Re: [Freesurfer] Flipping Thickness Matrices

2023-03-22 Thread Wighton, Paul 
Hi Anam

Sorry for the lag.  mris_left_right_register takes as input surfaces, not the 
overlays or thicknesses.

To flip an overlay file, here is what I would do.  Maybe others can chime in on 
weather this makes sense or if there is an easier way.  

I'd start by running mris_left_right_register.  Then, I would use read_surf.m 
to load in the original, and registered surfaces, eg lh.right and 
lh.sphere.left_right.  Then, I would go through each vertex in lh.right and 
find the corresponding (or closest) vertex in lh.sphere.left_right.  This 
correspondence will define a mapping you could then apply to the overlays.

-Paul


From: Anam Anzak 
Sent: Wednesday, March 15, 2023 3:52 AM
To: Wighton, Paul; Freesurfer@nmr.mgh.harvard.edu
Cc: Bernardo Pimentel
Subject: Re: Flipping Thickness Matrices

External Email - Use Caution

Dear Paul,

Thank you for your reply! Just one thing we haven't really figured out... does 
mris_left_right_register take as input the thickness (mgh) files or the 
surfaces? I've been trying but can't really apply it to the thickness files. In 
theory, we would really just like to flip the thickness matrix right->left... 
is mris_left_right_register something we should apply upstream of the thickness 
file generation?

Thank you and all the best,
Bernardo and Anam

--
Bernardo Pimentel
Neurology Resident
Department of Neurology - Christian-Doppler University Hospital
Paracelsus Medical University
Salzburg, Austria

Miss Anam Anzak MBBS PhD MRCS PGCCE
NIHR Clinical Lecturer (Neurosurgery)
Specialty Registrar in Neurosurgery, London deanery

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

Sent: 07 March 2023 21:31
To: Freesurfer@nmr.mgh.harvard.edu 
Cc: Bernardo Pimentel 
Subject: Re: [Freesurfer] Flipping Thickness Matrices

Hi Anam,

Check out mris_left_right_register.  It's not super well documented, but it 
takes as input the right and left hemispheres, inflated onto a sphere, and 
outputs the left hemisphere registered to the right and the right hemisphere 
registered to the left, also inflated onto a sphere.

If you'd like to do this in matlab, perhaps looking at the code for 
mris_left_right_regsiter would help
https://github.com/freesurfer/freesurfer/blob/dev/mris_left_right_register/mris_left_right_register.cpp

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Anam Anzak 

Sent: Tuesday, March 7, 2023 4:00 PM
To: Freesurfer@nmr.mgh.harvard.edu
Cc: Bernardo Pimentel
Subject: [Freesurfer] Flipping Thickness Matrices

External Email - Use Caution

Dear FreeSurfer Community,

Has anyone had any success with solving the below problem:

I am dealing with brain lesions which may present on the left or right 
hemisphere of the brain.


  1.  I wish to 'FLIP' RIGHT sided hemispheres (which contain lesions) to the 
LEFT side, so I ultimately can collate all my data and analyse brain 
hemispheres that are IPSILATERAL or CONTRALATERAL to the side of the brain 
lesion.
  2.  When I use the Flip function below, the matrix generated seems to be 
correct, HOWEVER the subsequent IMAGE generated from the matrix, appears 
incorrect (it is not at all a mirror image of the original image).
  3.  NOTE: My matrices include a Lesion Mask and a Medial Wall Mask (I am 
interested in examining Cortical Thickness values of all the cortex EXCEPT the 
lesion and medial wall (tentorium and ventricles etc).

Here are the commands used, for eg. 'subject 1':


%% 4b. Load the binary Lesion masks RIGHT


right_lesion_filelist= strcat(P, '/Oedema_masks_bin/', Imaging_Code, 
'_rh_fsaverage5_bin.mgh');


% load RIGHT lesion masks into a matrix

right_lesions   = SurfStatReadData([right_lesion_filelist]);
right_lesions = ~right_lesions;

% create a left hemisphere matrix filled with 1s
left_hemisphere = ones(17,10242)

% concatenate horizontally lesions masks (L) with right hemisphere matrix
fullbrain_with_right_lesions = horzcat(left_hemisphere, right_lesions)

