Re: [Freesurfer] Insula gyral and sulcal images
Dear Alexander, Right now, you can access the following labels in the aparc.a2009 parcellation (see http://www.ncbi.nlm.nih.gov/pubmed/20547229 for details): - G_Ins_lg_and_S_cent_ins : groups the Long insular gyri and the central sulcus of the insula - G_insular_short : groups the Short insular gyri - S_circular_insula_ant, S_circular_insula_inf, S_circular_insula_sup for the anterior, inferior and superior parts of the circular sulcus of the insula You can access these labels by loading the aparc.a2009 file ; the stats (including thickness) are located into the stats directory of you subject, in the ?h.aparc.a2009s.stats files. Sincerely -- Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - De: "Aleksander Dionisio" À: freesurfer@nmr.mgh.harvard.edu Envoyé: Samedi 31 Janvier 2015 01:04:56 Objet: [Freesurfer] Insula gyral and sulcal images Hello, first time posting after several google searches. Could anyone help to answer if there is a way to have a detailed reconstruction of the insula cortex with the gyral and sulcal anatomy? Details would include thickness of each sulcus and gyrus etc? How could this be achieved if there is such a way. Many thanks! === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2014). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer Courses 2015
Hi we will organize one in Tours, Loire Valley France next may, with the Boston team sincerely Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > Le 30 juil. 2015 à 10:22, Charalambous, Thalis > a écrit : > > To whom it may concern, > > My name is Thalis and I am about to start my PhD at University College London > (UCL). FreeSurfer is going to be a very useful tool and for this reason I am > thinking of attending the course that will take place in Boston between the > 28/09/2015-1/10/2015. > However, I would like to ask whether there are any other courses taking place > in Europe in the next couple of months that would be more convenient for me > to attend. > > Regards, > > Thalis Charalambous > > > ___ > 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 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] freesurfer atlases/versions
Hi Narly You are right: The anatomical parcellation is the same (aparc.a2009s) as the one included in the 4.5 FS version (see also http://surfer.nmr.mgh.harvard.edu/fswiki/DestrieuxAtlasChanges). Cheers -- Christophe - Mail original - > De: "Narly Golestani" > À: freesurfer@nmr.mgh.harvard.edu > Envoyé: Vendredi 28 Décembre 2012 21:13:05 > Objet: [Freesurfer] freesurfer atlases/versions > > > > Dear all, > > I have a quick question re- the different atlases used by the > different versions of freesurfer. I'd like to know if there will be > any differences in the auditory cortex labelization process if we > use freesurfer version 4.5 and upwards. From the below post I have > the impression that version 4.5 and upwards (until 5.2?) all apply > similar rules for parcellating the 3 auditory cortex ROIs that we're > interested in (the transverse temporal gyrus and sulcus, and the > planum temporale). > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20932.html > > Thanks in advance for your input, > with best wishes, > Narly Golestani. > > ___ > 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] Tracula preprocessing step error
Hi I add the same problem; It finally worked : - using libreoffice instead of excel to transpose the bvec/bval files ; - with english as linguisitic parameter, - save the file as cvs document, with the filter parameters box checked - in the filer option choose "space" as field separator; " as text separator, "unicode UTF-8" as encoding cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - > De: "Anastasia Yendiki" > À: "Allison Gruber" > Cc: Freesurfer@nmr.mgh.harvard.edu > Envoyé: Mercredi 9 Janvier 2013 22:43:01 > Objet: Re: [Freesurfer] Tracula preprocessing step error > > > Hi Allison - Instead of using excel, I would use a unix-based text > editor, > whichever is available on the system where you are running the > analyses. > This way you can ensure that unix commands read your text files > properly. > > The 3 values for each diffusion gradient vector are its x, y, z > components, so I wouldn't change their order, unless you have reason > to > believe that the order is not correct the way it was given to you. > > Hope this helps, > a.y > > On Wed, 9 Jan 2013, Allison Gruber wrote: > > > Hi Anastasia, > > > > Thanks so much for your help. I was able to correct this problem in > > my > > configuration file. I have now run into another error- "bvecs and > > bvals don't have the same number of entries." I have read other > > postings about this error and can see that my bvec file is not > > formatted correctly when I import into Excel. However, I am not > > sure > > how to correctly fix this formatting. I know that I have 28 bval > > entries and > > 84 bvec entries, so the overall number is correct. I am just > > unclear on how > > to fix the formatting of the bvec file so that it corresponds > > correctly to > > the ordering in the bval file (which order the bvec entries should > > appear in > > within the three columns). Do you have any resources on this? > > > > Thank you again for your help, > > Allison > > > > Quoting Anastasia Yendiki : > > > >> > >> Hi Allison - The mri_convert command at the top of your log file > >> is > >> trying to convert the directory > >> /Users/Desktop/Tracula/diffusion_DTI to > >> a nifti file. From the name of that nifti file, it looks like it's > >> expecting to find a field map and not finding it. > >> > >> Hope this helps, > >> a.y > >> > >> On Tue, 8 Jan 2013, Allison Gruber wrote: > >> > >> > Dear Freesurfer experts, > >> > > >> > I have encountered the following error while running the tracula > >> > pre-processing command and was hoping you could help me > >> > understand how > >> > to correct this. > >> > > >> > Selection from log: > >> > > >> > mri_convert /Users/Desktop/Tracula/diffusion_DTI/ > >> > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz > >> > mri_convert /Users/Desktop/Tracula/diffusion_DTI/ > >> > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz > >> > corRead(): can't open file > >> > /Users/Desktop/Tracula/diffusion_DTI/COR-.info > >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > >> > reading from /Users/Desktop/Tracula/diffusion_DTI/... > >> > Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: > >> > Mon Apr > >> > 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 > >> > > >> > trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 > >> > > >> > Please let me know if this is not enough information. Thank you > >> > for > >> > your help. > >> > > >> > Allison > >> > ___ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > > >> >
Re: [Freesurfer] Divisions for "anterior" and "posterior" insula?
Hi Nassim I would say : > Anterior insula = "G_insular_short" > Posterior insula = "G_Ins_lg_and_S_cent_ins" I wouldn't add the circular sulcus of the insula which limits it from the surrounding frontal, parietal and temporal opercula cheers > -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - > De: "Nasim Maleki" > À: freesurfer@nmr.mgh.harvard.edu > Envoyé: Mercredi 13 Mars 2013 16:17:00 > Objet: [Freesurfer] Divisions for "anterior" and "posterior" insula? > > Hi all, > > I have a hard time relating the boundaries of the insula defined by > Freesurfer (Destrieux a2009s) with what is out there in the > literature. Most of what is out there is described in terms of > anterior and posterior insula, and I'm not sure if most of them > match well with what is described in Destrieux et al. paper > (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/?tool=pubmed) > as the "anterior" and "posterior" insula as described below: > > "The central sulcus of the insula ran antero-inferiorly from the > superior segment of the circular segment of the insula. It was a > small sulcus that was not always visible on its whole course on the > inflated views. It divided the insula in two parts: the short > insular gyri [G_insular_short, 18] (anterior) and the long insular > gyrus (posterior). Due to their small size, the central sulcus of > the insula and the long insular gyri were grouped in the same label > [G_Ins_lg_and_S_cent_ins, 17]." > > Based on these definitions, would it be fair to say: > Anterior insula = "G_insular_short" and "S_circular_insula_ant" > Posterior insula = "G_Ins_lg_and_S_cent_ins" and > "S_circular_insula_inf" > > Thank you for your help, > Nasim > ___ > 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] Definition of medial temporal lobe
Hi You would probably like to include : - the parahippocampal gyrus - the hippocampus - the amygdala but not the brain stem The question is more complex for the entorhinal area since it is a part of the parahippocampal gyrus. To make things simple : - the hippocampus lies at the superior aspect of the parahippocampal gyrus. At the level of the body of the hippocampus, this flat region is known as the subiculum - at the level of the hippocampus head, the anterior part of the parahippocampal gyrus is know as the piriform lobe, which itself divides in 2 parts : - the entorhinal area, that rostraly continues the subiculum, - and the uncal part of the piriform lobe that curves posteriorly to form the rostral part of the uncus So including the entorhinal + parahippocampal would include the entorhinal area twice ; the aparc.a2009s consider the PHG as a whole. cheers -- Christophe Destrieux, - Mail original - > De: "Akshay" > À: freesurfer@nmr.mgh.harvard.edu > Envoyé: Lundi 18 Mars 2013 14:59:03 > Objet: [Freesurfer] Definition of medial temporal lobe > Hello freesurfer experts, > I am doing some TBM analysis and I am looking for the definition of > Medial temporal lobe. According to the definitions I found out they > are > hippocampus+amygdala+brainstem+parahippocampal regions+entorhinal > region. > I can get hippocampus and amygdala ROI from aseg.mgz; however for > parahippocampal and entorhinal regions should i use aparc+aseg.mgz > and > aparc.a2009s+aseg.mgz? > Any help will be appreciated. > Best, > Akshay > ___ > 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 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] Merging PArcellation labels
Hi did you look at : https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014620.html cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - > De: "Anupa AV" > À: freesurfer@nmr.mgh.harvard.edu > Envoyé: Samedi 23 Mars 2013 10:36:06 > Objet: [Freesurfer] Merging PArcellation labels > Dear All, > Can anyone tell me how to merge the parcellation labels using > tksurfer.? For eg. How can I merge, Superior frontal gyrus, middle > frontal gyrus and caudal middle frontal gyrus. > ___ > 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 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] Where does a sulcus end and a gyrus begin in FreeSurfer?
