Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Very strange error in surface reconstruction after a2-cp
by Paola Valsasina 17 Dec '13

17 Dec '13

Dear FS experts, I have a very strange error after running autorecon2-cp. I never saw this kind of error with previous versions of FS. I run recon-all -all on my subject, and obtained very good surface reconstructions, with the exception of few excluded wm voxels (see attachment called "before autorecon2-cp"). I added few control points throughout the entire image (for a total of 20 control points) and I run -autorecon2-cp -autorecon3 on the same subject. The output I obtain is very bad (see attachment called "after autorecon2-cp"). How is it possible that adding 20 control points causes such a surface distortions?!! I never had this error with previous FS versions. Thank you for any suggestion. Kind regards, Paola

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Optimal registration
by Dídac Vidal 17 Dec '13

17 Dec '13

Hi, I'd like to ask whether there exist any (implemented/objective) measure to identify a correct surface reconstruction beyond the visual inspection in order to identify gross defect or wm/gm boundary. Thanks in advance. -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Faculty of Medicine University of barcelona

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Fw: Re: unpacksdcmdir: specifies unpacking rules from the command-line ERROR
by Rujing Zha 16 Dec '13

16 Dec '13

Hi Bruce, Thanks Bruce. Would you please help me deal with another two problems? The 1st one is : There is a excellent segmentation in -surfs after editing the pial and running -autorecon-pial. 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. Does this aseg image will influence my group thickness analysis if I donot process additionally? There are brainmask.mgz(pic 1) and aseg(pic 2) snapshots in the attachment. The 2nd one is : I could not visualize the inflated image properly by tksurfer. Here was the detailed describe: tksurfer yizhihui rh inflated I could see little thing in the tksurfer after typing the command above. The result can be got in picture 3 of the attachment and the standard output message can be seen in the picture 4. I had visualized it in the freeview tool by typing "freeview -f $SUBJETCS_DIR/yizhihui/surf/rh.inflated ". The result can be seen in picture 5. CentOS 5.8 is used in my server and I use "freesurfer-Linux-centos4-stable-pib-v5.3.0". Thanks in advance. All the best. 2013-12-17 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 发送时间：2013-12-16 23:57 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人："Rujing Zha"<charujing123(a)163.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Hi Rujing you can use either our FTP site or our file drop. Info for this is at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange and https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html cheers Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: > Hi Bruce, > Maybe 163 email has some problems. I will try my gmail to send you and Louis > my data. But I donot know whether your email can get attachment size 289M? > Thanks. > All the best. > > 2013-12-16 > > ____________________________________________________________________________ > Rujing Zha > > ____________________________________________________________________________ > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > 发送时间：2013-12-16 22:37 > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the > command-line ERROR > 收件人："Rujing Zha"<charujing123(a)163.com> > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > no, I didn't get it > On Mon, 16 Dec 2013, Rujing Zha wrote: > > > Dear Bruce, > > Thanks Bruce. That's all right. > > I want to know if I e-mail to you my subject's data successfully. The > > subject's image had a incorrect segmentation in surfs after recon-all. > > Thanks in advance. > > All the best. > > > > 2013-12-16 > > > > _________________________________________________________________________ > ___ > > Rujing Zha > > > > _________________________________________________________________________ > ___ > > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > 发送时间：2013-12-16 22:24 > > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the ?? ?> command-line ERROR > > 收件人："Rujing Zha"<charujing123(a)163.com> > > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > > > sorry, I don't know that code very well. Doug is probably the right one t > o > ?? ? > > help you > > Bruce > > > > > > On Mon, 16 Dec 2013, Rujing Zha wrote: > > > > > Dear Bruce, > > > I did setup the "-run 015" not "013" in unpacksdcmdir as I told in prev > io > > us > > > message. But it generated the "013" folder automatically after running ?? ? > > > unpacksdcdir, which made me so confused. > > > As it created the "013" folder, I guess unpacksdcmdir didnot recognized > > > > structure image correctly which was in the "15th" line of the scan.info > . > ?? ?> Thanks Bruce. > > > All the best. > > > > > > 2013-12-16 > > > > > > _______________________________________________________________________ > __ > > ___ > > > Rujing Zha > > > > > > _______________________________________________________________________ > __ > > ___ > > > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > > 发送时间：2013-12-16 22:12 > > > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from th > e > ?? ?> command-line ERROR > > > 收件人："Rujing Zha"<charujing123(a)163.com> > > > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > > but why are you giving recon-all the path to run 013 instead of 015? I ?? ? > ?? ?> don't know the fsfast file structure, but your scan.info says that 01 > 3 is > > > > ?? ?an EPI fun and 015 is the mprage > > > > > > On Sat, > > > 14 Dec 2013, Rujing Zha wrote: > > > > > > > Hi Bruce, > > > > It generated a 013 subfolder in after running this code "unpacksdcmdi > r > ?? ? > > > > -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3dana > t > ?? ?mg > > > z > > > > 001.mgz". It is 15 that I can see the number of t1_mpr_ns_sag_iso_zh > an > > g > > ?? ?in > > > > the unpack.log. > > > > Then I ran "recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liuj > un > > ha > > > o", > > > > and it finished without error. > > > > "recon-all -s liujunhao -all" was run and ERROR would be displayed: ?? ? > > > > ERROR: input(s) cannot have multiple frames! > > > > The recon-all.log unpack.log and scan.info were unloaded in the attac > hm > > en > > > t. > > > > Thanks. > > > > All the best. > > > > > > > > 2013-12-14 > > > > > > > > _____________________________________________________________________ > __ > > __ > > > ___ > > > > Rujing Zha > > > > > > > > > > > _______________________________________________ > > > 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 He > lp > > Li > > > 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 > p > > ro > > > perly > > > dispose of the e-mail. > > > > > > > > > > > > > > _______________________________________________ > 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. > > >

