Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Re: [Freesurfer] {Filename?} Re: Re: recon-all CTABreadASCII error
by charujing123 13 Feb '14

13 Feb '14

Hi Bruce, I did try, but I am so sorry that size of the attachment is too big to send in the mail list. All the best. Rujing Zha 2014-02-13 charujing123 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 发送时间：2014-02-13 22:00 主题：Re: {Filename?} Re: Re: [Freesurfer] recon-all CTABreadASCII error 收件人："charujing123"<charujing123(a)163.com> 抄送： Hi Rujing can you cc the list so that others can help? thanks Bruce On Thu, 13 Feb 2014, charujing123 wrote: > > Warning: This message has had one or more attachments removed > (recon-all.cmd). Please read the "NMR-MGH-Attachment-Warning.txt" > attachment(s) for more information. > > Hi Bruce, > Some output of recon-all can be got in the attachment. > Thanks Bruce. > Rujing Zha > > 2014-02-13 > > ____________________________________________________________________________ > charujing123 > > ____________________________________________________________________________ > 发件人："charujing123"<charujing123(a)163.com> > 发送时间：2014-02-13 21:48 > 主题：Re: [Freesurfer] recon-all CTABreadASCII error > 收件人："Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu> > 抄送："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Hi Bruce, > I ran this code succefully last year. But I cannot completely this command > in recent days as errors just above. There is nothing change in the server > during this time. According this ERROR information, I asked administrator to > delete some files in the /tmp folder and change the write access. But it was > still report similar error. And I ran this command as root, then it > terminated as a similar situation. > Thanks Bruce. > All the best. > Rujing Zha > > 2014-02-13 > > ____________________________________________________________________________ > charujing123 > > ____________________________________________________________________________ > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > 发送时间：2014-02-13 21:33 > 主题：Re: [Freesurfer] recon-all CTABreadASCII error > 收件人："charujing123"<charujing123(a)163.com> > 抄送："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Hi Rujing > > do you have write access to /tmp? Or is it full maybe? > > Bruce > On Thu, 13 Feb 2014, > charujing123 wrote: > > > Dear FS experts, > > It represents this message in the command window after ran "recon-all > > -autorecon-pial -s CON_EIU01 -no-isrunning": > > Reading annotation reading colortable from annotation file... > > colortable with 36 entries read originally/autofs/space/terrier_001/users > /nicks/freesurfer/average/colortable_desikan > > _killiany.txt) > > CTABwriteFileASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not > > > open for writing > > > > Seg base 1000 Permission denied > > CTABreadASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not open > > > file > > No such file or directory > > ERROR: reading /tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab > > Linux centos2 2.6.18-308.20.1.el5xen #1 SMP Tue Nov 13 11:03:56 EST 2012 ?? ?> x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s CON_EIU04 exited with ERRORS at Thu Feb 13 14:01:12 CST 2014 > > > > > Thanks. > > All the best. > > Rujing Zha > > > > 2014-02-13 > > > > _________________________________________________________________________ > ___ > > charujing123 > > > > > > > The information in this e-mail is intended only for the person to whom it i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > >

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recon-all CTABreadASCII error
by charujing123 13 Feb '14

13 Feb '14

Dear FS experts, It represents this message in the command window after ran "recon-all -autorecon-pial -s CON_EIU01 -no-isrunning": Reading annotation reading colortable from annotation file... colortable with 36 entries read originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) CTABwriteFileASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not open for writing Seg base 1000 Permission denied CTABreadASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab Linux centos2 2.6.18-308.20.1.el5xen #1 SMP Tue Nov 13 11:03:56 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CON_EIU04 exited with ERRORS at Thu Feb 13 14:01:12 CST 2014 Thanks. All the best. Rujing Zha 2014-02-13 charujing123

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Re: [Freesurfer] recon-all CTABreadASCII error
by charujing123 13 Feb '14

13 Feb '14

Hi all, All the information can be got in the attachment. Thanks. All the best. Rujing Zha 2014-02-13 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-02-13 13:53 主题：[Freesurfer] recon-all CTABreadASCII error 收件人："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Dear FS experts, It represents this message in the command window after ran "recon-all -autorecon-pial -s CON_EIU01 -no-isrunning": Reading annotation reading colortable from annotation file... colortable with 36 entries read originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) CTABwriteFileASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not open for writing Seg base 1000 Permission denied CTABreadASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab Linux centos2 2.6.18-308.20.1.el5xen #1 SMP Tue Nov 13 11:03:56 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CON_EIU04 exited with ERRORS at Thu Feb 13 14:01:12 CST 2014 Thanks. All the best. Rujing Zha 2014-02-13 charujing123

