Re: [Freesurfer] issue with mri_vol2surf

[Douglas N. Greve]

Those thresholds apply to both pos and neg. Eg, what you have there will 
show values between +0.1 and +250 AND between -0.1 and -250. It appears 
that you don't have any negative values in that map


On 11/22/2023 1:34 PM, Atena Akbari wrote:


External Email - Use Caution

Screenshot 2023-11-22 at 1.32.53 PM.png
 doesn't allow me to adjust the threshold to negative values, for 
example t-values between -3 and 3.


On Wed, Nov 22, 2023 at 1:26 PM Douglas N. Greve 
 wrote:


Have you tried adjusting the threshold. Open the configure overlay
option. Also, sending a pic would be helpful (and the contents of
tk.dat)

On 11/22/2023 11:29 AM, Atena Akbari wrote:


External Email - Use Caution

Dear freesurfer team,

I want to overlay the activation map that I got from SPM on the
inflated surface. The command I use is:


"mri_vol2surf    --mov    spmT_funcmap.nii     --ref
 subj01/mri/orig.mgz.   --reg    tk.dat --hemi rh   --o   
flodername"


in which, I got the registration file (tk.dat) by aligning my
functional mean image to the orig.mgz in tkregisterfv.


now the problem is when I overlay the activation map on the
inflated surface, I can only see the voxels with positive
t-values. I can't see the negative ones. I cannot change the
threshold values provided by "configure overlay" to negative
values. Also, changing the "z-score" option next to the overlay
configuration doesn't make any difference. can you help me with
this, please?


Thanks a lot,

Atena


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
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
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline


<*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline

>
.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://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
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 

Re: [Freesurfer] issue with mri_vol2surf

[Atena Akbari]

External Email - Use Caution

[image: Screenshot 2023-11-22 at 1.32.53 PM.png]
 doesn't allow me to adjust the threshold to negative values, for example
t-values between -3 and 3.

On Wed, Nov 22, 2023 at 1:26 PM Douglas N. Greve 
wrote:

> Have you tried adjusting the threshold. Open the configure overlay option.
> Also, sending a pic would be helpful (and the contents of tk.dat)
>
> On 11/22/2023 11:29 AM, Atena Akbari wrote:
>
> External Email - Use Caution
> Dear freesurfer team,
>
> I want to overlay the activation map that I got from SPM on the inflated
> surface. The command I use is:
>
>
> "mri_vol2surf--mov spmT_funcmap.nii --ref
>  subj01/mri/orig.mgz.   --regtk.dat--hemi rh   --oflodername"
>
>
> in which, I got the registration file (tk.dat) by aligning my
> functional mean image to the orig.mgz in tkregisterfv.
>
>
> now the problem is when I overlay the activation map on the inflated
> surface, I can only see the voxels with positive t-values. I can't see the
> negative ones. I cannot change the threshold values provided by "configure
> overlay" to negative values. Also, changing the "z-score" option next to
> the overlay configuration doesn't make any difference. can you help me with
> this, please?
>
>
> Thanks a lot,
>
> Atena
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1IVPIDMFljkbz03OWhhpL1VpAXdX7qCtOHbekm0TiQFRGhN6pDQSWMYqFMIg11x7H0RSn55S0mPKkcGBfgShDP4Fa1uJGvv471Pu7A3lvXY03naNTsfXmoVy1gE75cKQsOU0JolHEvTZQ3RUy7NKl6mob802-R1J8lHPmdpAQYi8cQ3IuOzLsR7uoWqjzINd7rLry7o93NtTv6gI3CLqN56QnaJcTM6r_bPY3Czb-f2QMJgOiuggpckVZTpsW64nmItJn9SxHgNbqNY5y0WuNE70ew-iq046b_Nmg3mcrOETzh0FFrIfOoB8WpO-XAzFGos3eBKRHQX9CCRxPvioOKQ/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 contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1P0Nb7TleS5WyZJu-srhx4FTx8V-yKXC6caZoWiHRciFkMiTVRveY3mckTiQUbHyEwZtJAVyJmSBir2L6fG6yYUf-k_NFt2fIsgZzvmwM6PeQW36670jLmpRz3oA_L4sG8F1pSfLtwUfXT6xVGaJ2pYQnsDNox5aT51A9Syuc7cXoLW5P0yL5XthqjTdONXbgHCI9wZi6d57x9CG6s06kCl0Boja8N7t8IokkeDCdtMnqEpALkfA3qc2c04ekb8RLkU5F36hYO1S2-nyiZXyZIsM0dfNB46yd1jAALCmh1bAFAnToieKOT-eucGl9bFRgfxziMWp30ZUGffcOJvN5-A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1P0Nb7TleS5WyZJu-srhx4FTx8V-yKXC6caZoWiHRciFkMiTVRveY3mckTiQUbHyEwZtJAVyJmSBir2L6fG6yYUf-k_NFt2fIsgZzvmwM6PeQW36670jLmpRz3oA_L4sG8F1pSfLtwUfXT6xVGaJ2pYQnsDNox5aT51A9Syuc7cXoLW5P0yL5XthqjTdONXbgHCI9wZi6d57x9CG6s06kCl0Boja8N7t8IokkeDCdtMnqEpALkfA3qc2c04ekb8RLkU5F36hYO1S2-nyiZXyZIsM0dfNB46yd1jAALCmh1bAFAnToieKOT-eucGl9bFRgfxziMWp30ZUGffcOJvN5-A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


tk2.dat
Description: Binary data
___
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] issue with mri_vol2surf

