added 
browser extension.  I’m not aware that a firewall enabled on your machine 
or your ISP would otherwise block javascript from running.
If your current browser does not work, you could do a clean install of some 
browser you do not currently have installed on your machine (w/o changing its 
default preference settings).   Choices for chrome based browsers you 
might not already have installed could be Vivaldi or Opera.  You could 
search for "download Vivaldi" or "download Opera" and go directly to that 
vendors web site and download the installer.
- R.

On Sep 6, 2023, at 09:21, lizhao...@sjtu.edu.cn 
wrote:External Email - Use 
CautionHi there,   
  I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A 
license is required yet I could not get the license.txt from my e-mail. 
After filling the form from MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/registration.html, a 
registration error occured (see below).  Is there something wrong for 
my internet? Or what could I do to get the license?     A few 
words from you may help me a lot. Thanks in 
advance.Best!Lizhao 
Du School of Biomedical Engineering, Shanghai Jiao Tong universitylizhao...@sjtu.edu.cn ___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
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.

[Freesurfer] freesurfer data analysis and visualization

2023-09-06 Thread Pukovisa Prawiroharjo 
External Email - Use Caution

anyone have suggestion data visualization from freesurfer volumetric.
i need visualization of 2 volume before and after of the same individual
patient and between 2 groups in a research. i've found some paper use
pysurfer, anyone have other suggestions and tutorioal / reading and code
about how to use those ?

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

2023-09-06 Thread Iglesias Gonzalez, Juan E. 
External Email - Use Caution

Thanks for the interest in our work, Anton!
We don’t have a template in MNI space, sorry (it’s on the to-do list, but 
buried among many other items). But you can always segment the template with 
the atlas 😃
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1g6gun1nsf1mJ716coy3hC0-u-AbQGpxPhF54AmyF1MXqwLGsXL6lOU88WkafhE45WQjr5dBsIqHgNNZLIeXnankF0J8iSvDybiJJcUgaL1RJqirBI9sopHaCw8Ikx9FExl1zvnifC08PA_PiIog5ne79NQQtTTCz0RzVJ8zQ04RI3KWmOVy7PQM5SnbatgBHz__sIJIvKp1A1_0V0rlv9E2UGBtGQTmsDVv1D6T1ATU1I4wHMoPGPOMOVYJIzU-XzAcf58Ei41kQpa3Uu_knYA/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Dr. Anton Jakovcic 

Date: Wednesday, September 6, 2023 at 10:10 AM
To: freesurfer 
Cc: Seyma Bayrak 
Subject: [Freesurfer] FreeSurfer hippo-amygala module
External Email - Use Caution

Dear all,

here is Anton - a PhD candidate from Max Planck Institute for Human Cognitive 
and Brain Research in Leipzig, Germany.

Using FreeSurfer module segment_subregions, I successfully segmented amygdala 
for individual HCP subjects. Thanks a lot for developing it!

Currently, I am trying to get a group-level or a MNI-level segmentation to 
build a representative figure.
Do you think, is it possible to segment amygdala in MNI-registration template?
Any help/suggestion is appreciated.

Kind regards
Anton Jakovcic

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/15IKvTflStKRntjxa_pEzE-1YbPTVajzeFFSGFUaS63YChriz8tAZ1yjlQylfCegrU5SE_Oehtt93JpsweNM2tYb0qkNncoxjoKtTmJmW6RTQusK_rtzpm6-LrALxhOP0Z6t3yl8g1WFY1gNHEnlsJIMXpNqMiL_rNV_PRlKc-DMY4cjdNmUR__M_HRf9N0t4JmloX0ltQP0Gem5n1cp1AE52FQz7qt3Aeu1SNeMTEaHbCcIDVvaLB7xXPh1Nz-YolSKm2_Nvf5tqcRGlB1GGdw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
___
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.

[Freesurfer] keep T1w matrix size during recon-all (without zero-padding)

2023-09-06 Thread Rona Haker 
External Email - Use Caution

Hi,
Can recon-all be performed without zero-padding the final matrix aparc+aseg
in order to keep the original T1w matrix size?
This will greatly help me in further analyses.
Thank you!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.

[Freesurfer] FreeSurfer hippo-amygala module

2023-09-06 Thread Dr. Anton Jakovcic 
External Email - Use Caution

Dear all,

here is Anton - a PhD candidate from Max Planck Institute for Human Cognitive 
and Brain Research in Leipzig, Germany.

Using FreeSurfer module segment_subregions, I successfully segmented amygdala 
for individual HCP subjects. Thanks a lot for developing it!

