Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster?
If I use mri_binarize or mri_cor2label is not working (I understand that the clusters are not stored as individual vertexes in the .mgh file but I don't know what the format is.
Thanks in advance! Gari
PD: I am on a VPN and tksurfer is not working for manually creating a label with the contour of the cluster.
Hi Gari, you can use mri_annotation2label doug
On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:
Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster?
If I use mri_binarize or mri_cor2label is not working (I understand that the clusters are not stored as individual vertexes in the .mgh file but I don't know what the format is.
Thanks in advance! Gari
PD: I am on a VPN and tksurfer is not working for manually creating a label with the contour of the cluster.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug! Could you give me an example please? I cannot get it to work, with this command I get a zero label...
mri_annotation2label --subject fsaverage --hemi lh --annotation lh.mc-z.abs.sig.cluster.mgh --labelbase lh.mc_mycluster
thanks again! Gari
On Thu, Aug 15, 2013 at 4:44 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Gari, you can use mri_annotation2label doug
On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:
Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster?
If I use mri_binarize or mri_cor2label is not working (I understand that the clusters are not stored as individual vertexes in the .mgh file but I don't know what the format is.
Thanks in advance! Gari
PD: I am on a VPN and tksurfer is not working for manually creating a label with the contour of the cluster.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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.
Give it the annotation (.annot) file
On 08/15/2013 01:26 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Doug! Could you give me an example please? I cannot get it to work, with this command I get a zero label...
mri_annotation2label --subject fsaverage --hemi lh --annotation lh.mc-z.abs.sig.cluster.mgh --labelbase lh.mc_mycluster
thanks again! Gari
On Thu, Aug 15, 2013 at 4:44 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Gari, you can use mri_annotation2label doug On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster? If I use mri_binarize or mri_cor2label is not working (I understand that the clusters are not stored as individual vertexes in the .mgh file but I don't know what the format is. Thanks in advance! Gari PD: I am on a VPN and tksurfer is not working for manually creating a label with the contour of the cluster. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ 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.
Sorry Doug, I don't understand, I just have the cluster.mgh file with the MonteCarlo simulation results, is an .mgh file with a big significant cluster ( mc-z.abs.sig.cluster.mgh).
Is there a way to create a label for each of the significant clusters?
thanks again and sorry if the question is too trivial! Gari
On Thu, Aug 15, 2013 at 7:32 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Give it the annotation (.annot) file
On 08/15/2013 01:26 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Doug! Could you give me an example please? I cannot get it to work, with this command I get a zero label...
mri_annotation2label --subject fsaverage --hemi lh --annotation lh.mc-z.abs.sig.cluster.mgh --labelbase lh.mc_mycluster
thanks again! Gari
On Thu, Aug 15, 2013 at 4:44 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
Hi Gari, you can use mri_annotation2label doug On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster? If I use mri_binarize or mri_cor2label is not working (I understand that the clusters are not stored as individual vertexes in the .mgh file but I don't know what the format is. Thanks in advance! Gari PD: I am on a VPN and tksurfer is not working for manually creating a label with the contour of the cluster. ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
There should also be a .annot file there too
On 08/15/2013 02:40 PM, Garikoitz Lerma-Usabiaga wrote:
Sorry Doug, I don't understand, I just have the cluster.mgh file with the MonteCarlo simulation results, is an .mgh file with a big significant cluster (mc-z.abs.sig.cluster.mgh).
Is there a way to create a label for each of the significant clusters?
thanks again and sorry if the question is too trivial! Gari
On Thu, Aug 15, 2013 at 7:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Give it the annotation (.annot) file On 08/15/2013 01:26 PM, Garikoitz Lerma-Usabiaga wrote: Thanks Doug! Could you give me an example please? I cannot get it to work, with this command I get a zero label... mri_annotation2label --subject fsaverage --hemi lh --annotation lh.mc-z.abs.sig.cluster.mgh --labelbase lh.mc_mycluster thanks again! Gari On Thu, Aug 15, 2013 at 4:44 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Hi Gari, you can use mri_annotation2label doug On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote: Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster? If I use mri_binarize or mri_cor2label is not working (I understand that the clusters are not stored as individual vertexes in the .mgh file but I don't know what the format is. Thanks in advance! Gari PD: I am on a VPN and tksurfer is not working for manually creating a label with the contour of the cluster. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Garikoitz Lerma-Usabiaga