Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder.
I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture).
Then, I used another methods as follows. Firstly, I converted the annotation file into some label files using mri_annotation2label command; Secondly, I created ROIs using these labels by mri_vol2roi. However, the masks also couldn't cover the gray matter.
Could anyone help me creat good masks? Thanks a lot!
Zhiwei
Try using mri_aparc2aseg. This is what creates aparc+aseg.mgz from the aparc annot. You can look in the recon-all.log file for the command line (just make sure to change the output file name too so that you don't overwrite aparc+aseg.mgz)
doug
On 11/24/2014 07:54 AM, wangzhiwei3233 wrote:
Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder.
I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture).
Then, I used another methods as follows. Firstly, I converted the annotation file into some label files using mri_annotation2label command; Secondly, I created ROIs using these labels by mri_vol2roi. However, the masks also couldn't cover the gray matter.
Could anyone help me creat good masks? Thanks a lot!
Zhiwei
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It works! Thanks, Doug.
At 2014-11-25 01:19:13, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Try using mri_aparc2aseg. This is what creates aparc+aseg.mgz from the aparc annot. You can look in the recon-all.log file for the command line (just make sure to change the output file name too so that you don't overwrite aparc+aseg.mgz)
doug
On 11/24/2014 07:54 AM, wangzhiwei3233 wrote:
Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder.
I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture).
Then, I used another methods as follows. Firstly, I converted the annotation file into some label files using mri_annotation2label command; Secondly, I created ROIs using these labels by mri_vol2roi. However, the masks also couldn't cover the gray matter.
Could anyone help me creat good masks? Thanks a lot!
Zhiwei
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi all, I have a problem with freeview and I am not sure about the command line to be used to view a mask. I have created an annot file and I would like to have a picture of the mask in the inflated brain with curvature. However when I use the annot file with tksurfer I am able to do so, but with freeview the brain become all black (not in the mask) when the annot file is used. I have read the freeview manual, but I did not fond help in using freeview with command line. Where can I find some help?
the command with tksurfer was:
tksurfer fsaverage lh inflated -curv -gray -annot mymask.annot
with freeview I tried this:
freeview -f fsaverage/surf/lh.inflated:overlay=lh.curv:overlay_threshold=2,5 :annot=mymask.annot -viewport 3d
thank you for any help!
Angela
Would it be possible to send us your annoy file? Are you using the latest dev version of freeview or the one with 5.3 release?
Best, Ruopeng
On Nov 29, 2014, at 4:51 AM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with freeview and I am not sure about the command line to be used to view a mask. I have created an annot file and I would like to have a picture of the mask in the inflated brain with curvature. However when I use the annot file with tksurfer I am able to do so, but with freeview the brain become all black (not in the mask) when the annot file is used. I have read the freeview manual, but I did not fond help in using freeview with command line. Where can I find some help?
the command with tksurfer was:
tksurfer fsaverage lh inflated -curv -gray -annot mymask.annot
with freeview I tried this:
freeview -f fsaverage/surf/lh.inflated:overlay=lh.curv:overlay_threshold=2,5 :annot=mymask.annot -viewport 3d
thank you for any help!
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thank you for your help please find attached the annot file I am using the 5.3 release
Angela
Would it be possible to send us your annoy file? Are you using the latest dev version of freeview or the one with 5.3 release?
Best, Ruopeng
On Nov 29, 2014, at 4:51 AM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with freeview and I am not sure about the command line to be used to view a mask. I have created an annot file and I would like to have a picture of the mask in the inflated brain with curvature. However when I use the annot file with tksurfer I am able to do so, but with freeview the brain become all black (not in the mask) when the annot file is used. I have read the freeview manual, but I did not fond help in using freeview with command line. Where can I find some help?
the command with tksurfer was:
tksurfer fsaverage lh inflated -curv -gray -annot mymask.annot
with freeview I tried this:
freeview -f fsaverage/surf/lh.inflated:overlay=lh.curv:overlay_threshold=2,5 :annot=mymask.annot -viewport 3d
thank you for any help!
