Re: [Freesurfer] adding grey matter
Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia ___ 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] adding grey matter
Hi Bruce, I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com Hi Bruce, I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia 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/**compliancelinehttp://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 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] adding grey matter
is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia 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 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] adding grey matter
Hi Claudia, Make sure you use the filedrop to upload your data https://gate.nmr.mgh.harvard.edu/filedrop2/ Cheers, Shantanu On Mon, April 29, 2013 9:53 am, Claudia Dacquino wrote: Hi Bruce, I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com Hi Bruce, I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia 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/**compliancelinehttp://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 -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] adding grey matter
Bruce, no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia 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/**compliancelinehttp://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 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] adding grey matter
then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia 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
Re: [Freesurfer] adding grey matter
Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia 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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient
Re: [Freesurfer] adding grey matter
visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that?
Re: [Freesurfer] adding grey matter
Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial
Re: [Freesurfer] adding grey matter
But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz it's labeled as white matter, could it be possible? 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white
Re: [Freesurfer] adding grey matter
Hi Claudia now I'm confused. Did you put control points in those voxels? You definitely, definitely must avoid putting them in voxels that contain anything other than WM. The pial surface will usually be incorrect if the white surface is incorrect, so the first thing to do is make sure it is right Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz it's labeled as white matter, could it be possible? 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used
Re: [Freesurfer] adding grey matter
I'm sorry Bruce I'm confusing you. The fact is that those areas are labelled as WM, so I thought those were white matter, but looking with more attention at wm.mgz I did realize that they could me no WM, as you seggested me, because they are too dark. I'm new and I'm learning by trial and error. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia now I'm confused. Did you put control points in those voxels? You definitely, definitely must avoid putting them in voxels that contain anything other than WM. The pial surface will usually be incorrect if the white surface is incorrect, so the first thing to do is make sure it is right Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz it's labeled as white matter, could it be possible? 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray
Re: [Freesurfer] adding grey matter
Hi Claudia if you upload your whole subject and send us some example voxel coords of where you are looking we will take a look Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: I'm sorry Bruce I'm confusing you.The fact is that those areas are labelled as WM, so I thought those were white matter, but looking with more attention at wm.mgz I did realize that they could me no WM, as you seggested me, because they are too dark. I'm new and I'm learning by trial and error. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia now I'm confused. Did you put control points in those voxels? You definitely, definitely must avoid putting them in voxels that contain anything other than WM. The pial surface will usually be incorrect if the white surface is incorrect, so the first thing to do is make sure it is right Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz it's labeled as white matter, could it be possible? 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your
Re: [Freesurfer] adding grey matter
I'm uploading my subjdir on FTP server. Thanks a lot. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia if you upload your whole subject and send us some example voxel coords of where you are looking we will take a look Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: I'm sorry Bruce I'm confusing you.The fact is that those areas are labelled as WM, so I thought those were white matter, but looking with more attention at wm.mgz I did realize that they could me no WM, as you seggested me, because they are too dark. I'm new and I'm learning by trial and error. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia now I'm confused. Did you put control points in those voxels? You definitely, definitely must avoid putting them in voxels that contain anything other than WM. The pial surface will usually be incorrect if the white surface is incorrect, so the first thing to do is make sure it is right Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz it's labeled as white matter, could it be possible? 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean?
Re: [Freesurfer] adding grey matter
my subjdir is on FTP server. thanks claudia 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com I'm uploading my subjdir on FTP server. Thanks a lot. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia if you upload your whole subject and send us some example voxel coords of where you are looking we will take a look Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: I'm sorry Bruce I'm confusing you.The fact is that those areas are labelled as WM, so I thought those were white matter, but looking with more attention at wm.mgz I did realize that they could me no WM, as you seggested me, because they are too dark. I'm new and I'm learning by trial and error. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia now I'm confused. Did you put control points in those voxels? You definitely, definitely must avoid putting them in voxels that contain anything other than WM. The pial surface will usually be incorrect if the white surface is incorrect, so the first thing to do is make sure it is right Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz it's labeled as white matter, could it be possible? 2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote: The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough,
