Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

-aseg image not in accordance with brainmask.mgz
by Rujing Zha 16 Dec '13

16 Dec '13

Hi Doug and Bruce, There is a excellent segmentation in -surfs after editing the pial and run -autorecon-pial by tkmedit and recon-all respectively. Some voxels was removed from the brainmask.mgz in editing the pial. However the -aseg image still have those voxels which I have removed from the brainmask.mgz. This is why? Do I need to run -autorecon3 to fix the aseg? There are brainmask.mgz(pic 1) and aseg(pic 2) snapshots in the attachment. Thanks. All the best. 2013-12-14 Rujing Zha

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A prblem of tksufer tool
by Xiaojun.Huang 15 Dec '13

15 Dec '13

Hi, I am processing the 3D PD patients brain now . After recon-all running, when I use the TKSurfer Tool to review the 3D brain, it is reverse and mistake the left and right. I test some other data and realized it may be something wrong with the Tksufer installing.How can I fix it? Thanks, Huang.

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Re: [Freesurfer] engineer position at the Karolinska Institute
by Ivanka Savic Berglund 15 Dec '13

15 Dec '13

Research Engineer position in Neuroscience Karolinska Institutet, Dept for Women’s and Children’s Health We are seeking a highly talented, innovative and enthusiastic researcher preferably with a PhD in physics and with experience of brain imaging (the latter is mandatory). The research will be conducted at Div of Behavioral Neurology at the Department of Neurology Karolinska Hospital and Dept of Womens and Childrens Health, Karolinska Institute, which is part of the Stockholm Brain Institute (SBI). Our team consists of physicians, physicists, psychologists and biomedical experts, and our laboratory has expertise in functional magnetic resonance imaging (fMRI), PET, and psychophysics. In addition, the Stockholm Brain Institute has MeG and TMS facilities. We have access to two state-of-the-art 3-Tesla MRI scanners and the latest generation of the PET scanner at Karolinska Institute and Hospital. The ideal candidate will have expertise in human brain imaging (PET, MRI), and mathematics, have knowledge about brain anatomy, and insight in experimental psychology. The applicant should have experience in MRI acquisition and analysis, excellent programming skills (eg Linux, Matlab, Python), basic knowledge of statistics and an appreciation of methodological issues in cognitive brain imaging. You will be thorough, efficient, a good communicator, and enjoy working as part of a diverse and energetic, interdisciplinary team. You will organize methodology workshops för PhD post doctoral students of the institution. You will also have many opportunities to own development including national and international workshops and meetings. The candidate is expected to work within the general framework of the research program and actively contribute teaching and improve the MR methodology, with respect to data post processing. It is important that the candidate can independently keep updated to the latest software and their advantages. Applicants should be able to demonstrate a consistently good academic record, including publications in international journals. Applicants are expected to have the knowledge of post processing of the MRI data including analysis of fMRI time series with calculations of functional connectivity, multivariate pattern analysis, analyses of structural connectivity and computational morphometry, and gene brain interaction. There are several on going research programs covering various fields (e.g., effect of chronic stress on the brain, impact of sex hormones and sex chromosome genes on cerebral physiology and behaviour, the underpinnings of human epilepsy) The position is for an initial 12-month period, with the possibility of a permanent contract. Applicants with a foreign PhD are welcome. Application process An application must contain the following documents in English: 1. Curriculum vitae and qualifications, presented in accordance with Karolinska Institutet’s qualifications portfolio (http://ki.se/meritportfolj ) 2. A complete list of publications 3. A summary of current work (no more than one page) 4. Verifications for crediting of illness, military service, work for labour unions or student organizations, parental leave or similar circumstances 5. Verification from the thesis defense committee or the equivalent (only if the thesis defense is scheduled within three months after the application deadline) The application is to be submitted on the NetRecruiter system. Application deadline: January 30, 2014 Start time is negotiable. For additional information, please contact Professor Ivanka Savic, E-mail: ivanka.savic-berglund(a)ki.se<mailto:ivanka.savic-berglund@ki.se> Ivanka Savic M.D., PhD Professor of Neurology Karolinska Institute Dept of Women’s and Children’s Health and Neurology Clinic,Karolinska Hospital, Q2:07 SE-171 76 STOCKHOLM, Sweden Telephone +46 8 517 773 41 +46 709 38 07 38 Fax +46 8 517 76 422 ivanka.savic-berglund(a)ki.se<mailto:ivanka.savic-berglund@ki.se> On Dec 15, 2013, at 9:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu>> <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Dura/pial reconstruction: FLAIR vs. multiecho (Bruce Fischl) 2. Re: Fwd: Re: Fwd: Re: Fwd: Some problems of the brain image after recon-all (Bruce Fischl) 3. Re: A prblem of tksufer tool (Bruce Fischl) 4. Re: Dura/pial reconstruction: FLAIR vs. multiecho (Watson, Christopher) ---------------------------------------------------------------------- Message: 1 Date: Sat, 14 Dec 2013 13:09:20 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho To: roberto.viviani(a)uni-ulm.de Cc: Andre van der Kouwe <andre(a)nmr.mgh.harvard.edu>, Freesurfer(a)nmr.mgh.harvard.edu, Eberhard.Pracht(a)dzne.de Message-ID: <alpine.LRH.2.03.1312141308350.17965(a)nmr.mgh.harvard.