% create medial wall mask for all subjects
r_whole_mask = repmat(mask, 17, 1)


% add the medial wall mask on the lesion masks

fullbrain_lesion_medialwall = fullbrain_with_right_lesions.*r_whole_mask

% apply matrix with lesion & medial wall to the thickness values
T_right = fullbrain_lesion_medialwall .* T_rightlesion

%% Flip the Right sided images to the left

% reverse the element in each row
subject1 = T_rig

[Freesurfer] Open Postdoctoral Positions in the Neuroscience of Meditation at Harvard/MGH

2023-03-22 Thread Eckman, Megan 
Dear Colleagues,

Research Fellow/postdoctoral positions are available in the Meditation Research 
Program at Harvard Medical School and Mass General in Boston, MA.

The successful candidate(s) will develop the neuroscience of advanced 
meditation using cutting-edge neuroimaging/electrophysiology. Please see the 
full description and instructions for applying 
here.

Please feel free to forward this announcement to anyone who may be interested.

Kind regards,

Megan


Megan Eckman (she/her)
Program Manager, Meditation Research Program, Massachusetts General Hospital
W​ebsite: https://meditation.mgh.harvard.edu
Email: meck...@mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
CNY Building #149
149 13th St., Charlestown, MA 02129-4522

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[Freesurfer] Intracranial electrode visualization in Freeview

2023-03-22 Thread Kerezoudis, Panagiotis, M.D., M.S. 
External Email - Use Caution

Hi,

I have completed the Freesurfer segmentation and parcellation in a patient that 
has intracranial electrodes.

I also have the electrode locations in various file formats (tsv, nii and pom).

Is there a way to visualize their location in Freeview and particularly in 3D?
For example, for 2D I can easily do that with microGL.

Thank you very much in advance!

Best,
Panos Kerezoudis
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[Freesurfer] the virtual machine RE: Password ubuntu password

2023-03-22 Thread Zhao, Don 
External Email - Use Caution

"login as the user "developer" in the login menu. Get the password by sending 
an email request to the freesurfer help list."
Hi, freesurfer help list.
May I have the password, please?
Thanks,
Don
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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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] Password ubuntu password

2023-03-22 Thread Zhao, Don 
External Email - Use Caution

I have followed the virtual machine setup for virtual box freesurfer 
installation; but it ask me the password for the developer account.
Which is the password?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bartlett, Rob
Sent: Wednesday, March 22, 2023 10:06 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault

[[***CAUTION*** This email originated from outside of Messiah University]]

External Email - Use Caution
I get the same error when trying to open any files with the .mgz extension that 
I have tried so far.


Kind regards,

Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://secure-web.cisco.com/171EG5Xbe71Hukd6GqPyZPvblqCEeoxzcg1EjZPHtSfNSxcrF_ary5F2DoFbVUYU1_MSzwS5v9rvsmWzXqslw7lirGPduR5HFRTdGWd4jiS1FbKYuFuLx3XZxzuqmddYK9gYH0-jf5mnT3uFnude2WmZuUkaGlUDiN3Nv1jAtb_G_Dlp9MRg_l72REi3idAej-HfHGJWzboPXPEvURKZKrOBTSlLXm6k9VZcrXiC82NQJ_I1FOz-WYIDARiaKvwUMvpXLATOr0uZurhCI9jpEguWYCOA85QnJJzgvU8mUMlbFv5Nws_iGEqiNor6JdmWGIEzmaEeu-z2FKmIQQxh4jg/http%3A%2F%2Fwww.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: 22 March 2023 13:38
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Have you tried loading a different volume in the same folder? Such as 
brain.mgz. Will you get the same error?


On Mar 22, 2023, at 6:50 AM, Bartlett, Rob 
mailto:r.bartle...@exeter.ac.uk>> wrote:

External Email - Use Caution
Hi Bruce,

No problem, thanks for getting back to me quickly.