Currently, I am trying to get a group-level or a MNI-level segmentation to 
build a representative figure.
Do you think, is it possible to segment amygdala in MNI-registration template?
Any help/suggestion is appreciated.

Kind regards
Anton Jakovcic

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] converting preprocessed surface functional data to volume

2023-09-06 Thread wangzhiwei3233 
External Email - Use Caution



Dear Doug,
Thank you for your replying.
I collected the data by myself using a SIEMENS machine. Sorry, what do you mean 
by mapping the time course.  I guess I am not trying to do that. I would like 
to do beta series analysis.
I used the command in its old way, and I mapped it to 2mm template. It is OK 
now. The time and space are both acceptable. The code is as follows, I will 
really appricate it if you can help me to check the code.


mri_surf2vol --hemi ${hemi} --o 
${ROOTDIR}/$isub/bold/${irun}/spmRibbon${hemi}/${iVolume} --projfrac 0 
--fillribbon  --template ${SUBJECTS_DIR}/fsaverage/mri.2mm/brain.mgz \
--reg  ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat --surfval 
${ROOTDIR}/$isub/bold/${irun}/spm${hemi}/${iVolume}


Best,
Zhiwei


>Message: 5
>Date: Sun, 20 Aug 2023 17:23:52 -0400
>From: "Douglas N. Greve" 
>Subject: Re: [Freesurfer] converting preprocessed surface functional
>   data to volume
>To: freesurfer@nmr.mgh.harvard.edu
>Message-ID: 
>Content-Type: text/plain; charset="utf-8"
>
>External Email - Use Caution
>
>where did the functional data come from? Are you trying to map the time 
>courses? That usually does not work that well as your resulting image 
>will be huge. One thing to do is to map it to a cropped volume (most of 
>the 256^3 is outside the brain) and or also map it to 2mm instead of 1mm.
>
>On 8/13/2023 11:02 PM, wangzhiwei3233 wrote:
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer experts,
>> I am going to convert the preprocessed surface functional data to 
>> volume in fsaverage space so that I can used the processed data in SPM 
>> for further analysis, for example, beta series analysis. I tried 
>> mri_surf2vol, it worked. But it is time consuming. It takes around 5 
>> minutes per 10 volumes. In addition, the result volume is too big 
>> (67MB/ volume for 256*256*256 matrix, 1mm resolution). My data 
>> contains about??70800 brain volumes, so the needed time is about 
>> 40days and the storage space is about 7TB , which is unacceptable. The 
>> code is? as follows:
>>
>> /mri_surf2vol --o 
>> ${Dir_Subj_fMRI}/$isub/bold/${irun}/Ribbon/${iVolume} --subject 
>> fsaverage --so ${SUBJECTS_DIR}/fsaverage/surf/lh.white 
>> ${Dir_Subj_fMRI}/$isub/bold/${irun}/LH/${iVolume} --so 
>> ${SUBJECTS_DIR}/fsaverage/surf/rh.white 
>> ${Dir_Subj_fMRI}/$isub/bold/${irun}/RH/${iVolume} /
>> /
>> /
>> Are there methods with faster speed and outputing volumes with lower 
>> resolution?
>>
>> Best,
>> Zhiwei

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

[Freesurfer] registration error (reCAPTCHA not checked)

2023-09-06 Thread lizhao...@sjtu.edu.cn 
External Email - Use Caution


Hi there, 
I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A 
license is required yet I could not get the 
license.txt from my e-mail. After filling the form from 
https://secure-web.cisco.com/174jctt4T-x9hrxRO4K0cJXM-oWXh3mvxRN7Dqptum9XXFmAROsUsZNANm3rE31_EYYEeP3ioEgVxt5jyzH4G3YuFL-a4JyQFIgEw_MwifteHFzhX6f8f1OPmnGqrAGxnHCkaXkm725sK9F3nMA4hNpdOaBYezP-2CF4da5cNKejE1Enb4TJeQMB_sjOKnACpyXjrAZN8tAFZiBueOe2NqK8rLeVojEkfZRHkz02wLFB6T6BhM6VuorrhnYB23Chdvo13jIh_O0lDFUfJDxFUNk433T1qafXWyIOMIm8jZaeRMA7Tsg3l4sQUVqp4BUiJjNgGdp4IRi8h-XwaFXcCSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html,
 a registration 
error occured (see below).  Is there something wrong for my internet? Or what 
could I do to get the license? 
A few words from you may help me a lot. Thanks in advance.




Best!
Lizhao Du
 
School of Biomedical Engineering, Shanghai Jiao Tong University
lizhao...@sjtu.edu.cn 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.