Freesurfer

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30070 discussions

display bilateral pial surface by tksurfer
by tulu 11 Feb '07

11 Feb '07

Dear freesurfer experts, Can I use tksurfer to display two surface volume ? how to display bilateral pial surface from same subject under tksurfer ? Thanks replay Sincerely Kl chen

2 1

error with mri_ca_register
by Binyam Nardos 09 Feb '07

09 Feb '07

Hi Nick, I keep getting the same error with mri_ca_register. I have now tried this with two different subjects and they both fail at about the same stage. I have checked both brainmask.mgz files in tkmedit for any skull stripping or talairach registration errors and they look fine. Like you had recommended, I have also checked the messages in the /var/log directory but found nothing to suggest that the system was running out of memory. I'm fresh out of ideas. Please let me know if there's any other thing that comes to mind. I've attached the logs again for reference. Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thu 2/8/2007 3:31 PM To: Binyam Nardos Subject: RE: [Freesurfer] error with mri_ca_register Binyam, My run of mri_ca_register using the stable rh9 build of freesurfer also completed successfully, so I was not able to recreate the segfault problem you are seeing. One thing I just learned is that you can view the file: /var/log/messages and check it for messages that say "Out of Memory". This sort of message would appear if a freesurfer binary (or any other) is unable to allocate memory. You will need root or sudo access to read the file on your system. Nick On Wed, 2007-02-07 at 16:46 -0600, Binyam Nardos wrote: > Nick, > upgrading my RAM is definitely on top of my list. As far as the > documentation that I mentioned, I don't think it's something you can > update. I just remembered that I had seen that on the > Dale/Fischl/Sereno 1999 paper (Cortical Surface-Based Analysis I), > which, I know is pretty old, vis-a-vis all the time-consuming changes > that I'm sure have been implemented since then. In any case, I think > the paper reads "The entire procedure, from intensity normalization, > through segmentation, tessellation, and inflation, runs completely > automatically in about 1.5h on current PC architectures ..." > > Binyam > > Binyam Nardos > Cognitive Rehabilitation Research Group > Washington University School of Medicine Box # 8505 > 4444 Forest Park Blvd > St. Louis, MO 63108 > Office: (314) 454-7795 > Fax: (314) 286-1601 > > > > The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. > > > ______________________________________________________________________ > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Wed 2/7/2007 4:35 PM > To: Binyam Nardos > Subject: RE: [Freesurfer] error with mri_ca_register > > > > The mri_ca_register step typically takes about 10 hours to complete. > It > took 9 hours 37 minutes on the 2GHz machine I ran it on yesterday. > > Also, 1GB of RAM is pretty low. All of our machines have at least 2GB > (our minimum recommended), most 4GB. This might actually be the > source > of your problem, as our code does not check when it runs out of memory > (very bad, I know). I'll know more when this second run completes. > But > if it is at all possible to upgrade to 2GB or 4GB of RAM, I *highly* > recommend it. I know with certainty that when someone on the mailing > list upgraded from 512MB to 2GB, these sorts of problems disappeared. > > Can you point me to the documentation that says the segmentation takes > 2-3 hours to complete? I'd like to update that. > > > On Wed, 2007-02-07 at 16:20 -0600, Binyam Nardos wrote: > > thanks Nick, > > I tried processing another subject yesterday and again got stuck > > somewhere around mri_ca_register, I believe it said (segmentation > > error ... sorry I dont' have the details because I'm in windows > world > > right now.) In any case, I had another quick question for you: > > I am running Freesurfer on ubuntu, which is installed on a separate > HD > > on my computer. Some of my specs are 1GB RAM, 3.2GHz dual processor. > > In some of the documetation that I've read, a typical pc takes about > > 2-3 hours for complete segmentation. It's been taking me about 3 > times > > that (i'm actually yet to fully segment a subject successfuly ). But > > is this normal? > > > > thanks again, > > Binyam > > > > Binyam Nardos > > Cognitive Rehabilitation Research Group > > Washington University School of Medicine Box # 8505 > > 4444 Forest Park Blvd > > St. Louis, MO 63108 > > Office: (314) 454-7795 > > Fax: (314) 286-1601 > > > > > > > > The contents of this e-mail message and any attachments are intended > solely for the addressee(s) named in this message. This communication > is intended to be and to remain confidential and may be subject to > applicable physician/patient and/or work product privileges. If you > are not the intended recipient of this message, or if this message has > been addressed to you in error, please immediately alert the sender by > reply e-mail and then delete this message and its attachments. > > > > > > > ______________________________________________________________________ > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > Sent: Wed 2/7/2007 4:10 PM > > To: Binyam Nardos > > Subject: RE: [Freesurfer] error with mri_ca_register > > > > > > > > Binyam, > > > > I was able to run mri_ca_register successfully with this subject, > but > > I > > was using a 'development' build (not the one used publicly), and