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Roberto I think a T2-space FLAIR is your best bet. We have very little experience with other FLAIR and/or/ T2s, but those seem to work well. They are *much* higher SNR than the T2* maps that one can get from an memprage where the last echo is only around 7ms. cheers Bruce On Sat, 14 Dec 2013, roberto.viviani(a)uni-ulm.de wrote: Dear all, starting from the version of March of this year, FreeSurfer supports the use of co-acquired FLAIR images to separate the dura from the gray matter. Some years ago, the idea about solving the same problem was to use multi-echo MPRAGE images. I am starting a new project, in which I am planning to acquire structural images, and I would like to know something more about these two ways of addressing the dura problem. -- is there any experience on the superiority of the FLAIR approach, or is there any published evaluation of it / comparison with the MEMPRAGE approach (such as the van der Kouwer et al. 2008 paper on the MEMPRAGE) (I looked for it in scholar.google but could not find it) -- are you planning to support the multi echo approach in the future, or is it going to be discontinued I will also be very interested to hear from anyone who has had any experience with the FLAIR approach, or both. Best wishes, Roberto Roberto Viviani University of Ulm, Germany _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 2 Date: Sat, 14 Dec 2013 13:15:55 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fwd: Re: Fwd: Re: Fwd: Some problems of the brain image after recon-all To: "Xiaojun.Huang" <lvdosha(a)gmail.com> Cc: Freesurfer(a)nmr.mgh.harvard.edu Message-ID: <alpine.LRH.2.03.1312141315450.17965(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" sorry, I don't think I got it. How did you send it? On Fri, 13 Dec 2013, Xiaojun.Huang wrote: Hi Bruce, I Have sent the raw data to you and I find if it is the problem of tksurfer Installing? Can it result in the problem? How can I Fix it? Thanks, Xiaojun. -------- ???? -------- ??: Re: [Freesurfer] Fwd: Re: Fwd: Some problems of the brain image after recon-all ??: Tue, 10 Dec 2013 08:22:36 -0500 (EST) ???: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> ???: Xiaojun.Huang <lvdosha(a)gmail.com> yes, or the whole subject dir so I can diagnose what went wrong cheers Bruce On Tue, 10 Dec 2013, Xiaojun.Huang wrote: Hi Bruce, I wonder if I need to upload the 3d raw data to you, If you need them. Best, Huang. ? 2013/12/7 0:12, Bruce Fischl ??: it comes up upside down in tksurfer without pressing any buttons or anything? Never seen that before - if you upload the subject I'll take a look cheers Bruce On Fri, 6 Dec 2013, Xiaojun.Huang wrote: hi all, I am processing the 3D PD patients brain now . After recon-all running, the segmentations of the GM and WM is not accurate although the original dat a is normal. additionally, when I use the TKSurfer Tools to review the 3 D brain,it is rev erse. More informations and images as follows: -------- ???? -------- ??: Re: [Freesurfer] Fwd: Some problems of the brain image after recon-all ??: Thu, 05 Dec 2013 12:45:10 +0800 ???: Xiaojun.Huang <lvdosha(a)gmail.com> ???: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi Bruce, Sorry for reply late. The data were provided by a hospital and the input data were 3D images.Some image informations as followed(eg.PDSub_02): 0008,103E,Series Description=Ax 3D VBM 0008,1090,Manufacturer's Model Name=SIGNA EXCITE 0018,0000,Acquisition Group Length=484 0018,0020,Scanning Sequence=GR 0018,0021,Sequence Variant=SS\SP\SK 0018,0022,Scan Options=FAST.GEMS\EDR.GEMS\FILTERED.GEMS 0018,0023,MR Acquisition Type=3D 0018,0025,Angio Flag=N 0018,0050,Slice Thickness=1 0018,0080,Repetition Time [TR, ms]=7.652 0018,0081,Echo Time [TE, ms]=3.312 0018,0082,Inversion Time=0 0018,0083,Number of Averages=1 0018,0084,Imaging Frequency=127.755675 0018,0085,Imaged Nucleus=1H 0018,0086,Echo Number= 0018,0087,Magnetic Field Strength=3 0018,0088,Spacing Between Slices=1 0018,0091,Echo Train Length=1 0018,0093,Percent Sampling=100 0018,0094,Percent Phase Field View=100 0018,0095,Pixel Bandwidth=97.6562 0018,1020,Software Version=12\LX\MR Software release.12.0.M5A.0819.a 0018,1030,Protocol Name=PDD-YANGWANQUN/4 0018,1310,Acquisition Matrix=0, 256, 228, 0 0018,1312,Phase Encoding Direction=ROW 0018,1314,Flip Angle=13 0018,1315,Variable Flip Angle Flag=N 0028,0010,Rows=512 0028,0011,Columns=512 It comes up in the proper orientation in tkmedit in three orientations a s attachment(eg.coromaland saggital view). Tanks, Xiaojun. ? 