Hi Daniel for the aparc.a2009 atlas : - The average convexity sulco-gyral threshold vas usually set to 0 for the lateral cortex, and to 0.18 for the medial cortex. - The average convexity value was negative for the whole insula (located deeply in the lateral sulcus/fossa). For the insular region, we used the mean curvature in a similar way: vertices with a positive mean curvature value were considered sulcal, and vertices with non positivevalues were considered gyral. for more detail you can have a look to Destrieux C, Fischl B, Dale A, Halgren E. Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. Neuroimage 2010; 53: 1-15. cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - > De: "Daniel Yang" > À: "Bruce Fischl" > Cc: freesurfer@nmr.mgh.harvard.edu > Envoyé: Lundi 22 Avril 2013 23:31:36 > Objet: Re: [Freesurfer] Where does a sulcus end and a gyrus begin in > FreeSurfer? > > Thanks, Bruce! > > The average-convexity-crossing-zero idea makes good sense. > > Also I can see the segmentation/parcellation label in tkmedit when I > move > my cursor. That makes it clear which label is which. > > Best, > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > > > > > > On 4/22/13 5:01 PM, "Bruce Fischl" > wrote: > > >Hi Daniel > > > >we have had various neuroanatomists make that decision, but the > >typical > >measure used is the average convexity or sulc (stored in ?h.sulc). > >Where > >it > >crosses 0 is where the changeover is usually deemed to be > > > >cheers > >Bruce > > > > > >On Mon, 22 Apr 2013, Yang, Daniel wrote: > > > >> Dear FreeSurfer Experts and Users, > >> > >> This is probably a basic question, so please bear with me. > >> > >> I'm looking at the Coronal view in tkmedit, and I am wondering how > >> does > >> FreeSurfer knows where a gyrus ends and a sulcus begins (and vice > >>versa). > >> > >> For example, I'm looking at the superior temporal sulcus. But I'm > >> not > >>sure > >> how FS figures out which part is superior temporal gyrus, middle > >>temporal > >> gyrus, or superior temporal sulcus? > >> > >> Thanks! > >> Daniel > >> > >> > >> > >> > >> > > > > > >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
[Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016
Dear FreeSurfers, It is our pleasure to welcome you the FreeSurfer course organized in Tours, Loire Valley, France, 2016 26-27th may. This event is coorganized by the brain and imaging laboratory, INSERM U930-Université François Rabelais of Tours (France) and by the Martinos Center for Biomedical Imaging in Charlestown, MA (USA) which develops and distributes FreeSurfer. <http://freesurfer.net/> This course will be limited to 64 participants. It will focus on surface-based analysis of individual and group morphological data and on tractographic analysis using FreeSurfer tools. This course will be organized in the Ecole Polytechnique de l'Université de Tours For online registration, please visit : http://freesurfer2016.sciencesconf.org/?lang=en See you in Tours next May C Destrieux, F Andersson, L Barantin, S Love, M Sta, C Tauber Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ 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] Planum temporale measurement
Hi Adam, sorry for the delay in my answer The aparc.a2009s is based on the anatomical rules we published in Neuroimage in 2010: - There are 2 separate labels : one is sulcal, for the posterior part of the lateral fissure (Lat_Fis-post), the other one is gyral, for the planum temporale (G_temp_sup-Plan_tempo) - I’m not quite sure to understand the second part of the question : in my mind the lateral fissure can be divided in 3 segments (anterior, middle, posterior), and the posterior one is more or less ascending. There was only a single label (Lat_Fis-post) for the posterior segment of the lateral fissure I hope it helps — Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours Service de Neurochirurgie Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours - France Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau: christophe.destri...@univ-tours.fr Web : http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> > Le 5 févr. 2016 à 01:19, Adam David Felton a > écrit : > > Hello, > > I checked the listserv history, but couldn't find an answer to my question: > > With the 2009 parcellation scheme, 1) does the planum temporale parcellation > include the posterior ascending ramus (which Destrieux et al. 2010 seems to > imply) and 2) does the planum temporale include the posterior descending > ramus? > > > > Thank you! > > > > > Adam > ___ > 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 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] FreeSurfer Course Tours, France, 26-27/05/2016
Dear Caroline could you please resend it in english or in French ; I’m not too familiar with Flamish ; ) thanks Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > Le 12 févr. 2016 à 09:53, Caroline Beelen a > écrit : > > Dag Jolijn, > > Heb jij je al aangemeld voor onderstaande Freesurfer course? Er is volgens > mij nog steeds niets van die andere beschikbaar, dus ik twijfel ook om te > gaan (zou wel nuttig zijn!). Al is het een beetje achter de feiten aan… > > Vriendelijke groet, > > Caroline > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Christophe Destrieux > Verzonden: woensdag 3 februari 2016 18:00 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016 > > Dear FreeSurfers, > > It is our pleasure to welcome you the FreeSurfer course organized in Tours, > Loire Valley, France, 2016 26-27th may. > This event is coorganized by the brain and imaging laboratory, INSERM > U930-Université François Rabelais of Tours (France) and by the Martinos > Center for Biomedical Imaging in Charlestown, MA (USA) which develops and > distributes FreeSurfer. <http://freesurfer.net/> > This course will be limited to 64 participants. It will focus on > surface-based analysis of individual and group morphological data and on > tractographic analysis using FreeSurfer tools. > This course will be organized in the Ecole Polytechnique de l'Université de > Tours > For online registration, please visit : > http://freesurfer2016.sciencesconf.org/?lang=en > <http://freesurfer2016.sciencesconf.org/?lang=en> > See you in Tours next May > C Destrieux, F Andersson, L Barantin, S Love, M Sta, C Tauber > > > Christophe Destrieux, > Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais > de Tours > http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> > > Service de Neurochirurgie > et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 > Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > > > ___ > 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 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] FreeSurfer Course Tours, France, 26-27/05/2016
Bon problem ; I guessed it was something like this ; ) Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > Le 12 févr. 2016 à 11:02, Caroline Beelen a > écrit : > > Hi Christophe, > > Apologies, I wanted to forward the mail but instead replied to it. ;) > > Regards, Caroline > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Christophe Destrieux > Verzonden: vrijdag 12 februari 2016 10:45 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016 > > Dear Caroline > could you please resend it in english or in French ; I’m not too familiar > with Flamish ; ) > thanks > > Christophe Destrieux, > Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais > de Tours > http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> > > Service de Neurochirurgie > et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 > Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > > > Le 12 févr. 2016 à 09:53, Caroline Beelen <mailto:caroline.bee...@ppw.kuleuven.be>> a écrit : > > Dag Jolijn, > > Heb jij je al aangemeld voor onderstaande Freesurfer course? Er is volgens > mij nog steeds niets van die andere beschikbaar, dus ik twijfel ook om te > gaan (zou wel nuttig zijn!). Al is het een beetje achter de feiten aan… > > Vriendelijke groet, > > Caroline > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] Namens Christophe Destrieux > Verzonden: woensdag 3 februari 2016 18:00 > Aan: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Onderwerp: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016 > > Dear FreeSurfers, > > It is our pleasure to welcome you the FreeSurfer course organized in Tours, > Loire Valley, France, 2016 26-27th may. > This event is coorganized by the brain and imaging laboratory, INSERM > U930-Université François Rabelais of Tours (France) and by the Martinos > Center for Biomedical Imaging in Charlestown, MA (USA) which develops and > distributes FreeSurfer. <http://freesurfer.net/> > This course will be limited to 64 participants. It will focus on > surface-based analysis of individual and group morphological data and on > tractographic analysis using FreeSurfer tools. > This course will be organized in the Ecole Polytechnique de l'Université de > Tours > For online registration, please visit : > http://freesurfer2016.sciencesconf.org/?lang=en > <http://freesurfer2016.sciencesconf.org/?lang=en> > See you in Tours next May > C Destrieux, F Andersson, L Barantin, S Love, M Sta, C Tauber > > > Christophe Destrieux, > Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais > de Tours > http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> > > Service de Neurochirurgie > et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 > Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > ___ > 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 > a
Re: [Freesurfer] Reference about: MeanCurv, GausCurv, FoldInd, CurvInd?