I > was > > running on a 64bit system. So this problem is not a blatant bug in > > the > > code. > > > > I am going to re-run mri_ca_register again, this time using the rh9 > > stable build (which is what you used) to see if I can get it to > > segfault > > (the problem that you are encountering). > > > > Nick > > > > > > On Tue, 2007-02-06 at 12:01 -0600, Binyam Nardos wrote: > > > thanks Nick > > > > > > Binyam > > > > > > Binyam Nardos > > > Cognitive Rehabilitation Research Group > > > Washington University School of Medicine Box # 8505 > > > 4444 Forest Park Blvd > > > St. Louis, MO 63108 > > > Office: (314) 454-7795 > > > Fax: (314) 286-1601 > > > > > > > > > > > > The contents of this e-mail message and any attachments are > intended > > > solely for the addressee(s) named in this message. This > > communication > > > is intended to be and to remain confidential and may be subject to > > > applicable physician/patient and/or work product privileges. If > you > > > are not the intended recipient of this message, or if this message > > has > > > been addressed to you in error, please immediately alert the > sender > > by > > > reply e-mail and then delete this message and its attachments. > > > > > > > > > > > > -----Original Message----- > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > > Sent: Tue 2/6/2007 11:41 AM > > > To: Binyam Nardos > > > Subject: RE: [Freesurfer] error with mri_ca_register > > > > > > Binyam > > > > > > I've received the files and will have a look at them today. > > > > > > Nick > > > > > > > > > On Tue, 2007-02-06 at 11:32 -0600, Binyam Nardos wrote: > > > > Hi Nick, > > > > I have just uploaded the 4 mgz files for the subject. I hope > > that's > > > > what you were looking for. I checked the skull-strip and > talairach > > > > registration and it looks fine. > > > > > > > > > > > > > > > > thanks, > > > > Binyam > > > > > > > > Binyam Nardos > > > > Cognitive Rehabilitation Research Group > > > > Washington University School of Medicine Box # 8505 > > > > 4444 Forest Park Blvd > > > > St. Louis, MO 63108 > > > > Office: (314) 454-7795 > > > > Fax: (314) 286-1601 > > > > > > > > > > > > > > > > The contents of this e-mail message and any attachments are > > intended > > > > solely for the addressee(s) named in this message. This > > > communication > > > > is intended to be and to remain confidential and may be subject > to > > > > applicable physician/patient and/or work product privileges. If > > you > > > > are not the intended recipient of this message, or if this > message > > > has > > > > been addressed to you in error, please immediately alert the > > sender > > > by > > > > reply e-mail and then delete this message and its attachments. > > > > > > > > > > > > > > > > -----Original Message----- > > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > > > Sent: Tue 2/6/2007 11:18 AM > > > > To: Binyam Nardos > > > > Cc: Freesurfer Mailing List > > > > Subject: Re: [Freesurfer] error with mri_ca_register > > > > > > > > Binyam, > > > > > > > > The recon-all.log indicates that mri_ca_register hit a > > segmentation > > > > fault, which is bad. Can you send me the subject data so that I > > can > > > > try > > > > to recreate this segfault in a debugger? You can upload to me > via > > > the > > > > filedrop: > > > > > > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > In the meantime, also look at the brainmask.mgz file with > tkmedit > > > and > > > > confirm that it is skull-stripped and that the cerebellum is > > > attached. > > > > Also check the talairach registration with tkregister2. > > > > > > > > Nick > > > > > > > > > > > > On Tue, 2007-02-06 at 10:39 -0600, Binyam Nardos wrote: > > > > > hi all, > > > > > I just ran autorecon2 on one of our subjects (for the second > > time, > > > > > after getting a similar error, i.e. ERROR: mri_ca_register > with > > > non- > > > > > zero status. I just rerun recon-all with -autorecon2 without > > > > > removing/changing anything produced by the previous > autorecon2). > > > Is > > > > > there any logical place to start to fix the problem or do I > have > > > to > > > > > rerun mri_ca_register as shown below: > > > > > > > > > > mri_ca_register -align -nobigventricles -mask brainmask.mgz -T > > > > > transforms/talairach.lta > > > > > norm.mgz /usr/local/freesurfer//average/RB_all_2006-02-15.gca > > > > > transforms/talairach.m3z > > > > > > > > > > I have attached the recon-all log for reference. > > > > > Please advise, > > > > > > > > > > thanks, > > > > > Binyam > > > > > > > > > > > > > > > Binyam Nardos > > > > > Cognitive Rehabilitation Research Group > > > > > Washington University School of Medicine Box # 8505 > > > > > 4444 Forest Park Blvd > > > > > St. Louis, MO 63108 > > > > > Office: (314) 454-7795 > > > > > Fax: (314) 286-1601 > > > > > > > > > > > > > > > > > > > > The contents of this e-mail message and any attachments are > > > intended > > > > > solely for the addressee(s) named in this message. This > > > > communication > > > > > is intended to be and to remain confidential and may be > subject > > to > > > > > applicable physician/patient and/or work product privileges. > If > > > you > > > > > are not the intended recipient of this message, or if this > > message > > > > has > > > > > been addressed to you in error, please immediately alert the > > > sender > > > > by > > > > > reply e-mail and then delete this message and its attachments. > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >

2 1

labels in matlab
by Nurunisa Neyzi 09 Feb '07

09 Feb '07

Hi, just a quick question, I am reading my annotation files into matlab following: [v, L, ct] = read_annotation(annotation_filename); Suppose N is the number of vertices. Then, (1) v = N x 1 vector, v(i) = i-1 (you can usually ignore v) (2) L = N x 1 vector, L(i) = label of ith vertex of mesh (3) ct = colortable structure But I cannot interpret the L vector. For example if the lable of a vertex is 126465, what's the label? Going back to the color table, we have R G B , is there are relationship between these L's and the R G B's?

1 1

[Fwd: Re: [Freesurfer] total brain volume]
by Derin Cobia 06 Feb '07

06 Feb '07

Not sure if this went through the first time yesterday, here it is again. Thanks. I've noticed that the gray matter volume output from mris_anatomical_stats (lh) vs. mris_volume (lh.pial) differs. Am I missing something? Do I need to run mris_volume for a different surface? Thanks. -Derin

2 5

mri_convert -ait
by Don Hagler 06 Feb '07

06 Feb '07

I was trying to warp a volume in atlas space (i.e. an ROI) to single subject space using mri_convert -ait ... (version = stable3) and ran into trouble. I found that mri_convert will quit if the data type is int (type 1) and will give strange results if data type is float (type 3). I was able to do what I needed by converting my input volume to uchar (type 0). For what I want to do, uchar works just fine, but is there some reason why it fails for floats? It might be helpful to include some kind of message in the help and maybe quit it the -ait option is used and the input datatype is not uchar. _________________________________________________________________ Laugh, share and connect with Windows Live Messenger http://clk.atdmt.com/MSN/go/msnnkwme0020000001msn/direct/01/?href=http://im…