2013/12/4 22:45, Bruce Fischl ??: Hi Xiaojun we need more details in order to help you. What was your input data? > What format was it in? Does it come up in the proper orientation in > tkmedit? What kind of acquisition (resolution, type, etc...) did you use ? cheers Bruce On Wed, 4 Dec 2013, Xiaojun.Huang wrote: -------- ???? -------- ??: Some problems of the brain image after recon-all ??: Tue, 03 Dec 2013 21:33:41 +0800 ???: Xiaojun.Huang <lvdosha(a)gmail.com> ???: Freesurfer(a)nmr.mgh.harvard.edu Hi, I am processing the 3D PD patients brain now . After recon-all >> running, the segmentations of the GM and WM is not accurate although the original data is normal. additionally, when I use the >> TKSurfer Tools to review the 3D brain,it is reverse. (eg. PDSub_02 in the attach files) It is the first time for me to use Freesurfer.I'm sorry for the >> trouble I'm giving you.And looking forward your reply. Thanks, Xiaojun 2013.12.3 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. ------------------------------ Message: 3 Date: Sat, 14 Dec 2013 13:17:24 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] A prblem of tksufer tool To: Rujing Zha <charujing123(a)163.com> Cc: Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu>, "Xiaojun.Huang" <lvdosha(a)gmail.com>, freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.03.1312141316240.17965(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Rujing can you describe your freeview problems again? thanks Bruce On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Huang, I have similar question with you. In my case, I cannot visualizing inflated image by tksurfer but freeview. Looking forward to someone's help. All the best. ? 2013-12-14 ____________________________________________________________________________ Rujing Zha ____________________________________________________________________________ ????"Xiaojun.Huang" <lvdosha(a)gmail.com> ?????2013-12-14?20:44 ???[Freesurfer] A prblem of tksufer tool ????"Freesurfer"<Freesurfer(a)nmr.mgh.harvard.edu> ??? ? Hi,? I?am?processing?the?3D?PD?patients?brain?now?.?After?recon-all?running,? when?I?use?the?TKSurfer?Tool?to?review?the?3D?brain,?it?is?reverse?and? mistake?the?left?and?right.?I?test?some?other?data?and?realized?it?may? be?something?wrong?with?the?Tksufer?installing.How?can?I?fix?it?? Thanks,? Huang.? _______________________________________________? 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?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.? ? ------------------------------ Message: 4 Date: Sat, 14 Dec 2013 18:33:32 +0000 From: "Watson, Christopher" <Christopher.Watson(a)childrens.harvard.edu> Subject: Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, "roberto.viviani(a)uni-ulm.de" <roberto.viviani(a)uni-ulm.de> Cc: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu>, Andre van der Kouwe <andre(a)nmr.mgh.harvard.edu>, "Eberhard.Pracht(a)dzne.de" <Eberhard.Pracht(a)dzne.de> Message-ID: <C598595A8153064A89C29B0A55A55949487A4349(a)CHEXMBX2A.CHBOSTON.ORG> Content-Type: text/plain; charset="us-ascii" I only have anecdotal evidence based on 4 subjects, but I found that using the FLAIR results in much better surface reconstruction than the multiecho. In my experience (with kids age 12-16), the pial surface was underestimated when I used the multiecho. ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Saturday, December 14, 2013 1:10 PM To: roberto.viviani(a)uni-ulm.de Cc: Andre van der Kouwe; Freesurfer(a)nmr.mgh.harvard.edu; Eberhard.Pracht(a)dzne.de Subject: Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho Hi Roberto I think a T2-space FLAIR is your best bet. We have very little experience with other FLAIR and/or/ T2s, but those seem to work well. They are *much* higher SNR than the T2* maps that one can get from an memprage where the last echo is only around 7ms. cheers Bruce On Sat, 14 Dec 2013, roberto.viviani(a)uni-ulm.de wrote: Dear all, starting from the version of March of this year, FreeSurfer supports the use of co-acquired FLAIR images to separate the dura from the gray matter. Some years ago, the idea about solving the same problem was to use multi-echo MPRAGE images. I am starting a new project, in which I am planning to acquire structural images, and I would like to know something more about these two ways of addressing the dura problem. -- is there any experience on the superiority of the FLAIR approach, or is there any published evaluation of it / comparison with the MEMPRAGE approach (such as the van der Kouwer et al. 2008 paper on the MEMPRAGE) (I looked for it in scholar.google but could not find it) -- are you planning to support the multi echo approach in the future, or is it going to be discontinued I will also be very interested to hear from anyone who has had any experience with the FLAIR approach, or both. Best wishes, Roberto Roberto Viviani University of Ulm, Germany _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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. ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 118, Issue 28 *******************************************

