Re: [Freesurfer] Entorhinal Cortex segmentation and volume
Hi Melina Sorry for the delay in responindg, can you tell us a bit more about the acquisition? They look very grainy and low contrast. Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: > Thank you both for your respond. > 1. I have attached you some pictures. Like douglas wrote it corresponds to > white matter in aseg, but is more often labelled as "none" than "cortex > unknown". So is this "normal" and can I trust those borders? Or would you > rather advise to control aseg and aparc segmentation to estimate the > entorhinal cortex segmentation? > > 2. You're right, Bruce, in freeview the exvivo label it just follows the > surface. So I'll try mri_label2vol. > > Cheers Melina > > Am 16.02.2015 um 16:33 schrieb Douglas Greve: >> On 2/16/15 9:31 AM, Bruce Fischl wrote: >>> Hi Melina >>> >>> 1. Can you send us a picture? I'm not sure given your description, >>> although the surfaces can be arbitrary in the hippocampus/amygdala and >>> should be ignored there. >> This corresponds to the "cortex unknown" label in aparc (and is >> probably labeled WM in the aseg). This is normal. >>> 2. You should be able to use mri_label2vol for this. Note that you can >>> load >>> the label itself directly into freeview if you want without needing to run >>> label2vol (but it will follow the white surface I believe and not fill the >>> ribbon) >>> >>> cheers >>> Bruce >>> >>> On Mon, 16 Feb 2015, Melina Lehnerer wrote: >>> Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as "none" or "ctx-?h-unknown". Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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 >>> >>> >> ___ >> 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
Re: [Freesurfer] Entorhinal Cortex segmentation and volume
Yes, that is normal On 2/16/15 11:42 AM, Melina Lehnerer wrote: Thank you both for your respond. 1. I have attached you some pictures. Like douglas wrote it corresponds to white matter in aseg, but is more often labelled as none than cortex unknown. So is this normal and can I trust those borders? Or would you rather advise to control aseg and aparc segmentation to estimate the entorhinal cortex segmentation? 2. You're right, Bruce, in freeview the exvivo label it just follows the surface. So I'll try mri_label2vol. Cheers Melina Am 16.02.2015 um 16:33 schrieb Douglas Greve: On 2/16/15 9:31 AM, Bruce Fischl wrote: Hi Melina 1. Can you send us a picture? I'm not sure given your description, although the surfaces can be arbitrary in the hippocampus/amygdala and should be ignored there. This corresponds to the cortex unknown label in aparc (and is probably labeled WM in the aseg). This is normal. 2. You should be able to use mri_label2vol for this. Note that you can load the label itself directly into freeview if you want without needing to run label2vol (but it will follow the white surface I believe and not fill the ribbon) cheers Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as none or ctx-?h-unknown. Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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 ___ 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.
Re: [Freesurfer] Entorhinal Cortex segmentation and volume
Hi Melina 1. Can you send us a picture? I'm not sure given your description, although the surfaces can be arbitrary in the hippocampus/amygdala and should be ignored there. 2. You should be able to use mri_label2vol for this. Note that you can load the label itself directly into freeview if you want without needing to run label2vol (but it will follow the white surface I believe and not fill the ribbon) cheers Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as none or ctx-?h-unknown. Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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] Entorhinal Cortex segmentation and volume
Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as none or ctx-?h-unknown. Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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] Entorhinal Cortex segmentation and volume
On 2/16/15 9:31 AM, Bruce Fischl wrote: Hi Melina 1. Can you send us a picture? I'm not sure given your description, although the surfaces can be arbitrary in the hippocampus/amygdala and should be ignored there. This corresponds to the cortex unknown label in aparc (and is probably labeled WM in the aseg). This is normal. 2. You should be able to use mri_label2vol for this. Note that you can load the label itself directly into freeview if you want without needing to run label2vol (but it will follow the white surface I believe and not fill the ribbon) cheers Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as none or ctx-?h-unknown. Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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 ___ 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.