this was : Van Essen, D.C., Drury, H.A., 1997. Structural and functional analyses of human cerebral cortex using a surface-based atlas. J Neurosci 17, 7079–102. Cheers — Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours Service de Neurochirurgie Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours - France Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau: christophe.destri...@univ-tours.fr Web : http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> > Le 20 févr. 2016 à 19:22, Bruce Fischl a écrit : > > Hi Marta > > A 2D surface (like the cortical white or pial models) has two principal > curvatures at each point - one in the direction of maximum curvature and one > in the direction of minimum curvature - typically denoted k1 and k2. The mean > curvature is the average of these H=(k1+k2)/2 and the Gaussian curvature is > the product of them K=(k1 * k2). So, MeanCurv is the integral of the > absolute value of H and GausCurv is the integral of the absolute value of K. > FoldInd and CurvInd are two indices proposed by David Van Essen in a paper > from years ago that we also compute. Sorry, I don't have the right reference > handy, perhaps someone else on the list does? > > cheers > Bruce > > > On Tue, 16 Feb 2016, Karas, Marta wrote: > >> H! >> I am working with data which is an output from the FreeSurfer processing. >> I would like to kindly ask you to refer me to materials / precise >> "mathematical" definitions that could help to understand what are the >> following parameters: >> * MeanCurv - Integrated Rectified Mean Curvature, >> * GausCurv - Integrated Rectified Gaussian Curvature, >> * FoldInd - Folding Index, >> * CurvInd - Intrinsic Curvature Index. >> (I have been trying to google but not been successful, unfortunately.) >> Kind regards, >> Marta Karas, M.S. >> Research Assistant, Department of Biostatistics >> Richard M. Fairbanks School of Public Health and School of Medicine >> Indiana University >> tel: 317-665-4551 >> email: mka...@iu.edu > ___ > 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 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] Freesurfer course in Tours, France, 26-27 May 2016
Dear colleagues, It is our pleasure to host a FreeSurfer course in Tours, Loire Valley, France, 26-27 may. This event is coorganized by the brain and imaging laboratory, INSERM U930-Université François Rabelais of Tours (France) and by the Martinos Center. It will be limited to 64 participants and will focus on surface-based analysis of individual and group morphological data and on tractographic analysis using FreeSurfer tools. See you in Tours next May! Registration and information : http://freesurfer2016.sciencesconf.org/?lang=en — Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours Service de Neurochirurgie Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours - France Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau: christophe.destri...@univ-tours.fr Web : http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> ___ 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] Insula annotation on cortical surface
Hi in the aparc.a2009s atlas several labels correspond to the insula : - Short insular gyri (G_insular_short) - Long insular gyrus and central sulcus of the insula were grouped together (G_Ins_lg_and_S_cent_ins) since the central sulcus of the insula was not deep enough to be seen on its whole length there are also 3 labels for the circular sulcus of the insula limiting this region from frontal, temporal and parietal lobes: -Anterior segment (S_circular_insula_ant) -Inferior segment (S_circular_insula_inf) -Superior segment (S_circular_insula_sup) For a detailed list (table 1) and anatomical description of these labels, you can have a look to : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/?tool=pubmed cheers -- -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - > De: "Jie Shi" > À: freesurfer@nmr.mgh.harvard.edu > Envoyé: Lundi 2 Janvier 2012 01:25:21 > Objet: [Freesurfer] Insula annotation on cortical surface > Hi, does anyone know whether the insula area has an annotation on the > cortical surface segmented by FreeSurfer as isthmus, posterior > cingulate, etc? Thanks a lot. > Jie > ___ > 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 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] Destrieux atlas 2002
Hi Holger The problem with older atlases is that the labeling was not accurate enough, which explains why we had to group several label in the 2009 version Using older version is probably not a good idea. I don't exactly know what you want to do but I can tell that if several “transverse” temporal gyri were present, only the most anterior was included in [G_temp_sup-G_T_transv], which is supposed to corresponds to primary auditory cortex . Additional, more posterior, secondary "transverse temporal gyri" were included in the parcellation planum temporale [G_temp_sup-Plan_tempo] since they are made of secondary auditory cortex you can have a look to - http://surfer.nmr.mgh.harvard.edu/fswiki/DestrieuxAtlasChanges and - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/?tool=pubmed I don't know if it helps cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - > De: "Holger Klein" > À: freesurfer@nmr.mgh.harvard.edu > Envoyé: Mardi 3 Janvier 2012 19:34:30 > Objet: [Freesurfer] Destrieux atlas 2002 > Dear freesurfers, dear Mr. Destrieux, > I have a question concerning the destrieux atlas 2002: I need a > distinct label " G_temp_sup-G_temp_transv_and_interm_S" , which is > only available in this atlas version. I tried using "? > .atlas2002_simple.gcs", but this atlas does not output the requested > label - but the labels of the default ?.aparc.annot. How can I get the > mentioned label (with the original boundaries of this region). > Would be glad about any help, THX > Holger > ___ > 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 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] insula on medial surface
Hi Michael the limen insula explanation sounds ok, even if it's extension on the medial surface seem really large. would you have a snapshot to look on the volume to which structure this label anatomically corresponds to ? Also did you had a look to the results of the insula aparc with the 2009a atlas? cd -- Christophe Destrieux, Directeur du Département Communication et Multimédia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - De: "Michael Harms" À: "Freesurfer support list" Cc: "Ron KILLIANY" Envoyé: Jeudi 7 Août 2014 22:18:49 Objet: Re: [Freesurfer] insula on medial surface I'm not itching to re-process this data so I like that explanation as well. I think my main concern is that that bit of insula label seems somewhat arbitrary and inconsistent, in that some subjects have this bit of medial tissue labelled as insula, whereas others don't. (Even within the same subject, it isn't consistent between the two hemispheres). I guess it is just a matter of the sulcal variability and atlas labeling resulting in variability in that particular region. Presumably, Ron must have labelled that bit of tissue as "insula" in some subjects, but not others?? Ron: It would be great to hear what kind of "rule" you applied when labeling the individual subjects in the atlas in that particular region when deciding whether it should be considered insula or medial/lateral orbitofrontal. thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 8/7/14 2:52 PM, "Bruce Fischl" wrote: >wow, I like that answer much more than "it's a bug"! Can we go with >Paul's explanation? > > >Bruce > >On Thu, 7 Aug 2014, Paul Beach wrote: > >> I asked a neuroanatomist and insula expert on my campus about this a >>while >> back and this was his response: >> "This is the region of the "limen insulae" that you will remember Dr. >>Heimer >> referring to often in the brain dissection course. The insula is >>defined as >> cortex which is covered by a lid of other cortical lobes, frontal, >>parietal >> and temporal. They all fold over except at the inferior frontal end >>where a >> little bit of the surface of otherwise insular cortex is not covered, >>and >> this little corner peeks out. This is the limeninsula which neighbors >>the >> olfactory cortex on the inferior surface of the frontal lobe and the >>medial >> surface of the temporal lobe, and is olfactory cortex itself. Since it >>is >> not covered over, it technically might not be considered really >>"insular" >> but it is obviously in continuity with, and not separated by any kind of >> sulcus or other landmark, from the rest of the insular covered cortex. >>So we >> are left with no secure boundary line between insular cortex and >>inferior >> frontal and medial temporal cortex in this corner. It looks like >>Freesurfer >> has decided to call it all insular, and with good functional reasons." >> >> >> Cheers, >> >> >> >> On Thu, Aug 7, 2014 at 3:32 PM, Bruce Fischl >> >> wrote: >> Hi Mike >> >> I'm not sure - I think the insula was an additional label that >> Ron Killiany added. I'll cc Ron to see if he has any insight. It >> certainly looks too medial to me. >> >> I would also check on the white surface just to make sure that >> it's not a quirk of the inflation. If the aseg looks right we >> could certainly put together some simple auto-editing to correct >> this kind of thing >> >> cheers >> Bruce >> >> >> On Thu, 7 Aug 2014, Harms, Michael wrote: >> >> >> Hi, >> An astute RA, while reviewing the aparc+aseg.mgz of brains >> processed with FS >> 5.3, noticed a fair number of instances, where the insula >> label "wraps >> around" pretty medially, where she was expecting to see >>