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research engineer position at the Karolinska Institute
by Ivanka Savic Berglund 15 Dec '13

15 Dec '13

Ivanka Savic M.D., PhD Professor of Neurology Karolinska Institute Dept of Women’s and Children’s Health and Neurology Clinic,Karolinska Hospital, Q2:07 SE-171 76 STOCKHOLM, Sweden Telephone +46 8 517 773 41 +46 709 38 07 38 Fax +46 8 517 76 422 ivanka.savic-berglund(a)ki.se<mailto:ivanka.savic-berglund@ki.se>

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Dura/pial reconstruction: FLAIR vs. multiecho
by roberto.viviani＠uni-ulm.de 14 Dec '13

14 Dec '13

Dear all, starting from the version of March of this year, FreeSurfer supports the use of co-acquired FLAIR images to separate the dura from the gray matter. Some years ago, the idea about solving the same problem was to use multi-echo MPRAGE images. I am starting a new project, in which I am planning to acquire structural images, and I would like to know something more about these two ways of addressing the dura problem. -- is there any experience on the superiority of the FLAIR approach, or is there any published evaluation of it / comparison with the MEMPRAGE approach (such as the van der Kouwer et al. 2008 paper on the MEMPRAGE) (I looked for it in scholar.google but could not find it) -- are you planning to support the multi echo approach in the future, or is it going to be discontinued I will also be very interested to hear from anyone who has had any experience with the FLAIR approach, or both. Best wishes, Roberto Roberto Viviani University of Ulm, Germany

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Fwd: Re: Fwd: Re: Fwd: Some problems of the brain image after recon-all
by Xiaojun.Huang 14 Dec '13