2 1

surface back to the subject native space
by anqi 06 Feb '07

06 Feb '07

I wonder whether there is a way to convert surfaces back to the subject native space. Thanks! Anqi Qiu Center for Imaging Science The Johns Hopkins University -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Tuesday, February 06, 2007 11:43 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 36, Issue 10 Send Freesurfer mailing list submissions to freesurfer(a)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: tkregister2:views mixed up. (Chacko Cherian) 2. Re: tkregister2:views mixed up. (Doug Greve) 3. Re: brainmask.mgz problems (Bruce Fischl) 4. error with mri_ca_register (Binyam Nardos) ---------------------------------------------------------------------- Message: 1 Date: Mon, 5 Feb 2007 15:47:55 -0800 (PST) From: Chacko Cherian <chacko_cherian(a)yahoo.com> Subject: Re: [Freesurfer] tkregister2:views mixed up. To: Doug Greve <greve(a)nmr.mgh.harvard.edu> Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <570151.930.qm(a)web35315.mail.mud.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 Yes,It is perfectly fine with the --regheader optionmwhich means no problem with geometry info. But how do I fix the talairach.xfm? Thanks a lot! Chacko. --- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > I mean to just load the orig.mgz into tkmedit and see if it is > oriented correctly. Assuming that it is oriented correctly, then it > sounds like the talairach transform is messed up pretty badly. > When you run > tkregister2, try adding --regheader. This will ignore the info in the > talairaach.xfm file and force it to use the geometry info. it will > likely be very far off, but the basic orientation should be ok. > > Chacko Cherian wrote: > > >It has the problem in tkmedit,after I load the transform..i checked > >brainmask.img and T1.img after loading the transform and they had > >this > problem..The > >header and geometry info look fine.. > > > > > >--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > > > > > > >>That means that the geometry info in the file is messed up. Where > >>did the data come from? Are the dicoms messed up too? > >> > >>Chacko Cherian wrote: > >> > >> > >> > >>>No, It has the same problem in tkmedit too. > >>> > >>> > >>>--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > >>> > >>> > >>> > >>> > >>> > >>>>Does it view correctly in tkmedit? > >>>> > >>>>Chacko Cherian wrote: > >>>> > >>>> > >>>> > >>>> > >>>> > >>>>>Hello ALL, > >>>>> > >>>>>Has anybody had trouble with tkregister2..I > >>>>> > >>>>> > >>loaded > >> > >> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>the > >>>> > >>>> > >>>> > >>>> > >>>>>transform and the coronal and horizontal views > >>>>> > >>>>> > >>are > >> > >> > >>>>>mixed up.Coronal view of the subject is coupled > >>>>> > >>>>> > >>>>> > >>>>> > >>>>with > >>>> > >>>> > >>>> > >>>> > >>>>>the horizontal view of the talairach volume. > >>>>> > >>>>>Thanks in advance > >>>>>Regards, > >>>>> > >>>>>Chacko. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>_____________________________________________________________________ >>>_______________ > >>> > >>> > >>>> > >>>> > >>>> > >>>> > >>>>>TV dinner still cooling? > >>>>>Check out "Tonight's Picks" on Yahoo! TV. > >>>>>http://tv.yahoo.com/ > >>>>>_______________________________________________ > >>>>>Freesurfer mailing list > >>>>>Freesurfer(a)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 > >>>>Phone Number: 617-724-2358 > >>>>Fax: 617-726-7422 > >>>> > >>>>In order to help us help you, please follow the steps in: > >>>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>>> > >>>> > >>>>_______________________________________________ > >>>>Freesurfer mailing list > >>>>Freesurfer(a)nmr.mgh.harvard.edu > >>>> > >>>> > >>>> > >>>> > >>>> > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>______________________________________________________________________ >>______________ > >> > >> > >>>Never miss an email again! > >>>Yahoo! Toolbar alerts you the instant new Mail > >>> > >>> > >>arrives. > >> > >>http://tools.search.yahoo.com/toolbar/features/mail/ > >> > >> > >>> > >>> > >>> > >>> > >>-- > >>Douglas N. Greve, Ph.D. > >>MGH-NMR Center > >>greve(a)nmr.mgh.harvard.edu > >>Phone Number: 617-724-2358 > >>Fax: 617-726-7422 > >> > >>In order to help us help you, please follow the steps in: > >>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >> > >> > >>>_______________________________________________ > >>> > >>> > >>Freesurfer mailing list > >>Freesurfer(a)nmr.mgh.harvard.edu > >> > >> > >> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > >_______________________________________________________________________ >_____________ > >Never miss an email again! > === message truncated === ____________________________________________________________________________ ________ Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ------------------------------ Message: 2 Date: Mon, 05 Feb 2007 20:20:04 -0500 From: Doug Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] tkregister2:views mixed up. To: Chacko Cherian <chacko_cherian(a)yahoo.com> Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <45C7D7C4.2070908(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" You can start with that one and fix it by hand (which is a hassle). We are working on ways to make the talairach more robust. BTW, if you run tkregister2 again after fixing it, you should not include the --regheader as that will ignore your previous edits. doug Chacko Cherian wrote: >Yes,It is perfectly fine with the --regheader optionmwhich means no >problem with geometry info. >But how do I fix the talairach.xfm? > >Thanks a lot! > >Chacko. >--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > > >>I mean to just load the orig.mgz into tkmedit and see if it is >>oriented correctly. Assuming that it is oriented correctly, then it >>sounds like the talairach transform is messed up pretty badly. >>When you run >>tkregister2, try adding --regheader. This will ignore the info in the >>talairaach.xfm file and force it to use the geometry info. it will >>likely be very far off, but the basic orientation should be ok. >> >>Chacko Cherian wrote: >> >> >> >>>It has the problem in tkmedit,after I load the transform..i checked >>>brainmask.img and T1.img after loading the transform and they had >>>this >>> >>> >>problem..The >> >> >>>header and geometry info look fine.. >>> >>> >>>--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>> >>> >>> >>>>That means that the geometry info in the file is messed up. Where >>>>did the data come from? Are the dicoms messed up too? >>>> >>>>Chacko Cherian wrote: >>>> >>>> >>>> >>>> >>>> >>>>>No, It has the same problem in tkmedit too. >>>>> >>>>> >>>>>--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Does it view correctly in tkmedit? >>>>>> >>>>>>Chacko Cherian wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>Hello ALL, >>>>>>> >>>>>>>Has anybody had trouble with tkregister2..I >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>loaded >>>> >>>> >>>> >>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>the >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>transform and the coronal and horizontal views >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>are >>>> >>>> >>>> >>>> >>>>>>>mixed up.Coronal view of the subject is coupled >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>with >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>the horizontal view of the talairach volume. >>>>>>> >>>>>>>Thanks in advance >>>>>>>Regards, >>>>>>> >>>>>>>Chacko. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>____________________________________________________________________ >>>>________________ >>>> >>>> >>>>> >>>>> >>>>> >>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>TV dinner still cooling? >>>>>>>Check out "Tonight's Picks" on Yahoo! TV. >>>>>>>http://tv.yahoo.com/ >>>>>>>_______________________________________________ >>>>>>>Freesurfer mailing list >>>>>>>Freesurfer(a)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 >>>>>>Phone Number: 617-724-2358 >>>>>>Fax: 617-726-7422 >>>>>> >>>>>>In order to help us help you, please follow the steps in: >>>>>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> >>>>>> >>>>>>_______________________________________________ >>>>>>Freesurfer mailing list >>>>>>Freesurfer(a)nmr.mgh.harvard.edu >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>>> >>>> >>>> >>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>_____________________________________________________________________ >>>_______________ >>> >>> >>>> >>>> >>>> >>>> >>>>>Never miss an email again! >>>>>Yahoo! Toolbar alerts you the instant new Mail >>>>> >>>>> >>>>> >>>>> >>>>arrives. >>>> >>>> >>>> >>>http://tools.search.yahoo.com/toolbar/features/mail/ >>> >>> >>>> >>>> >>>> >>>> >>>>> >>>>> >>>>> >>>>> >>>>-- >>>>Douglas N. Greve, Ph.D. >>>>MGH-NMR Center >>>>greve(a)nmr.mgh.harvard.edu >>>>Phone Number: 617-724-2358 >>>>Fax: 617-726-7422 >>>> >>>>In order to help us help you, please follow the steps in: >>>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>> >>>> >>>> >>>> >>>> >>>>>_______________________________________________ >>>>> >>>>> >>>>> >>>>> >>>>Freesurfer mailing list >>>>Freesurfer(a)nmr.mgh.harvard.edu >>>> >>>> >>>> >>>> >>>> >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >>> >>> >>> >>______________________________________________________________________ >>______________ >> >> >>>Never miss an email again! >>> >>> >=== message truncated === > > > > >_______________________________________________________________________ >_____________ >Finding fabulous fares is fun. >Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. >http://farechase.yahoo.com/promo-generic-14795097 > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