Re: [Freesurfer] insula on medial surface
Hi Michael, I looked at the 2 subjects you sent me : the insula label of the aparc/aseg parcellation is obviously too large : it includes the insula, the limen insulae and, from there it propagates to the anterior perforated space, just posterior to the orbital gyri, to join the subcallosal area. I don't know why, but I assume it is more linked to the original parcellation used to build the atlas than to the automatic labeling process since the other atlases you mentionned give quite correct results. if you need a more acurate parcelation of the insula you should maybe use one of these alternative parcellation schemes : - ?h.aparc.a2009s.annot / aparc.a2009s+aseg.mgz or ?h.aparc.DKTatlas40.annot give about the same result for the insula except that ?h.aparc.a2009s.annot / aparc.a2009s+aseg.mgz gives several labels for the whole insula (circular sulcus, long, short gyri). - Since ?h.aparc.DKTatlas40.annot insula label includes the long and short insular gyri but also part of the circular sulcus, its size is a bit larger than the sum of the long and short insular gyri of the ?h.aparc.a2009s.annot parcellation I hope it helped ; cheers -- Christophe Destrieux, Directeur du Département Communication et Multimédia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - De: "Michael Harms" À: "Michael Harms" , "Christophe Destrieux" , "Freesurfer support list" Cc: "Ron KILLIANY" Envoyé: Vendredi 8 Août 2014 18:04:06 Objet: Re: [Freesurfer] insula on medial surface Hi, In response to Christophe's question, I looked at the two other whole brain parcellation schemes -- DKTatlas40 and a2009s. In those two subjects at least, that medial region which is labelled "insula" in the aparc.annot is labelled (mostly) as medial/lateral orbitofrontal (with some even as rostralanteriorcingulate) in aparc.DKTatlas40.annot, and as G_subcallosal in aparc.a2009s.annot. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 8/8/14 10:30 AM, "Harms, Michael" wrote: > >Hi Christophe, >I uploaded both subjects that I showed the snapshots for yesterday into >the FS FTP drop site. (Do you have access to that?) > >cheers, >-MH > >-- >Michael Harms, Ph.D. > >--- >Conte Center for the Neuroscience of Mental Disorders >Washington University School of Medicine >Department of Psychiatry, Box 8134 >660 South Euclid Ave. Tel: 314-747-6173 >St. Louis, MO 63110 Email: mha...@wustl.edu > > > > >On 8/7/14 4:03 PM, "Christophe Destrieux" > wrote: > >>Hi Michael >>the limen insula explanation sounds ok, even if it's extension on the >>medial surface seem really large. would you have a snapshot to look on >>the volume to which structure this label anatomically corresponds to ? >>Also did you had a look to the results of the insula aparc with the 2009a >>atlas? >>cd >> >>-- >>Christophe Destrieux, >> >>Directeur du Département Communication et Multimédia >>http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651 >>1 >>59612 >> >>Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François >>Rabelais de Tours >>http://www.u930.tours.inserm.fr/ >> >>Service de Neurochirurgie >>et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé >>37032 Tours - France >>tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 >> >> >>- Mail original - >>De: "Michael Harms" >>À: "Freesurfer support list" >>Cc: "Ron KILLIANY" >>Envoyé: Jeudi 7 Août 2014 22:18:49 >>Objet: Re: [Freesurfer] insula on medial surface >> >> >>I'm not itching to re-process this data so I like that explanation as >>well. I think my main concern is that that bit of insula label seems >>somewhat arbitrary and inconsistent, in that some subjects have this bit >>of medial tissue labelled as insula, whereas others don't. (Even within >>the same subject, it isn'
[Freesurfer] 'lh_G_Ins_lg&S_cent_ins_volume' and 'lh_G_insular_short_volume'
External Email - Use Caution Hi Rujing Sorry for the late answer. These 2 labels correspond to the insula The insula is divided by the central sulcus of the insula (S_cent_ins_) into long insular gyri (G_Ins_lg) and short insular gyri (G_insular_short). Since the cortex lining the central sulcus of the insula was quite small, it has been grouped together with the the long insular gyri ( 'lh_G_Ins_lg&S_cent_ins_volume’) If you are interested in the volume of the whole insula you need to add the volumes of these two anatomical classes. For a complete list of anatomical classes and explanations on their anatomical meaning see : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/ Best Christophe Destrieux, Unité iBrain UMRS INSERM U1253, Université de Tours https://ibrain.univ-tours.fr/ <https://ibrain.univ-tours.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > Le 21 nov. 2018 à 17:12, Bruce Fischl a écrit : > > you are getting very popular! > > > -- Forwarded message -- > Date: Wed, 21 Nov 2018 14:30:13 +0800 > From: charujing123 > Reply-To: Freesurfer support list > To: "freesurfer@nmr.mgh.harvard.edu" > Subject: [Freesurfer] 'lh_G_Ins_lg&S_cent_ins_volume' and >'lh_G_insular_short_volume' > > > External Email - Use Caution > > Hi, what is difference between and 'lh_G_insular_short_volume'. Are > these both insula? > Thanks. > Rujing > > 2018-11-21 > > > charujing123 > ___ > 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] What is "...S_central" in Destrieux atlas?
External Email - Use Caution Right See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/> , table 1 Best > > Christophe Destrieux > Laboratoire d'anatomie - Faculte de Medecine > 10, bd Tonnelle - 37032 Tours > 02 47 36 61 36 > > > > >> Le 15 nov. 2018 à 01:49, Bruce Fischl a écrit : >> >> S_ is for sulcus and G_ is for gyrus, so S_central is the central sulcus. I >> think Christophe included a table in his paper (right Christophe?) >> >> cheers >> Bruce >>> On Wed, 14 Nov 2018, Colin Birkenbihl wrote: >>> >>>External Email - Use Caution >>> Dear all, >>> I am currently working with MRI features calculated with the Destrieux >>> atlas. >>> As an output I have features named like: >>> Vol_Right_S_Central >>> Vol_Left_G_precentral >>> or >>> Vol_Left_S_orbital-H_Shaped >>> I wanted to ask you, what these features stand for and if there is some >>> mapping of those feature >>> names to brain region names which are clearly interpretable. >>> If not, it would be great if you could tell me what the above mentioned >>> features refer to. >>> It would be great if you could help me. >>> Best wishes, >>> Colin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Zeroes for few regions in 'aparc.a2009s' parcellation.
External Email - Use Caution Hi Bruce and Vittal could be, but looks strange to me since the listed sulci seems quite consistant to me. Vittal could you put one of these subjets somewhere ; I could look at their cortical folding best — Christophe Destrieux, Unité « Imagerie et Cerveau » (iBrain) INSERM U1253, Université de Tours Service de Neurochirurgie Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours - France Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau: christophe.destri...@univ-tours.fr Web : http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> > Le 10 juil. 2018 à 15:59, Bruce Fischl a écrit : > > Hi Vittal > > Christophe (ccd) can confirm, but I believe that there are areas in his > parcellation that don't occur in every subject (rare folding variants). > > cheers > Bruce > > On Tue, 10 Jul 2018, vittal korann wrote: > >> External Email - Use Caution >> Hello Freesurfer developers, >> I ran recon-all command to extract all subjects stats. Here I'm mainly >> targetting the surface area, >> volume, thickness and mean curve for all subjects. >> " recon-all -i /filepath/file/ -s /subjectid/ -all " this was the command i >> used. >> Now the problem is that I'm getting zeroes for the surface area which is >> parcellated from >> 'aparc.a2009s' and it occurred for a large number of subjects. >> The command for converting stats to .txt is given below: >> aparcstats2table --hemi lh --subjects 004 008 --parc aparc.a2009s --meas >> area --tablefile lh.a2009s. >> area.txt >> lh_G&S_frontomargin_area >> lh_G&S_occipital_inf_area >> lh_G&S_paracentral_area >> lh_G&S_subcentral_area >> lh_G&S_transv_frontopol_area >> lh_G&S_cingulAnt_area >> I wanted to know the reason for getting these zeroes. Could anyone plz help >> me out in this regard. >> Thanks in advance! >> Best >> Vittal >> > > > 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.
