[Freesurfer] overlay activation map on flattened surface

2024-02-22 Thread Atena Akbari 
External Email - Use Caution

Hello Freesurfer team,

I have flattened the occipital patch using "mris_flatten -w 10
subj04/surf/lh.occip.patch.3d subj04/surf/lh.occip.flattened" and it worked
without any error and I can load the flattened patch in freeview. However, I
have difficulty overlaying the activation map onto the flattened surface.
Is the following command correct for this purpose?
(mri_vol2surf --mov   spmT_0001.nii --out  subj04/surf/lh.bold.flat.mgz
 --reg  fsl_reg.dat.lta   --surf occip.flattened  --hemi   lh)

Many thanks,

Atena
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Re: [Freesurfer] issue with mri_vol2surf

2023-11-22 Thread 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
>
> ___
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>  .
>


tk2.dat
Description: Binary data
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[Freesurfer] issue with mri_vol2surf

2023-11-22 Thread 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
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Re: [Freesurfer] license issue with the updated version

2023-11-18 Thread Atena Akbari 
External Email - Use Caution

Thanks a lot, Yujing, I updated the FS_LICENSE accordingly, but when I want
to load a surface in freeview I get the following error:

QObject::killTimer: Timers cannot be stopped from another thread
QObject::~QObject: Timers cannot be stopped from another thread

also, with tkregister2 or tkregisterfv I don't get the GUI, it gives me the
"MRIread failed" error. I appreciate your help.

All the best,
Atena

On Sat, Nov 18, 2023 at 1:00 PM Huang, Yujing 
wrote:

> Hi Atena,
>
>
>
> Can you check if you have environment variable FS_LICENSE set?
>
> >echo $FS_LICENSE
>
>
>
> Set FS_LICENSE to your license file in 7.4.1,
>
> >export FS_LICENSE=
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Atena Akbari
> *Sent:* Friday, November 17, 2023 6:06 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] license issue with the updated version
>
>
>
> *External Email - Use Caution*
>
> Dear freesurfer team
>
>
>
> I have uninstalled the previous versions of freesurfer on my mac (Sonoma
> 14.1), and have installed a new version 7.4.1 based on the step by step
> freesurfer installation info on the website. I have set the freesurfer home
> directory as follows:
>
>
>
> export FREESURFER_HOME=/Applications/freesurfer/7.4.1/
>
> export SUBJECTS_DIR=path/to/my/data
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>
>
> and the license is in the /Applications/freesurfer/*MailScanner has
> detected a possible fraud attempt from "7.4.1" claiming to be* *
> MailScanner warning: numerical links are often malicious:* 7.4.1.
> <http://7.4.1.> But when I run a freesurfer command I get the following
> error:
>
>
>
> ERROR: FreeSurfer license file /Applications/freesurfer/7.2.0/license.txt
> not found.
>
> QObject::killTimer: Timers cannot be stopped from another thread
>
> QObject::~QObject: Timers cannot be stopped from another thread
>
> /Applications/freesurfer/7.4.1//bin/freeview: line 2:  2938 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>
>
>
> Could you help me with this issue?
>
>
>
> thanks so much.
>
>
>
> Best,
>
> Atena
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> e-mail contains patient information, please contact the Mass General
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>  <
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>  .
>
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[Freesurfer] license issue with the updated version

2023-11-17 Thread Atena Akbari 
External Email - Use Caution

Dear freesurfer team

I have uninstalled the previous versions of freesurfer on my mac (Sonoma
14.1), and have installed a new version 7.4.1 based on the step by step
freesurfer installation info on the website. I have set the freesurfer home
directory as follows:

export FREESURFER_HOME=/Applications/freesurfer/7.4.1/

export SUBJECTS_DIR=path/to/my/data

source $FREESURFER_HOME/SetUpFreeSurfer.sh


and the license is in the /Applications/freesurfer/7.4.1. But when I run a
freesurfer command I get the following error:


ERROR: FreeSurfer license file /Applications/freesurfer/7.2.0/license.txt
not found.

QObject::killTimer: Timers cannot be stopped from another thread

QObject::~QObject: Timers cannot be stopped from another thread

/Applications/freesurfer/7.4.1//bin/freeview: line 2:  2938 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"


Could you help me with this issue?


thanks so much.


Best,

Atena
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