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Variability in bedpostx output
by jwaugh＠nmr.mgh.harvard.edu 13 Feb '14

13 Feb '14

Hello all, I have run bedpostx on a series of DTI scans over ~1 year, the earlier ones in stable 5.1 and later ones in 5.3. I'm seeing quite a lot of variability in intensity from the earlier to later versions - re-running bedpostx in 5.3 on an older scan and comparing with 5.1 yields up to 10% variation in intensity at any given voxel between versions. I've been comparing the mean_f1 images by subtracting the (new - old) using fslmaths. The differences are not isolaed to surfaces, but can also be deep in the white matter or parenchyma. Has anyone else seen this? Thanks, Jeff

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Tracula version and download problem
by Clive Wong 12 Feb '14

12 Feb '14

Hi, I just want to confirm, is that I can use the new trac-all with the data processed in the original FS5.3 trac-all? And, I just want to download the new trac-all, but I have problem to connect to the ftp server. I can login to the server, but it does not response to any command. Please advise. Best, Clive

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Fwd: Problems dipslaying annotations in freeview
by Laura Taylor 12 Feb '14

12 Feb '14

Hi Ruopeng and freesurfer folks, I am still having trouble loading annotations in freeview, similar to what I mentioned before. When I load 'rh.aparc.a2009s.annot' in freeview, the annotation loads onto the LEFT hemisphere and is tye-died in appearance. In contrast, 'lh.aparc.a2009s.annot' loads correctly onto the left hemisphere and looks normal. I have had this problem with many of my subjects. Can you help with this?? Thank you, Laura ---------- Forwarded message ---------- Date: Thu, Jan 2, 2014 at 9:53 AM Subject: Fwd: [Freesurfer] Problems dipslaying annotations in freeview To: rpwang(a)nmr.mgh.harvard.edu Hi Ruopeng, I am forwarding the messages I sent to the freesurfer mailing list and that Doug suggested I ask you. Basically when I try and load an annotation in freeview, the rh loads properly (looks normal and is on the correct hemisphere), but the lh loads onto the rh and is tye-died in appearance. Can you help with this? Thanks, Laura ---------- Forwarded message ---------- From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Date: Wed, Dec 18, 2013 at 2:14 PM Subject: Re: [Freesurfer] Problems dipslaying annotations in freeview Cc: freesurfer(a)nmr.mgh.harvard.edu oh, if the lh annot is being loaded onto the rh surface, then that will definitely create the tye-died appearance.* Maybe Ruopeng can weigh in on the freeview issue.* doug On 12/18/2013 04:53 PM, Laura wrote: > Hi Douglas, > > I would go to the annotation drop down menu in freeview, select > l/rh.aparc.a2009s.annot and then it would freeze. I can't seem to > reproduce that problem today, but for every subject that I load an > annotation for now, the rh annotation loads properly,* but the lh > annotation loads onto the right hemisphere and is tye-died in appearance.* > > Thanks, > > Laura > > > On Tue, Dec 17, 2013 at 11:57 AM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > So when you say you cannot load it, what do you mean? > doug > > > > > On 12/17/2013 02:55 PM, Laura Taylor wrote: > > Hi Douglas, > > I checked the status of each subject once recon-all was > completed (by looking in the terminal window before I closed > it). Each of my roughly 90 subects had the message > "/recon-all -s/ subjectID /finished without error/ at date and > time". > > > When I look at the recon-all.log file the same message is > there at the end. Is there somewhere else where i should look > for an error message?? > > Thank you, > Laura > > > On Tue, Dec 17, 2013 at 10:44 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > For the subject that you were not able to load the annot, > did you > check the recon-all log file? Did recon-all complete properly? > doug > > > On 12/17/2013 01:35 PM, Laura wrote: > > Hi again, Douglas and freesurfer experts. > > Unfortunately my problem cannot be explained by having > made > manual edits and then not finishing recon-all. When I > load > subjects that I did not manually edit, I am either > unable to > load an annotation file (specifically > r/lh.aparc.a2009s.annot) > at all, or I can load it but have problems with the > output. > When I am able to load an image I get a the same tye-died > appearing surface for one hemisphere (and it is > projected onto > the opposite hemisphere that the label is for) or I get a > proper surface when I load the label for the other > hemisphere > (and it appears on the correct hemisphere). > > Can you help at all with this? > > Thank you, > > Laura > > > On Tue, Dec 10, 2013 at 11:45 AM, Laura Taylor > >>>> wrote: > > Hi, yes thank you both. That is exactly what the > problem was. > > Laura > > > On Tue, Dec 10, 2013 at 11:12 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Yep, looks like your annot is out of sync with the > surfaces > > On 12/10/2013 01:51 PM, Chris Watson wrote: > > I've seen this happen after making manual > edits and > then not > finishing > > a re-run of recon-all. > > Chris > > > > On 12/10/2013 02:00 PM, Laura Taylor wrote: > >> Hi, > >> > >> I'm trying to load lh.aparc.a2009s.annot > onto the > lh pial > surface of > >> a subject. When I use the freeview gui and > select > >> lh.aparc.a2009s.annot under the annotations > menu a > strange > >> multicolored surface is loaded. It looks like > something > that has > >> been tie-dyed and not like the examples of > parcellation > that are > >> shown on some of the freesurfer pages. > >> > >> I have attached a screenshot of the output > that I get. > >> > >> Any help would be appreciated. > >> > >> Thank you, > >> > >> Laura > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended > only for the > person to whom it is > >> addressed. If you believe this e-mail was > sent to > you in > error and the e-mail > >> contains patient information, please > contact the > Partners > Compliance HelpLine at > >> http://www.partners.org/complianceline . > If the > e-mail was > sent to you in error > >> but does not contain patient information, > please > contact > the sender and properly > >> dispose of the e-mail. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/ > BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Fwd: How to avoid tumour from being segmented out
by Melanie Morrison 12 Feb '14