14 Dec '13

Hi Bruce, I Have sent the raw data to you and I find if it is the problem of tksurfer Installing? Can it result in the problem? How can I Fix it? Thanks, Xiaojun. -------- 原始消息 -------- 主题: Re: [Freesurfer] Fwd: Re: Fwd: Some problems of the brain image after recon-all 日期: Tue, 10 Dec 2013 08:22:36 -0500 (EST) 发件人: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 收件人: Xiaojun.Huang <lvdosha(a)gmail.com> yes, or the whole subject dir so I can diagnose what went wrong cheers Bruce On Tue, 10 Dec 2013, Xiaojun.Huang wrote: > Hi Bruce, > I wonder if I need to upload the 3d raw data to you, If you need them. > Best, > Huang. > 于 2013/12/7 0:12, Bruce Fischl 写道: >> it comes up upside down in tksurfer without pressing any buttons or >> anything? Never seen that before - if you upload the subject I'll take a >> look >> >> cheers >> Bruce >> On Fri, 6 Dec 2013, Xiaojun.Huang wrote: >> >>> hi all, >>> >>> I am processing the 3D PD patients brain now . After recon-all running, >>> the segmentations of the GM and WM is not accurate although the original >>> dat >>> a is normal. additionally, when I use the TKSurfer Tools to review the 3D >>> brain,it is rev >>> erse. >>> More informations and images as follows: >>> >>> -------- 原始消息 -------- >>> 主题: >>> Re: [Freesurfer] Fwd: Some problems of the brain image after recon-all >>> 日期: >>> Thu, 05 Dec 2013 12:45:10 +0800 >>> 发件人: >>> Xiaojun.Huang <lvdosha(a)gmail.com> >>> 收件人: >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> >>> Hi Bruce, >>> Sorry for reply late. >>> The data were provided by a hospital and the input data were 3D >>> images.Some image informations as followed(eg.PDSub_02): >>> >>> 0008,103E,Series Description=Ax 3D VBM >>> 0008,1090,Manufacturer's Model Name=SIGNA EXCITE >>> 0018,0000,Acquisition Group Length=484 >>> 0018,0020,Scanning Sequence=GR >>> 0018,0021,Sequence Variant=SS\SP\SK >>> 0018,0022,Scan Options=FAST.GEMS\EDR.GEMS\FILTERED.GEMS >>> 0018,0023,MR Acquisition Type=3D >>> 0018,0025,Angio Flag=N >>> 0018,0050,Slice Thickness=1 >>> 0018,0080,Repetition Time [TR, ms]=7.652 >>> 0018,0081,Echo Time [TE, ms]=3.312 >>> 0018,0082,Inversion Time=0 >>> 0018,0083,Number of Averages=1 >>> 0018,0084,Imaging Frequency=127.755675 >>> 0018,0085,Imaged Nucleus=1H >>> 0018,0086,Echo Number= >>> 0018,0087,Magnetic Field Strength=3 >>> 0018,0088,Spacing Between Slices=1 >>> 0018,0091,Echo Train Length=1 >>> 0018,0093,Percent Sampling=100 >>> 0018,0094,Percent Phase Field View=100 >>> 0018,0095,Pixel Bandwidth=97.6562 >>> 0018,1020,Software Version=12\LX\MR Software release.12.0.M5A.0819.a >>> 0018,1030,Protocol Name=PDD-YANGWANQUN/4 >>> 0018,1310,Acquisition Matrix=0, 256, 228, 0 >>> 0018,1312,Phase Encoding Direction=ROW >>> 0018,1314,Flip Angle=13 >>> 0018,1315,Variable Flip Angle Flag=N >>> 0028,0010,Rows=512 >>> 0028,0011,Columns=512 >>> >>> It comes up in the proper orientation in tkmedit in three orientations as >>> attachment(eg.coromaland saggital view). >>> >>> Tanks, >>> Xiaojun. >>> >>> >>> 于 2013/12/4 22:45, Bruce Fischl 写道: >>> > Hi Xiaojun >>> > >>> > we need more details in order to help you. What was your input data? > >>> What format was it in? Does it come up in the proper orientation in > >>> tkmedit? What kind of acquisition (resolution, type, etc...) did you use? >>> > >>> > cheers >>> > Bruce >>> > On Wed, 4 Dec 2013, Xiaojun.Huang wrote: >>> > >>> >> >>> >> >>> >> >>> >> -------- 原始消息 -------- >>> >> 主题: >>> >> Some problems of the brain image after recon-all >>> >> 日期: >>> >> Tue, 03 Dec 2013 21:33:41 +0800 >>> >> 发件人: >>> >> Xiaojun.Huang <lvdosha(a)gmail.com> >>> >> 收件人: >>> >> Freesurfer(a)nmr.mgh.harvard.edu >>> >> >>> >> >>> >> Hi, >>> >> >>> >> I am processing the 3D PD patients brain now . After recon-all >> >>> running, the segmentations of the GM and WM is not accurate >>> >> although the original data is normal. additionally, when I use the >> >>> TKSurfer Tools to review the 3D brain,it is reverse. (eg. >>> >> PDSub_02 in the attach files) >>> >> >>> >> It is the first time for me to use Freesurfer.I'm sorry for the >> >>> trouble I'm giving you.And looking forward your reply. >>> >> >>> >> Thanks, >>> >> Xiaojun >>> >> >>> >> 2013.12.3 >>> >> >>> >> >>> >> >>> >> >>> >> >>> > >>> > >>> > 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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import from caret
by Colin Reveley 14 Dec '13