Here is the output of -l against the file:

brainmask.mgz
-rw-rw-rw- 1 rob rob 1363253 Sep 30  2018 brainmask.mgz



Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://secure-web.cisco.com/171EG5Xbe71Hukd6GqPyZPvblqCEeoxzcg1EjZPHtSfNSxcrF_ary5F2DoFbVUYU1_MSzwS5v9rvsmWzXqslw7lirGPduR5HFRTdGWd4jiS1FbKYuFuLx3XZxzuqmddYK9gYH0-jf5mnT3uFnude2WmZuUkaGlUDiN3Nv1jAtb_G_Dlp9MRg_l72REi3idAej-HfHGJWzboPXPEvURKZKrOBTSlLXm6k9VZcrXiC82NQJ_I1FOz-WYIDARiaKvwUMvpXLATOr0uZurhCI9jpEguWYCOA85QnJJzgvU8mUMlbFv5Nws_iGEqiNor6JdmWGIEzmaEeu-z2FKmIQQxh4jg/http%3A%2F%2Fwww.exeter.ac.uk

Re: [Freesurfer] FreeSurfer Segmentation Fault

2023-03-22 Thread Bartlett, Rob 
External Email - Use Caution

I get the same error when trying to open any files with the .mgz extension that 
I have tried so far.


Kind regards,

Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/11On7gOdpigOmuygGY56ARMyr9yhP1a_j0p5BeqsZ8OgvVK-3VeBdHzPQkU6g6AujIrlnLXENFNv33eJR93kF6_oY-MKMU9CBIINa3IbasV9RXGSdkS_BVb1aF6cDi6skhqk-2IyXHCwiQ_oZ5N-049leIYaTit-UBX9z9Wljy-qpV1GGIubV17gP648dTQZhNM68P9P6sLmzXi9c2qgemjhciaXuckwIKSChzuICAVox6-l7AepcvApDgBiyBQYWiMbluf9EeKsDQxjhwqQl39klW1L-aZtHSyRNPZ3Ds_9RKAPtlrqRLhyaL7ks1GxgR3wYZ6EEevwN5QPIHIYkOw/http%3A%2F%2Fwww.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wang, Ruopeng 

Sent: 22 March 2023 13:38
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Have you tried loading a different volume in the same folder? Such as 
brain.mgz. Will you get the same error?

On Mar 22, 2023, at 6:50 AM, Bartlett, Rob 
mailto:r.bartle...@exeter.ac.uk>> wrote:

External Email - Use Caution

Hi Bruce,

No problem, thanks for getting back to me quickly.

Here is the output of -l against the file:

brainmask.mgz
-rw-rw-rw- 1 rob rob 1363253 Sep 30  2018 brainmask.mgz


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://secure-web.cisco.com/11On7gOdpigOmuygGY56ARMyr9yhP1a_j0p5BeqsZ8OgvVK-3VeBdHzPQkU6g6AujIrlnLXENFNv33eJR93kF6_oY-MKMU9CBIINa3IbasV9RXGSdkS_BVb1aF6cDi6skhqk-2IyXHCwiQ_oZ5N-049leIYaTit-UBX9z9Wljy-qpV1GGIubV17gP648dTQZhNM68P9P6sLmzXi9c2qgemjhciaXuckwIKSChzuICAVox6-l7AepcvApDgBiyBQYWiMbluf9EeKsDQxjhwqQl39klW1L-aZtHSyRNPZ3Ds_9RKAPtlrqRLhyaL7ks1GxgR3wYZ6EEevwN5QPIHIYkOw/http%3A%2F%2Fwww.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Sent: 21 March 2023 18:52

Re: [Freesurfer] FreeSurfer Segmentation Fault

2023-03-22 Thread Wang, Ruopeng 
Have you tried loading a different volume in the same folder? Such as 
brain.mgz. Will you get the same error?

On Mar 22, 2023, at 6:50 AM, Bartlett, Rob 
mailto:r.bartle...@exeter.ac.uk>> wrote:

External Email - Use Caution

Hi Bruce,

No problem, thanks for getting back to me quickly.

Here is the output of -l against the file:

brainmask.mgz
-rw-rw-rw- 1 rob rob 1363253 Sep 30  2018 brainmask.mgz


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
www.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Sent: 21 March 2023 18:52
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Oh, sorry, should have read to the end of my inbox before responding.  What 
does ls -l show for that file?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 12:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault



External Email - Use Caution
Hi Ruopeng,



This is the command I have been using: freeview 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz



I get the same result when I open freeview and select the volume through the 
GUI.



Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
www.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_S_Mlgb7T3r_w0vxOAw4p78Yx8KkNV9hz4nzEpYmRyBSC0rItAr094f0ftSA4TDMuQXIXnXKSC2TFWnfEOuB5c2DMw8w-BKhQvV2SUUojLRHK9zByMvvmDZl27FP5JnBEUT-E6ZKCbWZfq0We5LG8f4V47lL8NK8MtFmfHGji9h22vnsQxOrUV8sP3hKRQHEXm4u-BH_xZiFoh09oumIHv2E8NuO-9MiJiL2GaK6MhmNu3MyoOtAMdv13SGVsZ_CNa1BBzjLcrlDP6npzevH55ZtmHFALKXugbpJ2U4A/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
attachments immediately. The University will not accept responsibility for the 
accuracy/completeness of this email and its attachments.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Tuesday, March 21, 2023 1:35 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer]

Re: [Freesurfer] FreeSurfer Segmentation Fault

2023-03-22 Thread Bartlett, Rob 
External Email - Use Caution

Hi Bruce,

No problem, thanks for getting back to me quickly.

Here is the output of -l against the file:


brainmask.mgz

-rw-rw-rw- 1 rob rob 1363253 Sep 30  2018 brainmask.mgz



Kind regards,

Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/1yutBkt5hXhgLKg69R5m3lB60Vj9CohXvvYObck-pTgGNEaDA2-3a9UaPwvspO5Su0Ul-G0w_teCqMbsv_um9Z5yBX6vK6k7uaydp2-NH642Od-uJRrVkPKMGmaGKKquSi7Lnt1uGd5DcGoISePP0PYKv-8ZndKX8EZqpgdC-i6_y4xKPABD9i_Z0KURH2C7--Tf42G8KDjjjIFxRp5xPHb7dyCS5MD-8VDKAgT_DNukIo4g9KsebNEMom57Z5_H-H0qgkZLBSLQHP_omhmzpiy2DzpDl0Cwk0fprWCkLosa9Hsub3F3P5ekTEhuQXStD/http%3A%2F%2Fwww.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce R.,PHD 

Sent: 21 March 2023 18:52
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.


Oh, sorry, should have read to the end of my inbox before responding.  What 
does ls -l show for that file?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 12:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault



External Email - Use Caution

Hi Ruopeng,



This is the command I have been using: freeview 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz



I get the same result when I open freeview and select the volume through the 
GUI.



Kind regards,

Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/1yutBkt5hXhgLKg69R5m3lB60Vj9CohXvvYObck-pTgGNEaDA2-3a9UaPwvspO5Su0Ul-G0w_teCqMbsv_um9Z5yBX6vK6k7uaydp2-NH642Od-uJRrVkPKMGmaGKKquSi7Lnt1uGd5DcGoISePP0PYKv-8ZndKX8EZqpgdC-i6_y4xKPABD9i_Z0KURH2C7--Tf42G8KDjjjIFxRp5xPHb7dyCS5MD-8VDKAgT_DNukIo4g9KsebNEMom57Z5_H-H0qgkZLBSLQHP_omhmzpiy2DzpDl0Cwk0fprWCkLosa9Hsub3F3P5ekTEhuQXStD/http%3A%2F%2Fwww.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE

[http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_S_Mlgb7T3r_w0vxOAw4p78Yx8KkNV9hz4nzEpYmRyBSC0rItAr094f0ftSA4TDMuQXIXnXKSC2TFWnfEOuB5c2DMw8w-BKhQvV2SUUojLRHK9zByMvvmDZl27FP5JnBEUT-E6ZKCbWZfq0We5LG8f4V47lL8NK8MtFmfHGji9h22vnsQxOrUV8sP3hKRQHEXm4u-BH_xZiFoh09oumIHv2E8NuO-9MiJiL2GaK6MhmNu3MyoOtAMdv13SGVsZ_CNa1BBzjLcrlDP6npzevH55ZtmHFALKXugbpJ2U4A/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]

This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
attachments immediately. The University will not accept responsibility for the 
accuracy/completeness of this email and its attachments.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Tuesday, March 21, 2023 1:35 PM
To: Freesurfer support list 
mailto:freesurfer