[Freesurfer] nonlabeled vertices in bert
Hello, 1) I reiterate my question, because i cannot continue processing. Some vertices are not labeled in the rh.aparc.annot in bert as 35643,36746,37788. 2) The parcels of my subject are not connex. Below is the detail on my first email. Thank you very much for answering me De : Ben Hamida Cammoun Leila Faiza Envoyé : jeudi 6 octobre 2011 14:53 À : Objet : nonconnexity and holes in parcels Hello, I am using freesurfer v5.1.0 (on ubuntu). when processing reconall on my data I notice on the parcellation aparc.annot two strange points: some isolated small regions not annotated, as well as the non connexity of some parcels. I checked the bert aparc.annot on inflated surface and I found the same problem of non connexity, for instance some medialorbitofrontal labeled vertices (vertex index 108562) in rostralanteriorcingulate, or vertex num 103429 labeled as insula in lateralorbitofrontal parcel. In lingual there is also a small hole without annotation like vertices: 35643,36746,37788. is this normal? if yes, how can we correct that? thanks in advance ___ 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] Rejoindre mon réseau sur LinkedIn
LinkedIn Huiguang He souhaite se connecter à vous sur LinkedIn : -- Freesurfer, Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Huiguang He http://www.linkedin.com/e/-qq80um-gtldw1um-5w/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/blk/I115482657_65/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYRdBYTdjoOe3gRcj59bPlOdT91s5ZjbPkQdz0RdzwMdjgLrCBxbOYWrSlI/EML_comm_afe/?hs=falsetok=0sSDmefvRlfQY1 Voir le profil de Huiguang He http://www.linkedin.com/e/-qq80um-gtldw1um-5w/rsn/72703165/ArO9/?hs=falsetok=1yeuyNQ31lfQY1 -- ___ 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] nonlabeled vertices in bert
Can you and us a picture? Cheers Bruce On Oct 10, 2011, at 7:08 AM, Ben Hamida Cammoun Leila Faiza leila.camm...@epfl.ch wrote: Hello, 1) I reiterate my question, because i cannot continue processing. Some vertices are not labeled in the rh.aparc.annot in bert as 35643,36746,37788. 2) The parcels of my subject are not connex. Below is the detail on my first email. Thank you very much for answering me De : Ben Hamida Cammoun Leila Faiza Envoyé : jeudi 6 octobre 2011 14:53 À : Objet : nonconnexity and holes in parcels Hello, I am using freesurfer v5.1.0 (on ubuntu). when processing reconall on my data I notice on the parcellation aparc.annot two strange points: some isolated small regions not annotated, as well as the non connexity of some parcels. I checked the bert aparc.annot on inflated surface and I found the same problem of non connexity, for instance some medialorbitofrontal labeled vertices (vertex index 108562) in rostralanteriorcingulate, or vertex num 103429 labeled as insula in lateralorbitofrontal parcel. In lingual there is also a small hole without annotation like vertices: 35643,36746,37788. is this normal? if yes, how can we correct that? thanks in advance ___ 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] Cerebellum pail surface
Hi, I'm trying to get red and green lines for cerebellum.. How can I do?. There are green and red lines for the cortex. Should I re-convert the data? Thank you. ___ 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] WM hypointensities and corpus callosum mislabeling
Hello, In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there fixes that don't involve manually doctoring the mislabelings (such as setting a particular flag for recon)? I am quite new to FS so please forgive any rudimentary misunderstandings. Thank you! Warren -- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ 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] retinotopy description
hi michelle, the Sereno et al. 1995 Science paper has details about the phase encoded retinotopic data analysis, especially in the endnotes of the article. also for more details you can look at the MATLAB code embedded in the command 'selfreqavg', which is used for the basic retinotopy analysis and is quite readable. hope this helps, -jon On Wed, 21 Sep 2011, Michelle Umali wrote: Hi Freesurfers. Is there text describing the retinotopy analysis in Freesurfer mathematically? Thanks. Michelle ___ 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] selfreqavg
Hi Jon, Thanks! I have a question about when selfreqavg. When do I use selfreqavg? Is it called when I run fieldsign-sess or do I have to run it in addition to the below? I've been doing the following: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj09 -force selxavg3-sess -a rtopy.self.lh -s sj09 selxavg3-sess -a rtopy.self.rh -s sj09 fieldsign-sess -a rtopy.self.lh -occip -s sj09 fieldsign-sess -a rtopy.self.rh -occip -s sj09 Thanks for your help. Michelle On Mon, Oct 10, 2011 at 5:30 PM, Jonathan Polimeni j...@nmr.mgh.harvard.edu wrote: hi michelle, the Sereno et al. 1995 Science paper has details about the phase encoded retinotopic data analysis, especially in the endnotes of the article. also for more details you can look at the MATLAB code embedded in the command 'selfreqavg', which is used for the basic retinotopy analysis and is quite readable. hope this helps, -jon On Wed, 21 Sep 2011, Michelle Umali wrote: Hi Freesurfers. Is there text describing the retinotopy analysis in Freesurfer mathematically? Thanks. Michelle 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] WM hypointensities and corpus callosum mislabeling
Hi Warren can you send us some images to show us what you mean? Or upload an example dataset for us to look at? cheers Bruce On Mon, 10 Oct 2011, Warren Winter wrote: Hello, In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there fixes that don't involve manually doctoring the mislabelings (such as setting a particular flag for recon)? I am quite new to FS so please forgive any rudimentary misunderstandings. Thank you! Warren -- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ 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] nonlabeled vertices in bert
Hi Ben if the unlababeled vertices are in non-cortical regions, e.g. on the midline, then this is normal. We also only enforce connectivity by removing small regions. If there are multiple large parts to a parcel, we don't relabel it as this can occur using some anatomical definitions. We can't tell if your case is right without seeing it though cheers Bruce On Mon, 10 Oct 2011, Ben Hamida Cammoun Leila Faiza wrote: Hello, 1) I reiterate my question, because i cannot continue processing. Some vertices are not labeled in the rh.aparc.annot in bert as 35643,36746,37788. 2) The parcels of my subject are not connex. Below is the detail on my first email. Thank you very much for answering me De : Ben Hamida Cammoun Leila Faiza Envoyé : jeudi 6 octobre 2011 14:53 À : Objet : nonconnexity and holes in parcels Hello, I am using freesurfer v5.1.0 (on ubuntu). when processing reconall on my data I notice on the parcellation aparc.annot two strange points: some isolated small regions not annotated, as well as the non connexity of some parcels. I checked the bert aparc.annot on inflated surface and I found the same problem of non connexity, for instance some medialorbitofrontal labeled vertices (vertex index 108562) in rostralanteriorcingulate, or vertex num 103429 labeled as insula in lateralorbitofrontal parcel. In lingual there is also a small hole without annotation like vertices: 35643,36746,37788. is this normal? if yes, how can we correct that? thanks in advance ___ 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.