[Douglas N. Greve]

Have you tried adjusting the threshold. Open the configure overlay 
option. Also, sending a pic would be helpful (and the contents of tk.dat)


On 11/22/2023 11:29 AM, Atena Akbari wrote:


External Email - Use Caution

Dear freesurfer team,

I want to overlay the activation map that I got from SPM on the 
inflated surface. The command I use is:



"mri_vol2surf    --mov  spmT_funcmap.nii     --ref    
 subj01/mri/orig.mgz.  --reg    tk.dat    --hemi rh   --o    flodername"



in which, I got the registration file (tk.dat) by aligning my 
functional mean image to the orig.mgz in tkregisterfv.



now the problem is when I overlay the activation map on the inflated 
surface, I can only see the voxels with positive t-values. I can't see 
the negative ones. I cannot change the threshold values provided by 
"configure overlay" to negative values. Also, changing the "z-score" 
option next to the overlay configuration doesn't make any difference. 
can you help me with this, please?



Thanks a lot,

Atena


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://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
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] issue with mri_vol2surf

[Atena Akbari]

External Email - Use Caution

Dear freesurfer team,

I want to overlay the activation map that I got from SPM on the inflated
surface. The command I use is:


"mri_vol2surf--mov spmT_funcmap.nii --ref
 subj01/mri/orig.mgz.   --regtk.dat--hemi rh   --oflodername"


in which, I got the registration file (tk.dat) by aligning my
functional mean image to the orig.mgz in tkregisterfv.


now the problem is when I overlay the activation map on the inflated
surface, I can only see the voxels with positive t-values. I can't see the
negative ones. I cannot change the threshold values provided by "configure
overlay" to negative values. Also, changing the "z-score" option next to
the overlay configuration doesn't make any difference. can you help me with
this, please?


Thanks a lot,

Atena
___
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] Issue with mri_vol2surf nearest interpolation

[Douglas N. Greve]

   External Email - Use Caution


Can you send the full terminal output?

On 8/4/2023 1:20 PM, Sun, Wendy wrote:


External Email - Use Caution

Good afternoon,
We are encountering an issue with getting non-integer values (input 
file has all integers) when using the “nearest” interpolation method 
in mri_vol2surf. Here is the command we ran:


mri_vol2surf --mov ${anatIn} --regheader ${REG} --hemi lh --projfrac 
0.5 --trgsubject fsaverage6 --o $Limg --reshape --interp nearest


The input file ${anatIn} has values ranging from 0 to 255 and are all 
integers. The ${REG} folder is created during recon-All.


We expected the output to be all integers, given the interpolation 
method, but we see non-integer values.


Do you know why this is the case and how to fix it?

Thank you,
Wendy

—
Wendy Sun
Graduate Student, Buckner Lab
PD Soros Fellow, 2020
Cambridge Integrated Clerkship 18
MD/PhD Candidate, HMS


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1eG2biXfg571B4PRL1u2qDkuLk5HGeAnHaQSH4ZHETJskNncqXqOZN8RKLlFpvt-uKkLwR_wLiLKTQWvTvlYKWOJctX4mRUWgM8I9byk9xyLm11EgXwDFaavCtCH2Av6OC5ZugwJCsJnbCmPwrE8EeRVZyT_b1j-X4ru8dtaw2GCUYMp_b_mE4P_FReqlpuhKvbWsFDMdnzCsd4QysvjrOOamZWzPQsedcAneSGqSLlsTR3eYVMPgHa1iWg4oYn0TBnVeVLiXUGG9InmOiuPS4Q/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] Issue with mri_vol2surf nearest interpolation

[Sun, Wendy]

External Email - Use Caution

Good afternoon,
We are encountering an issue with getting non-integer values (input file has 
all integers) when using the “nearest” interpolation method in mri_vol2surf. 
Here is the command we ran:

mri_vol2surf --mov ${anatIn} --regheader ${REG} --hemi lh --projfrac 0.5 
--trgsubject fsaverage6 --o $Limg --reshape --interp nearest

The input file ${anatIn} has values ranging from 0 to 255 and are all integers. 
The ${REG} folder is created during recon-All.

We expected the output to be all integers, given the interpolation method, but 
we see non-integer values.

Do you know why this is the case and how to fix it?

Thank you,
Wendy

—
Wendy Sun
Graduate Student, Buckner Lab
PD Soros Fellow, 2020
Cambridge Integrated Clerkship 18
MD/PhD Candidate, HMS

___
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.