[Freesurfer] PhD position avalaible in Torus, France : hisgh resolution Brainstem atlas
External Email - Use Caution Dear all, we have an open 3-year position for a PhD student in our lab in Tours, France beginning 2018, oct 1st. This student will work on a brainstem atlas from 11.7T exvivo MRI data. Details are included here : https://ibrain.univ-tours.fr/actualites/scientifiques/offres-de-recrutement/phd-position-development-of-a-multiscale-mri-atlas-of-the-human-brainstem-638411.kjsp?RH=1381307896713 <https://ibrain.univ-tours.fr/actualites/scientifiques/offres-de-recrutement/phd-position-development-of-a-multiscale-mri-atlas-of-the-human-brainstem-638411.kjsp?RH=1381307896713> Do not hesitate to distribute Christophe Destrieux, Unité iBrain UMRS INSERM U1253, Université de Tours http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ 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] Medial prefrontal cortex mPFC in Destrieux Atlas
External Email - Use Caution Hi Daiana It’s impossible to tell since the anatomical classes of this atlas are limited by the sulco-gyral pattern ; for instance the mPFC includes only part of the superior frontal gyrus (its medial aspect) but the superior frontal gyrus also include the SMA and pre SMA It's easier for the lateral parietal cortex which contains : G_pariet_inf-Angular G_pariet_inf-Supramar G_parietal_sup best > > Hi all, > > I am trying to find out which regions in Destrieux atlas would correspond to > mPFC? > > Any ideas ? > > Also for lateral parietal cortex .. > > Than you, > Daiana Christophe Destrieux, Unité iBrain UMRS INSERM U1253, Université de Tours https://ibrain.univ-tours.fr/ <https://ibrain.univ-tours.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Equivalent labels
Hi Fidel as stated in the paper you cited, the intralimbic gyrus is made of : prehippocampal rudiment, indusium griseum and hippocampus. Only the latter vas clearly visible on the MR scans used to build the atlas, but was not correctly unfolded. For this reason the intralimbic gyrus can not be automatically labelled on the surface. Nevertheless, Hippocampus is segmented by the volume autoparcellation. Similarly, Sulcus semi annularis was not correctly unfolded and was not labelled. Sorry about that -- Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - De: "FIDEL ALFARO ALMAGRO" À: freesurfer@nmr.mgh.harvard.edu Envoyé: Mercredi 12 Janvier 2011 16:20:10 Objet: [Freesurfer] Equivalent labels Hi Freesurfer experts, I would like to know what are the equivalent labels to - Gyrus Intralmibic - Sulcus semmi annularis In the label file FreeSurferColorLUT.txt. I have checked the paper "Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature" but the information there is not useful (e.g. indusium griseum does not appear in that file). Thanks and best regards. Fidel. ___ 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] Equivalent labels
not that I know, except for hippocampus which is available on the volume segmentation Bruce : am I right? cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - De: "FIDEL ALFARO ALMAGRO" À: "Christophe Destrieux" Cc: "FIDEL ALFARO ALMAGRO" , freesurfer@nmr.mgh.harvard.edu Envoyé: Mercredi 12 Janvier 2011 16:37:36 Objet: Re: [Freesurfer] Equivalent labels Hi mr Destrieux, Does this mean that those structures cannot be found in ANY segmentation or labelling made by freesurfer? Thanks again for your quick answer, Fidel. > Hi Fidel > > as stated in the paper you cited, the intralimbic gyrus is made of : > prehippocampal rudiment, indusium griseum and hippocampus. Only the latter > vas clearly visible on the MR scans used to build the atlas, but was not > correctly unfolded. For this reason the intralimbic gyrus can not be > automatically labelled on the surface. Nevertheless, Hippocampus is > segmented by the volume autoparcellation. > > Similarly, Sulcus semi annularis was not correctly unfolded and was not > labelled. > > Sorry about that > > > > > > -- > Christophe Destrieux, > > Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, > Université François Rabelais de Tours > http://www.u930.tours.inserm.fr/ > > Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé > 37032 Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > - Mail original - > De: "FIDEL ALFARO ALMAGRO" > À: freesurfer@nmr.mgh.harvard.edu > Envoyé: Mercredi 12 Janvier 2011 16:20:10 > Objet: [Freesurfer] Equivalent labels > > > Hi Freesurfer experts, > > I would like to know what are the equivalent labels to > > - Gyrus Intralmibic > - Sulcus semmi annularis > > In the label file FreeSurferColorLUT.txt. I have checked the paper > "Automatic parcellation of human cortical gyri and sulci using standard > anatomical nomenclature" but the information there is not useful (e.g. > indusium griseum does not appear in that file). > > Thanks and best regards. > > Fidel. > > ___ > 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] Equivalent labels
I meant : am i right to think that we don't have any other parcellation available showing the other labels Fidel would like to use ? (I thought that maybe somebody localized these structures in a way similar to what you did for the entorhinal cortex in your exvivo/invivo 2008 paper) cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - De: "Bruce Fischl" À: "Christophe Destrieux" Cc: "FIDEL ALFARO ALMAGRO" , freesurfer@nmr.mgh.harvard.edu Envoyé: Mercredi 12 Janvier 2011 18:45:51 Objet: Re: [Freesurfer] Equivalent labels yes, hippocampus is in the aseg On Wed, 12 Jan 2011, Christophe Destrieux wrote: > not that I know, except for hippocampus which is available on the volume > segmentation > > Bruce : am I right? > > cheers > > 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] Unknown label in Parcellation
that's right -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - > De: "Bruce Fischl" > À: "Pedro Paulo de Magalhães Oliveira Junior" > Cc: "Freesurfer Mailing List" > Envoyé: Mercredi 27 Avril 2011 21:57:01 > Objet: Re: [Freesurfer] Unknown label in Parcellation > I think unknown is the medial wall area that is non-cortical, so > should > be ignored > Bruce > On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior > wrote: > > > lh.aparc.stats > > > > 2011/4/27 Bruce Fischl > > > >> which parcellation are you using? > >> > >> > >> On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior > >> wrote: > >> > >> In one study we are conducting we found significant difference in > >> cortical > >>> thickness between the two groups in some areas. One of those areas > >>> are > >>> lh_unknown. > >>> > >>> Is this an error or it's a still unlabelled area? > >>> > >>> thanks > >>> > >>> Pedro Paulo Jr > >>> > >>> > >> > >> 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label
Hi Esther I had a look to the 2005 aparc for fsaverage and the intraparietal sulcus is indeed weird. Why don't you use the 2009 version of the atlas that includes major improvements ; this parcellation is fully described in Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. ; Destrieux C, Fischl B, Dale A, Halgren E. ; Neuroimage . 2010 Oct 15;53(1):1-15 I let Bruce or Doug answer the second part of your question ; cheers PS I attached a snapshot of the 2009 parcellation for the same hemi -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - De: "Esther Walton" À: freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 30 Mai 2011 23:41:24 Objet: [Freesurfer] S_intraparietal-and_Parietal_transverse.label Dear list, I am interested in the S_intraparietal-and_Parietal_transverse label from the Desitreux atlas using aparc.a2005s.annot. If I load this into fsaverage, it has three regions to it (see dark purple label in the attached screenshot): two big ones, very close to each other, connected by two narrow bridges, and another much smaller region more dorsally. Does this look fine to you?! Secondly, assuming this is ok, I created labels for each subject using mri_annotation2label and turned those labels into ROIs in standard space using mri_label2vol --label xx/label/lh.S_intraparietal-and_Parietal_transverse.label --temp xx/reg_standard/example_func.nii.gz --reg xx/reg/freesurfer/anat2std.register.dat --o xx/reg_standard/stats/lh.S_intraparietal-and_Parietal_transverse.nii.gz However, when I load this volume with: tksurfer fsaverage lh inflated -overlay lh.S_intraparietal-and_Parietal_transverse.nii.gz -mni152reg -fthresh 0.1 -fmax 1 it looks a bit off (see yellow label and red ROI in second screenshot). Would you think that's still ok taking into account the individual anatomy or did something go wrong somewhere? Thanks for your help, Esther ___ 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 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] Destrieux or Desikan/Ron Killiany