error with mri_ca_register
by Binyam Nardos 06 Feb '07

06 Feb '07

hi all, I just ran autorecon2 on one of our subjects (for the second time, after getting a similar error, i.e. ERROR: mri_ca_register with non-zero status. I just rerun recon-all with -autorecon2 without removing/changing anything produced by the previous autorecon2). Is there any logical place to start to fix the problem or do I have to rerun mri_ca_register as shown below: mri_ca_register -align -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer//average/RB_all_2006-02-15.gca transforms/talairach.m3z I have attached the recon-all log for reference. Please advise, thanks, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.

2 1

brainmask.mgz problems
by Catherine Hartley 05 Feb '07

05 Feb '07

Hi, I ran autorecon1 on a group of data consisting of a single set of mprage DICOMs per subject, acquired on a Siemens Allegra 3T scanner. Several of the brainmask.mgz images had large portions of the brainstem and cerebellum removed. A couple had portions of the neck which were not removed. The talairach transforms looked fine. A more experiened Freesurfer user suggested that adding control points and re-running the intensity normalization might fix this. I assume that I can follow the instructions here, http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fControlPoints but that I would need to edit the orig.mgz file and then run autorecon1-cp. Is this correct? My intended analysis (cortical thickness in PFC regions) does not depend upon these flawed regions, but I want to make sure these errors aren't indicative of some larger problem. Also, I know there have been issues with gradient warping with the Allegra. Do these problems sound like gradient warping symptoms? Thanks, Cate

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tkregister2:views mixed up.
by Chacko Cherian 05 Feb '07

05 Feb '07

Hello ALL, Has anybody had trouble with tkregister2..I loaded the transform and the coronal and horizontal views are mixed up.Coronal view of the subject is coupled with the horizontal view of the talairach volume. Thanks in advance Regards, Chacko. ____________________________________________________________________________________ TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/

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input registration matrix
by Chacko Cherian 05 Feb '07

05 Feb '07

Hello All, After making changes using tkregister2 the input registration matrix changes.IS there an 'optimum' input registration matrix that i should try to get.I notice that the closer the values(last column of the input reg matrix) are to zero the better the outcome. Thanks in advance. Chacko. ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097

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