12 Feb '14

Thanks, Melanie Morrison Begin forwarded message: > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Date: 12 February, 2014 1:21:56 PM EST > To: Melanie Morrison <melanie.morrison(a)hotmail.com> > Subject: RE: [Freesurfer] How to avoid tumour from being segmented out > > Hi Melanie > > can you cc the list so that others can answer? > > thanks > Bruce > On Wed, 12 Feb 2014, Melanie Morrison wrote: > >> Thanks. I can just do this manually? Can I over lay this on my anatomical >> map somehow so I can manually outline the correct boundaries. >> > Date: Wed, 12 Feb 2014 11:51:14 -0500 >> > From: fischl(a)nmr.mgh.harvard.edu >> > To: melanie.morrison(a)hotmail.com >> > CC: freesurfer(a)nmr.mgh.harvard.edu; astevens(a)nmr.mgh.harvard.edu >> > Subject: Re: [Freesurfer] How to avoid tumour from being segmented out >> > >> > Hi Melanie >> > >> > you should be able to fill it in in the wm.mgz volume in either tkmedit >> > or freeview (using 255 if in freeview - tkmedit will do this by default) >> > >> > cheers >> > Bruce >> > On >> > Wed, 12 Feb 2014, Melanie Morrison wrote: >> > >> > > Hi there, >> > > >> > > I am creating surfaces from my volume T1-weight scans so that I can run >> them >> > > in AFNI's SUMA program. >> > > Problem is that my tumour has been segmented out because its intensity >> and >> > > the intensity of its surround area is much lower that what is being >> > > segmented. >> > > >> > > How can I avoid this? Or edit this? I need my functional MRI data to be >> > > displayed around the tumour region which is now unfortunately cut out. >> > > (HELPP!!!) >> > > >> > > >> > > Thanks, >> > > Melanie Morrison >> > > >> > > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)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. >> > >>

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dt_recon error for Siemens mosaics image
by Gennan Chen 12 Feb '14

12 Feb '14

HI! All, I got an error when I ran dt_recon WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR000001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I can confirm it is Siemens mosaics format. Any idea how to by pass this?? -- Gennan Chen ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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local_gi problem
by krista kelly 12 Feb '14

12 Feb '14

Hello, I am trying to do local gyrification with freesurfer and am having trouble. I have the image processing toolbox and have set the path. I ran recon-all -s BV21 -localGI and it exited without errors. Yet, when I try to view it in tksurfer using tksurfer BV21 lh inflated -overlay lh.pial_lgi, I get this error: cannot find rh.pial_lgi (even though it is in the surfs folder). I can open the inflated brain in tksurfer and overlay lh.pial_lgi but there seems to be a problem where not all of the brain is colored in (please see attached pictures). I'm wondering if someone can help me with this problem, it's happened on more than one participant. When checking through the terminal, I found this at the beginning of the processing: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 I initially did recon-all -all using a linux on a virtual machine, however there wasn't enough working memory to do all of my analyses using linux, so I transferred all of my data to a mac and did the quality checks, extracted roi data (aparcstats2table) and ran glm analyses (qdec) from there. Do you think that the problem lies in the fact that recon-all was originally ran in Linux? I'd rather not do the local gyrification in Linux as I do not have matlab on that machine. Thanks! Krista