Hi Lars There is no atlas more accurate than the other one ; they just differ in anatomical convention. In fact the difference between the 2 nomenclatures comes from the definition of the parcellation: - Rahul used a gyral based atlas : ie a gyrus was defined as running between the bottoms of 2 adjacent sulci. - I used a different parcellation that first divided the cortex in gyral and sulcal, the limit between both being given by the curvature value of the surface. This technique provides a more complex parcellation, since sulcal labels were added to gyral ones In other words: * In my atlas, a gyrus only includes the cortex visible on the pial view, the hidden cortex (banks of sulci) are marked sulcus * in Rahul's: a gyrus includes the part visible on the pial view + adjacent banks of the sulci limiting this gyrus Your ROI mainly belongs to the cingulate sulcus, cingulate gyrus and pericallosal sulcus in my atlas. In Rahul's, since sulcal labels are "included" in gyri: * the superior bank of cingulate sulcus is transfered to superior frontal gyrus, and its inferior bank is transfered to the cingulate gyrus * similarly, the inferior bank of pericallosal sulcus is transfered to corpus callosum and its superior one is transfered to the cingulate gyrus I hope that my explanations are clear enough ; PS a new version of my atlas should be available soon with subdivision of the cingulate sulcus and gyrus according to the one proposed by voogt and al cheers Hi, I just mapped these on the fsaverage lh.inflated. By images of the folding patterns, do you mean pial or smoothwm images from fsaverage? Or do you mean data from single subjects? LMR > Date: Tue, 10 Mar 2009 08:01:31 -0400 > From: fis...@nmr.mgh.harvard.edu > To: lari...@gmail.com > CC: freesurfer@nmr.mgh.harvard.edu; destri...@med.univ-tours.fr; ra...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Destrieux or Desikan/Ron Killiany > > Hi Lars, > > you need to send images of the folding patterns for Christophe and Rahul > to decide. > > cheers, > Bruce > On Tue, 10 Mar 2009, Lars M. Rimol wrote: > > > Hi, > > I have an area of significance on the mesial surface of the hemisphere > > (please see attached tiffs). I would like to know if it is exclusively in > > the cingulate or in cingulate and SFG. The prolbem is that the two atlases > > don't agree. The upper more than half of this significant area is in SFG > > according to lh.aparc.annot and in cingulate gyrus and sulcus according to > > lh.aparc.a2005s.annot. > > > > I know there have been some issues before with cingulate and SFG in the > > Destrieux atals ( > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05399.html) > > but it's unlcear to me whether these have been resolved. As you can see from > > the tiffs, in lh.aparc.annot the significant area is inside the corpus > > callosum (a small part), caudal and rostral ant. cingulate, and SFG. In > > lh.aparc.a2005s.annot it is inside pericallosal sulcus, g. cingulate main > > part, s. cingulate main part, and only a very small part of it extends into > > SFG. > > These are substantially different interpretations. Is one atlas more > > accurate in this region? > > > > > > Thank you! > > > > -- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] test message
-- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical label values
Hi Gregory for the 2009 version of the sulco gyral based atlas (destrieux) you can find the list of labels in your freesurfer home : Simple_surface_labels2009.txt I'm not sure where the 2005 version was located in previous distributions of FS ; I attached the corresponding file cheers Hi, I am using the cortical labels mapped into the aparc+aseg volume for seeding qball imaging. i looked around and did not find a complete listing of the numerical values of all the cortical parcellation labels. I can of course load the aparc on the surface in tksurfer and map them to the aparc+aseg volume with save point-go to point for each one but would save me some time to just have a list. i.e. the LUT and stats files just have the subcortical stuff. thank you Greg. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 0 Unknown 0 0 0 0 1 Corpus_callosum 50 50 50 0 2 G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 3 G_cingulate-Isthmus 60 25 25 0 4 G_cingulate-Main_part 25 60 60 0 5 G_cuneus180 20 20 0 6 G_frontal_inf-Opercular_part220 20 100 0 7 G_frontal_inf-Orbital_part 140 60 60 0 8 G_frontal_inf-Triangular_part 180 220 140 0 9 G_frontal_middle140 100 180 0 10 G_frontal_superior 180 20 140 0 11 G_frontomarginal140 20 140 0 12 G_insular_long 21 10 10 0 13 G_insular_short 225 140 140 0 14 G_and_S_occipital_inferior 23 60 180 0 15 G_occipital_middle 180 60 180 0 16 G_occipital_superior20 220 60 0 17 G_occipit-temp_lat-Or_fusiform 60 20 140 0 18 G_occipit-temp_med-Lingual_part 220 180 140 0 19 G_occipit-temp_med-Parahippocampal_part 65 100 20 0 20 G_orbital 220 60 20 0 21 G_paracentral 60 100 60 0 22 G_parietal_inferior-Angular_part20 60 220 0 23 G_parietal_inferior-Supramarginal_part 100 100 60 0 24 G_parietal_superior 220 180 220 0 25 G_postcentral 20 180 140 0 26 G_precentral60 140 180 0 27 G_precuneus 25 20 140 0 28 G_rectus20 60 100 0 29 G_subcallosal 60 220 20 0 30 G_subcentral60 20 220 0 31 G_temporal_inferior 220 220 100 0 32 G_temporal_middle 180 60 60 0 33 G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 34 G_temp_sup-Lateral_aspect 220 60 220 0 35 G_temp_sup-Planum_polare65 220 60 0 36 G_temp_sup-Planum_tempolare 25 140 20 0 37 G_and_S_transverse_frontopolar 13 0 250 0 38 Lat_Fissure-ant_sgt-ramus_horizontal61 20 220 0 39 Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 40 Lat_Fissure-post_sgt61 60 100 0 41 Medial_wall 25 25 25 0 42 Pole_occipital 140 20 60 0 43 Pole_temporal 220 180 20 0 44 S_calcarine 63 180 180 0 45 S_central 221 20 10 0 46 S_central_insula21 220 20 0 47 S_cingulate-Main_part_and_Intracingulate183 100 20 0 48 S_cingulate-Marginalis_part 221 20 100 0 49 S_circular_insula_anterior 221 60 140 0 50 S_circular_insula_inferior 221 20 220 0 51 S_circular_insula_superior 61 220 220 0 52 S_collateral_transverse_ant 100 200 200 0 53 S_collateral_transverse_post10 200 200 0 54 S_frontal_inferior 221 220 20 0 55 S_frontal_middle141 20 100 0 56 S_frontal_superior 61 220 100 0 57 S_frontomarginal21 220 60 0 58 S_intermedius_primus-Jensen 141 60 20 0 59 S_intraparietal-and_Parietal_transverse 143 20 220 0 60 S_occipital_anterior61 20 180 0 61 S_occipital_middle_and_Lunatus 101 60 220 0 62 S_occipital_superior_and_transversalis 21 20 140 0 63 S_occipito-temporal_lateral 221 140 20
Re: [Freesurfer] extract aparc.anot area
Hi Grégory In the 2005 version of the sulco-gyral based atlas, you should find a label called "transverse temporal gyrus" that correspond to the most anterior one that is supposed to correspond to primary auditory cortex ; when posterior one(s) was(ere) present it(they) was(were) included into the planum temporale label We had several talks on the list with Narly Golestani ; you should find info's in : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11835.html cheers > > Hi everyone, > > I need to draw Heschl gyri on freesurfer pial surface of my subjects > but it’s not easy because this area is not directly visible. So: > > 1. Is there a simple mean to cut the surface to see more internal > areas with freesurfer tools (or other???) ? > > 2. Is it possible to extract only desired areas from the > “aparc.annot.a2005s” files and how to modify them manually? > > Thanks > > Grégory SIMON > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Destrieux boundaries Insular cortex
Hi Lena Here is the link to the HBM 2009 poster : http://www.nmr.mgh.harvard.edu/martinos/publications/posters/HBM-2009/HBM09-Destrieux-Sulcal.pdf Following is the "insula" section of the paper we are going to publish "On the inflated view, the insula was clearly limited by the circular sulcus of the insula divided in 3 segments: superior [S_circular_insula_sup, 49], horizontally limiting the insula from the subcentral and inferior frontal gyri, anterior [S_circular_insula_ant, 47], vertically limiting the insula from the orbital gyri, and inferior [S_circular_insula_inf, 48], obliquely limiting the insula from the superior aspect of the superior temporal gyrus. The lateral sulcus or fissure results from the juxtaposition of fronto-parietal and temporal opercula, and is classically divided in anterior, middle and posterior segments (Duvernoy et al., 1991). The superior and anterior segments of the circular sulcus of the insula anteriorly fused to form the anterior segment of lateral sulcus that rapidly splits into vertical [Lat_Fis-ant-Vertical, 40] and horizontal rami [Lat_Fis-ant-Horizont, 39]. Since the inflated representation widely separated the opercula bordering the insula, the middle segment of the lateral sulcus was missing on inflated reconstruction. Finally, the superior and inferior segments of the circular sulcus of the insula posteriorly merged to become the posterior segment of the lateral sulcus [Lat_Fis-post, 41], which curved superiorly to enter the inferior parietal lobule. The central sulcus of the insula ran antero-inferiorly from the superior segment of the circular segment of the insula. It was a small sulcus that was not always visible on its whole course on the inflated views. It divided the insula in two parts: the short insular gyri [G_insular_short, 18] (anterior) and the long insular gyrus (posterior). Due to their small size, the central sulcus of the insula and the long insular gyri were grouped in the same label [G_Ins_lg_and_S_cent_ins, 17]." I hope that it helped cheers Le 28 févr. 10 à 01:39, Lena Palaniyappan a écrit : Is there any reference available for tracking the boundaries of 5 parcellations within insula as given by Destrieux a2009s? Cheers Lena ___ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ 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