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Re: [Freesurfer] problem creating annotation using mri_sample_parc?
by Markus Gschwind 16 Dec '13

16 Dec '13

Dear Bruce or someone else, would you mind answering a little more in detail, please? I am stuck. There is hardly any thread about the command mris_sample_parc, but I need this function. 1) This file called "cma_parcellation_colors.txt", is an option for mris_sample_parc. Where does that file come from? How am I supposed to create it? 2) What is missing if the loading of the created annotation file onto a surface (in freeview) gives the following error, repeating for infinity 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 What does this error mean, at all? Thank you and please excuse my insisting! Markus 2013/12/14 Markus Gschwind <markus.gschwind(a)gmail.com> > Thank you Bruce, > > I read that mris_sample_parc "samples a volumetric parcellation onto a > surface". > > I understand that this is like creating from a file of the type of aseg a > corresponding file of the type of aparc.annot.ctab. > > Is this not true? Do I actually have to create the aparc.annot.ctab type > file manually and give this as the above mentionned file to the command? > The file is only an optional arguement though? > > Thanks again, Markus > > > 2013/12/14 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Hi Markus >> >> you need to create that file (or update FreeSurferColorLUT.txt) to >> reflect whatever you have in /Documents/myROIfile.mgz >> >> cheers >> Bruce >> >> >> On Sat, 14 Dec 2013, Markus Gschwind wrote: >> >> Dear Bruce, >>> Thank you for your answer. I have not yet gotten it correctly. >>> >>> 1) Where does that file come from? Should I create it? how? >>> >>> 2) what is missing in the command of mris_sample_parc? Why does it now >>> work? >>> >>> 3) what does the second error mean? >>> 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 >>> >>> Thanks in advance! >>> [cleardot.gif] >>> >>> Markus >>> >>> >>> 2013/12/13 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> Hi Markus >>> >>> that file translates indices/annotations into colors to display >>> and human reasable names. >>> >>> cheers >>> Bruce >>> On Fri, 13 Dec 2013, Markus Gschwind wrote: >>> >>> I can precise the question, actually there are >>> three: >>> >>> 1) ist the command correct? >>> >>> mris_sample_parc -v -sdir subject001 rh >>> ~/Documents/myROIfile.mgz rh.myROIfile.annot >>> >>> >>> 2) I do not understand the meaning of this claimed >>> file >>> cma_parcellation_colors.txt >>> >>> Actually this does not exist. In the Wiki >>> (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc) >>> it says that >>> there was an optional arguement >>> >>> -file <filename> >>> >>> use <filename> as translation (default: >>> 'cma_parcellation_colors.txt') >>> >>> >>> If I understand correctly, "translation" points ot a >>> problem of different >>> spaces, but the filename rather seems something like >>> a parcellation/atlas >>> color table? >>> >>> 3) The result of this problem seems to be that I >>> cannot annotate the surface >>> using the created annotation file. It gives this >>> error, which i do not >>> understand. >>> >>> >>> >>> 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. >>> >>> Can anyone help me find the problem? >>> >>> >>> Thank you in advance! >>> >>> Markus >>> >>> >>> >>> >>> 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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how to do regression rather than group comparison in freesurfer
by ryu＠nmr.mgh.harvard.edu 16 Dec '13

16 Dec '13

Dear All, Does anyone know how to run regression (with covariates of interest) in freesurfer. I know people usually do group comparison but I need to do regression with a continuous variable. Or do I have to use SPM? Cheers, Jacky

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-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>

1 0

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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Freesurfer December 2013