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Postdoc - ICM Paris - Morphometry using 7T MRI
by Olivier Colliot 12 Feb '14

12 Feb '14

Dear colleagues, Our team is looking for a postdoctoral fellow. Please find below the informations about the position. Many thanks Olivier Colliot _*Research topic: Computational anatomy of the hippocampus using very high resolution MRI at 7 Tesla: diffeomorphic registration and shape analysis *_The hippocampus is an anatomical structure of the brain which plays critical roles in different brain disorders including Alzheimer's disease and epilepsy. The hippocampus has the particularity of presenting a highly complex tridimensional organization with a large number of substructures, fields and layers. Current approaches for shape analysis of the hippocampus only consider its external boundary and do not model its complex internal architecture. Indeed, using conventional MRI at 1.5T or 3T, only the external boundaries of the hippocampus can be visualized and its internal subregions remain inaccessible. The advent of ultra-high field MRI (7T and higher) has opened new perspectives by providing increased signal-to-noise ratio, increased tissular contrast and increased spatial resolution, which allows visualizing in vivo tiny anatomical structures (~100-200 microns). New computational anatomy approaches are needed to handle these complex anatomical structures. The aim of this postdoctoral project is to develop new approaches for diffeomorphic registration and shape analysis of the internal structures of the hippocampus using 7T MRI data with very high spatial resolution. The developments will be based on the framework of large diffeomorphic deformations and matching of currents. New developments based on varifolds and functional currents will be performed in order to handle the complex shapes of the internal structures. The work will be done in collaboration with our partners at ENS de Cachan (Alain Trouvé) and Université Paris-Descartes (Joan Glaunès). The developed approaches will be applied to detect subtle alterations in patients with Alzheimer's disease and epilepsy in which 7T MRI has been acquired. These clinical applications will be done in collaboration with our partners at Neurospin, Pitié-Salpêtrière hospital, and University of Minnesota. _*Profile of the candidate *_The ideal candidate should have previous experience in the design of new methods for morphometry, shape analysis or registration of anatomical medical images. However, we will also consider outstanding scientific profiles in the fields of image processing/computer vision, without previous experience of the specific topics mentioned above. _*About the ARAMIS team*_ ARAMIS is a joint research team between CNRS, INRIA, Inserm and UPMC within the Brain and Spine Institute (ICM). The ICM (http://icm-institute.org/menu/foundation/mission?lang=en) is a recently created neuroscience center based in the Pitié-Salpêtrière hospital in Paris, which is the largest adult hospital in Europe and has a long tradition of neuroscience and neurology. The ICM brings together 500 researchers covering the whole field of neuroscience. ARAMIS is the methodological research team of the ICM. It is a multidisciplinary group (electrical engineering, computer science, neurology) with about 30 members. The team aims at designing new mathematical and computational approaches for the analysis of images and signals of the human brain. The key domains of expertise of the team are: i) automatic segmentation of brain structures; ii) shape analysis and longitudinal modeling; iii) machine learning; iv) analysis of brain connectivity. The team has developed advanced methods for the analysis of anatomical and functional neuroimaging data including the fully automatic approach SACHA to segment the hippocampus and the amygdala, pattern classification algorithms, the Deformetrica software for shape analysis, and graph-theory approaches to functional connectivity. The team also has strong expertise in the management of multi-center neuroimaging studies, including multi-site MRI harmonization, quality control and analysis of massive datasets. The team has close and enduring collaborations with different clinical teams of the ICM and the Pitié-Salpêtrière hospital to apply advanced image analysis approaches to neurological disorders, including Alzheimer's disease, epilepsy, fronto-temporal dementia, Parkinson's disease, Gilles de la Tourette syndrome. _*Contact information*_ Olivier Colliot - olivier.colliot(a)upmc.fr - http://cogimage.dsi.cnrs.fr/perso/colliot/ _*More information:*_ https://www.inria.fr/en/institute/recruitment/offers/post-doctoral-research…

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Freesurfer February 2014