Re: [Freesurfer] 2005 vs 2009 parcellations
Hi Frida I'm afraid I won't have any anatomical explanation for this smoothing, since most of the boundaries remained the same on the surfaces of the subjects used to train the atlas. I don't know if any minor changes occured in the labelling algorithm between these 2 versions ; maybe Bruce can tell. Cheers > hi > > aside from new ROIS (i.e. the cingulate being divided into 3 parts), > the 2009 looks like it has smoother/different boundaries than the 2005 > one, even for ROIs that remain the same as the 2005. what is that a > result of? > > thanks, frida > > -- > Frida E. Polli, PhD > Postdoctoral Fellow > Brain & Cognitive Sciences, MIT > 43 Vassar St., Room 46-4033 > Cambridge, MA 02139 > email: fpo...@mit.edu <mailto:fpo...@mit.edu> > tel: (617) 324 2897 > > > > ___ > 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. > -- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Using Freesurfer's label files to create one ROI
Hi Stephan You could use mris_translate_annotation with : ** : the subject you want to work on * *: the hemi you want to work on * *: your initial annotation file (ie the one containing Medial OFC, Lateral OFC, anterior part of the Cingulate) ** : a text file you have to create, that will list the labels( one per line) you want to group, and the new label you want to create. In fact you can't use the labels names but you have to use their RGB codes; each line will provide the input and output RGB values for instance the following file 221 220 60 223 220 60 221 220 160 223 220 60 221 220 100 223 220 60 will group 3 labels (with RGB codes 221 220 60, 221 220 160, and 221 220 100) in a single label (223 220 60) you can get the RGB value by clicking view->information->annotation on tksurfer interface after loading the surface and the annotation file. Be carefull not to use a RGB code previously used in your input annotation. You can get the RGB value of any label by clicking view->information->annotation on tksurfer interface after loading the surface and the annotation file. A field named annotation will be created on the interface with the RGV under brackets ** : the output annotation (the one you want to create, with labels grouped together) cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ 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] Question about getting fusiform stats
Hi Brian I don't know which parcellation you are using, but in the sulco-gyral parcellation (aparc.a2009s.annot), the fusiform appears as "G_oc- temp_lat-fusifor" cheers -CD Le 8 juin 10 à 21:56, Weisinger, Brian (NIH/OD) [E] a écrit : Hello I am trying to retrieve the fusiform volumes of a sample. I looked in the subject output files but didn't see any mention of the fusiform and when I searched the website so far all I could find involved fsl and functional data which mine is not. If it is possible to do could you please point me in the right direction to figure this out. Thank you for your help ___ 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 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] aparc.a2005s.annot errors?
Hi Yigal, n my previous post, I just did not realize that the a2009s version was not included in FS 4.5 package. It will be included in v5.0, to be released in a couple weeks. Nick made them available from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/fsaverage/label/ I hope that it helped Le 24 juin 10 à 08:53, Christophe Destrieux a écrit : Hi Yigal I had a look to fsaverage. There are obviously some mislabelling creating small "holes", especially in the cingulate region. I suggest you to use the a2009s parcellation avalaibel in the 4.5 FS distrib: 1/ this problem is soilved in this version, with a clear improvement of the automated labeling procedure (see attached picture), 2/ACC is directly labeled in this version of the atlas ; for details on the manual labelling process you can have a look to a paper to be published soon in Neuroimage Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. <http://www.ncbi.nlm.nih.gov/pubmed/20547229 >, Destrieux C, Fischl B, Dale A, Halgren E. Neuroimage. 2010 Jun 11. [Epub ahead of print] Cheer CD Hi, There are some "holes" in fsaverage lh cingulate labels in the a2005s annotation. For example, vertex 16631, between the cingulate gyrus and sulcus is part of the superior frontal gyrus label. Same with vertices 20390 and 141081. Is that an error? This is a problem for us because it creates holes in our ACC labels. Thanks, Yigal ___ 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. -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 <2009_Vs_2005.jpg>___ 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 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] Any update on releasing the source for FreeSurfer?
Hi Alex I'm running fs on debian boxes here and they run the freesurfer-Linux-centos4-stable-pub-vX.X.X version, without any need to recompile sources cheers > Hey Everyone, > I searched through the archives and it seems to be that there is an > intent to release FreeSurfer as open source eventually. However, the > most recent post about that that I could find was from a year or two > ago. Is there any update on this or plan for when this will happen? > The reason why I ask is that we're looking to run FreeSurfer on > Debian based systems, and it doesn't seem that you provide packages for > those systems. I would be happy to compile and package this software > and make it available to the community if the source was available, or > made available. > Thank you for your time. I look forward to hearing back from you. > > ---Alex > > ___ > 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. > > -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Description of frontal labels Destrieux 2009
Hi Antony and Lena they are mainly based on Duvernoy. We just published a paper describing the borders of each parcellation : Neuroimage. 2010 Jun 12. [Epub ahead of print] Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. Destrieux C <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Destrieux%20C%22%5BAuthor%5D>, Fischl B <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Fischl%20B%22%5BAuthor%5D>, Dale A <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Dale%20A%22%5BAuthor%5D>, Halgren E <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Halgren%20E%22%5BAuthor%5D>. Cheers > It is my understanding that these are defined based on the Duvernoy > atlas. If this is not the case, please let me know. > > Lena Palaniyappan wrote: > >> Dear Christophe and team >> >> I am writing up something on frontal measures derived from 2009 >> Destrieux atlas – I need to know the anatomical boundaries for >> frontomarginal, orbital H shaped sulcus, and the three inferior, >> middle and superior gyrus and sulcus: is there a place where I can >> find these descriptions? >> Cheers >> Lena >> >> >> On 06/07/2010 23:11, "Christophe Destrieux" >> wrote: >> >> Hi Alex >> >> I'm running fs on debian boxes here and they run the >> freesurfer-Linux-centos4-stable-pub-vX.X.X version, without any >> need to >> recompile sources >> >> cheers >> > Hey Everyone, >> > I searched through the archives and it seems to be that there is an >> > intent to release FreeSurfer as open source eventually. However, the >> > most recent post about that that I could find was from a year or two >> > ago. Is there any update on this or plan for when this will happen? >> > The reason why I ask is that we're looking to run FreeSurfer on >> > Debian based systems, and it doesn't seem that you provide >> packages for >> > those systems. I would be happy to compile and package this software >> > and make it available to the community if the source was >> available, or >> > made available. >> > Thank you for your time. I look forward to hearing back from you. >> > >> > ---Alex >> > >> > ___ >> > 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. >> > >> > >> >> >> -- >> Christophe Destrieux, >> >> Directeur du Département Communication et Multimedia >> >> http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/=1200651159612 >> >> <http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612> >> >> <http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612> >> >> >> Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé >> 37032 Tours - France >> tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> *Lena Palaniyappan >> *Clinical Lecturer & Honorary StR | Division of Psychiatry ( >> University of Nottingham) >> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH >> >> >> This message has been checked for viruses but the contents of an >> attachment may still contain software viruses which could damage your >> computer system: you are advised to perform your own checks. Email >> communications with the University of Nottingham may be monitor
Re: [Freesurfer] creation of special image...