Angela
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thanks. I can replicate the issue. I’ll look into it.
Best, Ruopeng
On Nov 30, 2014, at 12:45 PM, angela.favaro@unipd.it wrote:
thank you for your help please find attached the annot file I am using the 5.3 release
Angela
Would it be possible to send us your annoy file? Are you using the latest dev version of freeview or the one with 5.3 release?
Best, Ruopeng
On Nov 29, 2014, at 4:51 AM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with freeview and I am not sure about the command line to be used to view a mask. I have created an annot file and I would like to have a picture of the mask in the inflated brain with curvature. However when I use the annot file with tksurfer I am able to do so, but with freeview the brain become all black (not in the mask) when the annot file is used. I have read the freeview manual, but I did not fond help in using freeview with command line. Where can I find some help?
the command with tksurfer was:
tksurfer fsaverage lh inflated -curv -gray -annot mymask.annot
with freeview I tried this:
freeview -f fsaverage/surf/lh.inflated:overlay=lh.curv:overlay_threshold=2,5 :annot=mymask.annot -viewport 3d
thank you for any help!
Angela
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
<lh.mymap2.annot>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Angela,
The issue has been fixed. It is because your annotation has 0's which is corresponding to black color in the color table). I've made change in my code so it doesn't display 0's. The fix will be in tomorrow's dev build. If you are interested in trying it. You can download the dev version of freeview tomorrow.
Best, Ruopeng
On 11/30/2014 12:45 PM, angela.favaro@unipd.it wrote:
thank you for your help please find attached the annot file I am using the 5.3 release
Angela
Would it be possible to send us your annoy file? Are you using the latest dev version of freeview or the one with 5.3 release?
Best, Ruopeng
On Nov 29, 2014, at 4:51 AM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with freeview and I am not sure about the command line to be used to view a mask. I have created an annot file and I would like to have a picture of the mask in the inflated brain with curvature. However when I use the annot file with tksurfer I am able to do so, but with freeview the brain become all black (not in the mask) when the annot file is used. I have read the freeview manual, but I did not fond help in using freeview with command line. Where can I find some help?
the command with tksurfer was:
tksurfer fsaverage lh inflated -curv -gray -annot mymask.annot
with freeview I tried this:
freeview -f fsaverage/surf/lh.inflated:overlay=lh.curv:overlay_threshold=2,5 :annot=mymask.annot -viewport 3d
thank you for any help!
Angela
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ruopeng, thank you very much!
Hi Angela,
The issue has been fixed. It is because your annotation has 0's which is corresponding to black color in the color table). I've made change in my code so it doesn't display 0's. The fix will be in tomorrow's dev build. If you are interested in trying it. You can download the dev version of freeview tomorrow.
Best, Ruopeng
On 11/30/2014 12:45 PM, angela.favaro@unipd.it wrote:
thank you for your help please find attached the annot file I am using the 5.3 release
Angela
Would it be possible to send us your annoy file? Are you using the latest dev version of freeview or the one with 5.3 release?
Best, Ruopeng
On Nov 29, 2014, at 4:51 AM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with freeview and I am not sure about the command line to be used to view a mask. I have created an annot file and I would like to have a picture of the mask in the inflated brain with curvature. However when I use the annot file with tksurfer I am able to do so, but with freeview the brain become all black (not in the mask) when the annot file is used. I have read the freeview manual, but I did not fond help in using freeview with command line. Where can I find some help?
the command with tksurfer was:
tksurfer fsaverage lh inflated -curv -gray -annot mymask.annot
with freeview I tried this:
freeview -f fsaverage/surf/lh.inflated:overlay=lh.curv:overlay_threshold=2,5 :annot=mymask.annot -viewport 3d
thank you for any help!
Angela
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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angela.favaro＠unipd.it -
Douglas N Greve -
Ruopeng Wang -
wangzhiwei3233