Hi list and Anastasia. Thank you very much. mri_annotatiion2label works fine. Becouse I should run this command: label2surf -s <surface> -o <outputsurface> -l <labels> -s,--surf input surface -o,--out output surface -l,--labels ascii list of label files I should provide also surface file relatively to each .label previously created with mri_annotatiion2label. How can I do? Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 26-set-2013 0.57 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Import FS data to FSL
Try mri_annotation2label.
On Wed, 25 Sep 2013, stdp82@virgilio.it wrote:
For FSL guide:
I should transforms a group of labels into a surface
Usage:
label2surf -s <surface> -o <outputsurface> -l <labels>
Compulsory arguments (You MUST set one or more of):
-s,--surf input surface -o,--out output surface -l,--labels ascii list of label filesOptional arguments (You may optionally specify one or more of):
-v,--verbose switch on diagnostic messages -h,--help display this messagebut I should create a lh/rh.frontal.label and use it for label2surf.
With mdi_binarize I can create .nii.gz but no .label. Is that correct?
How I can do it?
Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 25-set-2013 17.49 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Import FS data to FSL
1 - Yes. 2 - You can use mri_aparc2aseg to grow the cortical labels into the white matter (say, by 2mm). The file that it will produce will be a volume file, so then you just run mri_binarize to extract specific labels. Make sure you save them in nifti format for FSL.
On Wed, 25 Sep 2013, stdp82@virgilio.it wrote:
Hi list,
I have 2 questions, please.
1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)?
2-I'd like to export cortical masks from FS to FSL.
An option is mri_binarize but this way failed in probtrackx (fsl). FSL list have advised me that I should use label2surf command to convert label to surface files.
Where could find the .label (according to FreeSurferColorLUT.txt) to build mask of frontal, parietal, motor, sensor, temporal and occipital lobes?
Do you have other ways that you advise me?
Thanks,
Stefano
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.
label2surf is an FSL command, so you can get a more authoritative answer on the FSL list, but I'd try one of the files in the surf/ directory, like lh.white or rh.white.
On Fri, 27 Sep 2013, stdp82@virgilio.it wrote:
Hi list and Anastasia.
Thank you very much. mri_annotatiion2label works fine.
Becouse I should run this command:
label2surf -s <surface> -o <outputsurface> -l <labels>
-s,--surf input surface -o,--out output surface -l,--labels ascii list of label files
I should provide also surface file relatively to each .label previously created with mri_annotatiion2label.
How can I do?
Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 26-set-2013 0.57 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Import FS data to FSL
Try mri_annotation2label.
On Wed, 25 Sep 2013, stdp82@virgilio.it wrote:
For FSL guide:
I should transforms a group of labels into a surface
Usage:
label2surf -s <surface> -o <outputsurface> -l <labels>
Compulsory arguments (You MUST set one or more of):
-s,--surf input surface
-o,--out output surface
-l,--labels ascii list of label files
Optional arguments (You may optionally specify one or more of):
-v,--verbose switch on diagnostic messages
-h,--help display this message
but I should create a lh/rh.frontal.label and use it for label2surf.
With mdi_binarize I can create .nii.gz but no .label. Is that correct?
How I can do it?
Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 25-set-2013 17.49 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Import FS data to FSL
1 - Yes. 2 - You can use mri_aparc2aseg to grow the cortical labels into the white matter (say, by 2mm). The file that it will produce will be a volume file, so then you just run mri_binarize to extract specific labels. Make sure you save them in nifti format for FSL.
On Wed, 25 Sep 2013, stdp82@virgilio.it wrote:
Hi list,
I have 2 questions, please.
1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)?
2-I'd like to export cortical masks from FS to FSL.
An option is mri_binarize but this way failed in probtrackx (fsl). FSL list have advised me that I should use label2surf command to convert label to surface files.
Where could find the .label (according to FreeSurferColorLUT.txt) to
build
mask of frontal, parietal, motor, sensor, temporal and occipital lobes?
Do you have other ways that you advise me?
Thanks,
Stefano
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
-
Anastasia Yendiki -
stdp82＠virgilio.it