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Hello Freesurfer Team, I am interested in using premotor, precentral gyrus and postcentral gyrus in my analysis. For the definition of the precentral gyrus and postcentral gyrus I use the following lines: fslmaths aparc+aseg.nii.gz -thr 1024 -uthr 1024 PreCG_L.nii.gz fslmaths aparc+aseg.nii.gz -thr 2024 -uthr 2024 PreCG_R.nii.gz fslmaths aparc+aseg.nii.gz -thr 1022 -uthr 1022 PostCG_L.nii.gz fslmaths aparc+aseg.nii.gz -thr 2022 -uthr 2022 PostCG_R.nii.gz
To define the premotor area I use the labels rh.BA6_exvivo.label and lh.BA6_exvivo.label according to the script below: bbregister --s SubID_FreeSurfer --mov nodif.nii.gz --reg lowb2orig.dat --dti --init-fsl mri_label2vol --label SubID_FreeSurfer /label/rh.BA6_exvivo.label --reg lowb2orig.dat --fillthresh .3 --hemi rh --subject SubID_FreeSurfer --o BA6_R.nii.gz --temp nodif.nii.gz --proj frac 0 1 .1
When I check the location of the resulted BA6 and precentral gyrus masks, there is an overlap. Could you please advise if there is any other way to define premotor area?
Thank you in advance, Evie
________________________________
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Is the problem that there is an overlap? The exvivo labels and aparc labels are not going to be mutually exclusive.
On 12/6/2021 5:34 PM, Tsolaki, Evangelia C. wrote:
External Email - Use Caution
Hello Freesurfer Team,
I am interested in using premotor, precentral gyrus and postcentral gyrus in my analysis.
For the definition of the precentral gyrus and postcentral gyrus I use the following lines:
fslmaths aparc+aseg.nii.gz -thr 1024 -uthr 1024 PreCG_L.nii.gz
fslmaths aparc+aseg.nii.gz -thr 2024 -uthr 2024 PreCG_R.nii.gz
fslmaths aparc+aseg.nii.gz -thr 1022 -uthr 1022 PostCG_L.nii.gz
fslmaths aparc+aseg.nii.gz -thr 2022 -uthr 2022 PostCG_R.nii.gz
To define the premotor area I use the labels rh.BA6_exvivo.label and lh.BA6_exvivo.label according to the script below:
bbregister --s SubID_FreeSurfer --mov nodif.nii.gz --reg lowb2orig.dat --dti --init-fsl
mri_label2vol --label SubID_FreeSurfer /label/rh.BA6_exvivo.label --reg lowb2orig.dat --fillthresh .3 --hemi rh --subject SubID_FreeSurfer --o BA6_R.nii.gz --temp nodif.nii.gz --proj frac 0 1 .1
When I check the location of the resulted BA6 and precentral gyrus masks, there is an overlap. Could you please advise if there is any other way to define premotor area?
Thank you in advance,
Evie
UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hello, Yes the problem is that there is an overlap between the premotor and motor area. Does FreeSurfer provide any other masks that can be used for the premotor area?
Thank you in advance, Evie
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Date: Friday, December 10, 2021 at 3:43 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Definition of Premotor Area
CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Is the problem that there is an overlap? The exvivo labels and aparc labels are not going to be mutually exclusive. On 12/6/2021 5:34 PM, Tsolaki, Evangelia C. wrote:
External Email - Use Caution Hello Freesurfer Team, I am interested in using premotor, precentral gyrus and postcentral gyrus in my analysis. For the definition of the precentral gyrus and postcentral gyrus I use the following lines: fslmaths aparc+aseg.nii.gz -thr 1024 -uthr 1024 PreCG_L.nii.gz fslmaths aparc+aseg.nii.gz -thr 2024 -uthr 2024 PreCG_R.nii.gz fslmaths aparc+aseg.nii.gz -thr 1022 -uthr 1022 PostCG_L.nii.gz fslmaths aparc+aseg.nii.gz -thr 2022 -uthr 2022 PostCG_R.nii.gz
To define the premotor area I use the labels rh.BA6_exvivo.label and lh.BA6_exvivo.label according to the script below: bbregister --s SubID_FreeSurfer --mov nodif.nii.gz --reg lowb2orig.dat --dti --init-fsl mri_label2vol --label SubID_FreeSurfer /label/rh.BA6_exvivo.label --reg lowb2orig.dat --fillthresh .3 --hemi rh --subject SubID_FreeSurfer --o BA6_R.nii.gz --temp nodif.nii.gz --proj frac 0 1 .1
When I check the location of the resulted BA6 and precentral gyrus masks, there is an overlap. Could you please advise if there is any other way to define premotor area?
Thank you in advance, Evie
________________________________
UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
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HI Evie
You can try thresholding the premotor area, or removing the intersection with precentral gyrus (or both)
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Tsolaki, Evangelia C. Sent: Monday, December 13, 2021 3:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Definition of Premotor Area
External Email - Use Caution Hello, Yes the problem is that there is an overlap between the premotor and motor area. Does FreeSurfer provide any other masks that can be used for the premotor area?
Thank you in advance, Evie
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Date: Friday, December 10, 2021 at 3:43 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Definition of Premotor Area
CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Is the problem that there is an overlap? The exvivo labels and aparc labels are not going to be mutually exclusive. On 12/6/2021 5:34 PM, Tsolaki, Evangelia C. wrote:
External Email - Use Caution Hello Freesurfer Team, I am interested in using premotor, precentral gyrus and postcentral gyrus in my analysis. For the definition of the precentral gyrus and postcentral gyrus I use the following lines: fslmaths aparc+aseg.nii.gz -thr 1024 -uthr 1024 PreCG_L.nii.gz fslmaths aparc+aseg.nii.gz -thr 2024 -uthr 2024 PreCG_R.nii.gz fslmaths aparc+aseg.nii.gz -thr 1022 -uthr 1022 PostCG_L.nii.gz fslmaths aparc+aseg.nii.gz -thr 2022 -uthr 2022 PostCG_R.nii.gz
To define the premotor area I use the labels rh.BA6_exvivo.label and lh.BA6_exvivo.label according to the script below: bbregister --s SubID_FreeSurfer --mov nodif.nii.gz --reg lowb2orig.dat --dti --init-fsl mri_label2vol --label SubID_FreeSurfer /label/rh.BA6_exvivo.label --reg lowb2orig.dat --fillthresh .3 --hemi rh --subject SubID_FreeSurfer --o BA6_R.nii.gz --temp nodif.nii.gz --proj frac 0 1 .1
When I check the location of the resulted BA6 and precentral gyrus masks, there is an overlap. Could you please advise if there is any other way to define premotor area?
Thank you in advance, Evie
________________________________
UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
_______________________________________________
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Fischl, Bruce -
Tsolaki, Evangelia C.