Re: [Freesurfer] Projection of markers from the scalp to cortical surfaces
Yes, I meant that the output labels were much less than the input ones and I would not expect this, but their position was correct. I will try to figure out if I did something wrong. Thank you! Eleonora 2013/4/4 Douglas Greve gr...@nmr.mgh.harvard.edu When you say it does not work, what do you mean? Did it not put the label in the right place? The number of vertices in the output label may be much less than in the input. label2label just finds the vertex that is closest to each label point. A multiple input label points may map to a single output label. doug On 4/3/13 4:24 PM, Eleonora Maggioni wrote: Dear Doug, thank you for the suggestion. I used the new file that you sent me exactly as in the example 4, but the labels which are effectively translated into the nearest vertex surface labels are few. I first selected the marker labels on the T1 image within tkmedit. As the labels are outside the head volume, I put the maximum distance --paint as 50 mm, to be sure that the distance is sufficient to find a surface vertex. But anyway is still does not works. Can this be due to the external position of the markers? Which kind of projection is done by mri_label2label? Thank you for your support! Eleonora 2013/4/2 Douglas N Greve gr...@nmr.mgh.harvard.edu Hi Eleonora, the easiest way to do this is to create a label of the electrodes, then use mri_label2label to map them to the nearest pial vertices. This ability to map volume labels to nearest surface vertices is broken in the current version. I've fixed this and put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2label Run it with --help and use Example 4. doug On 04/02/2013 08:19 AM, Eleonora Maggioni wrote: Hi Freesurfer experts, I am new to FreeSurfer and I have a question. I have markers of EEG electrodes on the T1 image of a subject and I want to project them from the scalp to his pial surface (that I reconstructed using the standard procedure). To do so, I manually selected the central point of each marker in tkmedit and I defined a control point. Then I red that control point with tksurfer on the corresponding pial surface. This should be the projection to the pial surface: is this procedure correct? If yes, in which coordinate system is the projection made? Thank you in advance, Kind regards, -- Eleonora Maggioni BioEngineering PhD student Politecnico di Milano Istituto E.Medea, Bosisio Parini (LC) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- Eleonora Maggioni BioEngineering PhD student Politecnico di Milano Istituto E.Medea, Bosisio Parini (LC) -- Eleonora Maggioni BioEngineering PhD student Politecnico di Milano Istituto E.Medea, Bosisio Parini (LC) ___ 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.
Re: [Freesurfer] Projection of markers from the scalp to cortical surfaces
When you say it does not work, what do you mean? Did it not put the label in the right place? The number of vertices in the output label may be much less than in the input. label2label just finds the vertex that is closest to each label point. A multiple input label points may map to a single output label. doug On 4/3/13 4:24 PM, Eleonora Maggioni wrote: Dear Doug, thank you for the suggestion. I used the new file that you sent me exactly as in the example 4, but the labels which are effectively translated into the nearest vertex surface labels are few. I first selected the marker labels on the T1 image within tkmedit. As the labels are outside the head volume, I put the maximum distance --paint as 50 mm, to be sure that the distance is sufficient to find a surface vertex. But anyway is still does not works. Can this be due to the external position of the markers? Which kind of projection is done by mri_label2label? Thank you for your support! Eleonora 2013/4/2 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Eleonora, the easiest way to do this is to create a label of the electrodes, then use mri_label2label to map them to the nearest pial vertices. This ability to map volume labels to nearest surface vertices is broken in the current version. I've fixed this and put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2label Run it with --help and use Example 4. doug On 04/02/2013 08:19 AM, Eleonora Maggioni wrote: Hi Freesurfer experts, I am new to FreeSurfer and I have a question. I have markers of EEG electrodes on the T1 image of a subject and I want to project them from the scalp to his pial surface (that I reconstructed using the standard procedure). To do so, I manually selected the central point of each marker in tkmedit and I defined a control point. Then I red that control point with tksurfer on the corresponding pial surface. This should be the projection to the pial surface: is this procedure correct? If yes, in which coordinate system is the projection made? Thank you in advance, Kind regards, -- Eleonora Maggioni BioEngineering PhD student Politecnico di Milano Istituto E.Medea, Bosisio Parini (LC) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Eleonora Maggioni BioEngineering PhD student Politecnico di Milano Istituto E.Medea, Bosisio Parini (LC) ___ 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.
Re: [Freesurfer] Projection of markers from the scalp to cortical surfaces
Hi Eleonora, the easiest way to do this is to create a label of the electrodes, then use mri_label2label to map them to the nearest pial vertices. This ability to map volume labels to nearest surface vertices is broken in the current version. I've fixed this and put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2label Run it with --help and use Example 4. doug On 04/02/2013 08:19 AM, Eleonora Maggioni wrote: Hi Freesurfer experts, I am new to FreeSurfer and I have a question. I have markers of EEG electrodes on the T1 image of a subject and I want to project them from the scalp to his pial surface (that I reconstructed using the standard procedure). To do so, I manually selected the central point of each marker in tkmedit and I defined a control point. Then I red that control point with tksurfer on the corresponding pial surface. This should be the projection to the pial surface: is this procedure correct? If yes, in which coordinate system is the projection made? Thank you in advance, Kind regards, -- Eleonora Maggioni BioEngineering PhD student Politecnico di Milano Istituto E.Medea, Bosisio Parini (LC) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