Hi At the begining of the surface atlas, I used such a code to "paint" rgb files on the surface before the painting/filling tools were developped in fs interface. I don't remember the name of the code ; Maybe Bruce does (I don't remember if he wrote it or if Anders did) ?. It worked by 1/creating the flat representation of the surface, 2/by exporting it as a rgb picture , 3/ editing this picture with photoshop, 4 importing it back in fs; cheers > It's not the same. As you can see in Doug's image the smile is hidden > by the sulci and it shows up when you inflate the surface. > - > Pedro Paulo de Magalhães Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br <http://www.netfilter.com.br> > -- For mobile: http://www.netfilter.com.br/mobile > > > > > On Thu, Aug 5, 2010 at 13:01, Christian Lambert > mailto:c.lamb...@fil.ion.ucl.ac.uk>> wrote: > > You can achieve it *very* easily using brain-visa package (see > attached) > > > Bruce Fischl wrote: > > the easiest would be to draw a label on the inflated surface > in tksurfer I would think. Or contract it out to Doug at some > exhorbitant rate :) > On Thu, 5 Aug 2010, Douglas N Greve wrote: > > > > There's no standard way to make that. That took a long > time ... > > Gonzalo Rojas Costa wrote: > > > Hi: > > How can I create an image such as the "Be happy" one > that appeared in the > last slide of "Surface-based Analysis: Intersubject > Registration and > Smoothing" PPT?... > > Sincerely, > > > > Gonzalo Rojas Costa > > > ___ > 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. > > > > > > > > ___ > 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. > > > > > ___ > 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. > -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question abt Destrieux atlas
Hi Rito The answer for the second question is yes : the stable 4.5.0 version includes the 2009 parcellation atlas (see http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) For the first one I'm not quite sure if running recon-all with the -cortparc2 <http://surfer.nmr.mgh.harvard.edu/fswiki/cortparc> -parcstats2 <http://surfer.nmr.mgh.harvard.edu/fswiki/parcstats> -aparc2aseg <http://surfer.nmr.mgh.harvard.edu/fswiki/aparc2aseg> is methodologically correct if yours subjects were reconstructed with 4.4.0 version ; Nick or Bruce could you answer this part? cheers > Hello Christophe > > My name is Rito and I am an avid freesurfer user. I realised that our > freesurfer version is not the latest one and doesnt create the parcellations > contained in Destrieux2009 atlas. > > I have run a lot of data using the 4.4 release. I have installed the latest > release of freesurfer but my question to you is > > 1) How do I get the 2009 parcellations on the data that I already ran through > with the 4.4 release ? > > 2) Also does the latest freesurfer release contain the parcellations reported > in you latest paper "Destrieux et al. Automatic parcellation of human > cortical gyri and sulci using standard anatomical nomenclature. NeuroImage > (2010)" ? > > Any help will be highly appreciated. > > Thanks > > Rito > > Ritobrato Datta, Ph.D. > Post Doctoral Fellow > Department of Neurology > Center for Functional Neuroimaging > University of Pennsylvania School of Medicine > 3rd Floor Gates Building > 3400 Spruce St. > Philadelphia > Pa 19104 > > > -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ 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] lh.aparc.a2005s: S_subcentral_ant label
Hi Bruce and Jenifer I had a look to bert's labelling ; The S_subcentral_ant label is not listed as a variable in the /stats/lh.aparc.a2005s output file just because this structure is absent for this subjects on the left hemisphere. I copied bellow a short description of the region : The subcentral gyrus, located at the lateral aspect of the brain joined the inferior part of the pre and post central gyri, it was inferiorly limited by the superior part of the circular sulcus of the insula while its superior boundary was the virtual line joining the inferior tip of the precentral, central and post central sulci. The anterior and posterior limits of the subcentral gyrus were two small sulci that may branch from the superior segment of the circular sulcus of the insula or may be independent, or absent : the */anterior/* [S_subcentral_ant] */and posterior/* [S_subcentral_post] /*subcentral *sulci./ The subcentral gyrus was limited from the inferior frontal gyrus (pars opercularis) by the anterior subcentral sulcus continued by a virtual line joining the inferior tip of the precentral sulcus. Similarly, it was posteriorly limited from the supramarginal gyrus by the posterior subcentral sulcus continued by the line running towards the inferior tip of the postcentral sulci. I hope it will help. Maybe Christophe can comment? Bruce On Wed, 23 Apr 2008, Juranek, Jenifer wrote: We recently started playing with the ?h.aparc.a2005s annotation files (fsv401). We noticed that in /freesurfer/subject/bert, the S_subcentral_ant label is not listed as a variable in the /stats/lh.aparc.a2005s output file. However, this variable name does *sometimes* appear in some of our study subjects. 1) Is this normal behavior? 2) Is it possible to add a FieldName index (analagous to the aseg.stats file) to facilitate detailed accountings of "empty" variables in the ?h.aparc.a2005s files? Many Thanks for any information you can provide, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_extract_label 4181
Hi Bruce and Markus S_temporal_transverse is constant and should be present on the surface ; cheers HI Markus, that's one of Christophe's labels, so would only be in the aparc.a2005s+aseg.mgz. Have you cheched the aparc.a2005s.annot on the surface to verify that it is present there? There are also some labels that don't appear on every subject, Christophe would know if this is one of them. cheers, Bruce On Wed, 10 Dec 2008, Markus Röhl wrote: Dear all, I used mri_extract_label recently to get NIfTI -binary maps for certain anatomical landmarks, e.g. the Gyrus temporalis inferior of the left hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt: mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz 1009 $FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz This works fine. Now I want to extract the labels of anatomical landmarks like 4181wm-rh-S_temporal_transverse I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz, aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I can find or how can I create the necessary segmentation volume? Regards, Markus -- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: AW: [Freesurfer] mri_extract_label 4181
Hi Markus I'mm not very familiar with the labels extraction , I can just answer you in anatomical terms ; the anatomical labelling sounds correct to me. Soory not to be more helpfull cheers Hi for the purpose of illustration I change to 3136 wm-lh-G_temp_sup-Planum_tempolare The corresponding gray matter part (1136) can seen in cortex.tiff. It is labeled green and can be found quite in the middle of the picture right from the red labeled S_temporal_transverse. The successful extraction of the 1136 ctx-lh-G_temp_sup-Planum_tempolare is shown in success.png. The corresponding white matter of this landmark (3136 wm-lh-G_temp_sup-Planum_tempolare) can also be seen on the right side of WM.tiff as a green labeled area superior of the pink labeled lateral aspect of G_temp_sup. (the 3181 wm-lh-S_temporal_transverse is also present as a very very small red labeled area between the small blue and green areas in the middle of WM.tiff). I am not able to extract 3136 and I think this seems to hold also for the other 3XXX or 4XXX wm-labels from aparc.a2005s+aseg.mgz. I extracted 2034 ctx-rh-transversetemporal from "aparc+aseg.mgz" and analog 4034 wm-lh-transversetemporal from "wmparc.mgz". I assumed that there must be a corresponding file of "aparc.a2005s+aseg.mgz" like "wmparc.a2005s+aseg.mgz" to extract white matter labels. "aparc.a2005s+aseg.mgz" seems to work only for ctx- but not for wm-labels, and I don't found something else. The problem is not subject-related. Regards, Markus -Ursprüngliche Nachricht- Von: Christophe Destrieux [mailto:[EMAIL PROTECTED] Gesendet: Mittwoch, 10. Dezember 2008 14:24 An: Bruce Fischl Cc: Markus Röhl; freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_extract_label 4181 Hi Bruce and Markus S_temporal_transverse is constant and should be present on the surface ; cheers HI Markus, that's one of Christophe's labels, so would only be in the aparc.a2005s+aseg.mgz. Have you cheched the aparc.a2005s.annot on the surface to verify that it is present there? There are also some labels that don't appear on every subject, Christophe would know if this is one of them. cheers, Bruce On Wed, 10 Dec 2008, Markus Röhl wrote: Dear all, I used mri_extract_label recently to get NIfTI -binary maps for certain anatomical landmarks, e.g. the Gyrus temporalis inferior of the left hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt: mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz 1009 $FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz This works fine. Now I want to extract the labels of anatomical landmarks like 4181wm-rh-S_temporal_transverse I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz, aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I can find or how can I create the necessary segmentation volume? Regards, Markus -- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