14 Dec '13

Hi - If one has a surface that is aligned to a volume in CARET, is it possible (or rather, is there a general procedure) to export the volume and the surface into freesurfer? The volume in CARET won't be conformed. It's header will define the origin such that CARET interprets a specific voxel/coordinate as the anterior commisure. The surface will be aligned to the volume in the sense that it's co-ordinates are with respect to that anterior commisure definition. What I need to do is run mri_convert -c to conform the volume, and then convert the surface to freesurfer format in such a way that it's now aligned to the conformed volume in freesurfer. Then I'd do some stuff (refine the surface) in freesurfer, and export the surface back to CARET. That's the general issue. Details include: the surface will need to be transformed so that it appears to freesurfer to be 1mm data, and the volume will have it's header changed so that it claims 1mm voxels (the data is higher resolution than 1mm). The problem can be considered as finding the inverse of Van Essen's Freesurfer to F99 pipeline. Or, "Surefit to Freesurfer" is a better way to look at it. The surfaces are *white and *pial though. It's some scaling, translating, conforming and format conversions. Other stuff is not a worry. connectome workbench, FS, CARET, FSL, MATLAB whatever are all relevant/involved tools hope can help Colin Reveley

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error loading surface on one machine, but not another
by Ryan Mruczek 13 Dec '13

13 Dec '13

Hi All I created surfaces for a particular subject on one machine, and subsequently copied the entire subjects surface directory to another machine (both running OSX, although different versions). On the second machine, I cannot load the lh surfaces files. For example % tksurfer LS lh white produces the following output and error (last line): tksurfer LS lh white subject is LS hemi is lh surface is white surfer: current subjects dir: /Users/rmruczek/MR_DATA/surfaces surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/rmruczek/MR_DATA/surfaces/LS/surf checking for nofix files in 'white' Reading image info (/Users/rmruczek/MR_DATA/surfaces/LS) Reading /Users/rmruczek/MR_DATA/surfaces/LS/mri/orig.mgz surfer: Reading header info from /Users/rmruczek/MR_DATA/surfaces/LS/mri/orig.mgz mrisFindNeighbors: /Users/rmruczek/MR_DATA/surfaces/LS/surf/lh.white: face[0].v[0] = 0, but face 0 not in vertex 0 face list This is a problem for all of the left hemisphere surfaces on the new machine. The same command executes fine on the original machine. Also, the right hemisphere surfaces load fine on the second machine. I've double checked that the files were copied completely and were not truncated. Has anyone experienced something similar or have an idea of what is going on? Thanks! Cheers, Ryan

2 3

segmentation incorrectly after recon-all
by Rujing Zha 13 Dec '13

13 Dec '13

Dear all, How can I fix the false segmentation in the attachment. Thanks. All the best. 2013-12-13 Rujing Zha

2 4

problem creating annotation using mri_sample_parc?
by Markus Gschwind 13 Dec '13

13 Dec '13

Dear all, I am trying to create a annotation file from a ROI_file with multiple ROIs with values form 1:10 using mris_sample_parc I had verified that myROIfile and subject001/surf/rh.white and also mri/T1.mgz loadable together in freeview (=same space). when running the command mris_sample_parc -v -sdir subject001 rh ~/Documents/myROIfile.mgz rh.myROIfile.annot it first starts well, but then complains about could not open translation file /Applications/freesurfer/cma_parcellation_colors.txt However when trying to load the created annotation file it gives me the same never endign error: CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory ... etc. I guess that the annotation is not on the surface, but what am I doing wrong? Thank you in advance, Markus

2 5

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