Sure. Right now I would like to extract the corpus callosum, as defined by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like to pick a voxel in the center of the CC and grow a region around it picking up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted single irregular ROI of the CC.
I am more of an EEG person, and have done this with EEG tools like EMSE and Brain Voyager. Thanks, -Jeff -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of freesurfer-requ...@nmr.mgh.harvard.edu Sent: Tuesday, August 10, 2010 5:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 78, Issue 18 Send Freesurfer mailing list submissions to 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-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@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: Red Hat vs. CentOs (Paul Raines) 2. Exec format error. Wrong Architecture. (Kristina Fanucci) 3. Re: Red Hat vs. CentOs (Don Hagler) 4. [freesurfer] a puzzling installation error (Glen Lee) 5. region seeding and growing (Eriksen, Jeffrey (Portland)) 6. Re: region seeding and growing (Bruce Fischl) 7. surface-based aal template (Zhangyuanchao) 8. File Format for talairach.m3z (Soon Hock Wei) ---------------------------------------------------------------------- Message: 1 Date: Mon, 9 Aug 2010 15:42:57 -0400 (EDT) From: Paul Raines <rai...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Red Hat vs. CentOs To: dah...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <pine.lnx.4.62.1008091542210.9...@gate.nmr.mgh.harvard.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Yes, it should be almost no different. On Mon, 9 Aug 2010 dah...@nmr.mgh.harvard.edu wrote: > Hi, > > I'd like to make sure that a Dell desktop with pre-installed RHEL would > work seamlessly with Freesurfer, equivalent to CentOS. Is this correct? > > Thanks, > Dahlia. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- --------------------------------------------------------------- Paul Raines email: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA ------------------------------ Message: 2 Date: Mon, 9 Aug 2010 15:44:07 -0400 From: Kristina Fanucci <kfanu...@nmr.mgh.harvard.edu> Subject: [Freesurfer] Exec format error. Wrong Architecture. To: freesurfer@nmr.mgh.harvard.edu Message-ID: <aanlktimj2qwfph3vy-_ngzn6zesmk8powgj6gbb74...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, I finished running autorecon1 pbsubmit -m kfanucci -l nodes=1:opteron -c "recon-all -i /autofs/cluster/mscat/users/kristina/MS-freesurfer/ms-dicom/MS_pt20_dico m/MEMPRAGE_4e/008/255000-000008-000049.dcm -subjid MS_pt20_recon -autorecon1" and then tried to look at the skull strip tkmedit MS_pt20_recon brainmask.mgz -aux T1.mgz but received this error: /autofs/cluster/mscat/users/kristina/MS-freesurfer/frozen-freesurfer-ver s03082010/stable/bin/tkmedit.bin: Exec format error. Wrong Architecture. Where did I go wrong? Thanks, Kristina -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2010080 9/a00c832f/attachment-0001.html ------------------------------ Message: 3 Date: Mon, 9 Aug 2010 13:06:41 -0700 From: Don Hagler <dhagle...@hotmail.com> Subject: Re: [Freesurfer] Red Hat vs. CentOs To: <rai...@nmr.mgh.harvard.edu>, <dah...@nmr.mgh.harvard.edu> Cc: freesurfer maillist <freesurfer@nmr.mgh.harvard.edu> Message-ID: <snt129-w506195486f73c6f8ae1f13a6...@phx.gbl> Content-Type: text/plain; charset="iso-8859-1" In my recent experience, no. There were problems with entering text in tksurfer/tkmedit when running on the pre-installed RHEL that went away when CentOS was installed later. > Date: Mon, 9 Aug 2010 15:42:57 -0400 > From: rai...@nmr.mgh.harvard.edu > To: dah...@nmr.mgh.harvard.edu > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Red Hat vs. CentOs > > > Yes, it should be almost no different. > > On Mon, 9 Aug 2010 dah...@nmr.mgh.harvard.edu wrote: > > > Hi, > > > > I'd like to make sure that a Dell desktop with pre-installed RHEL would > > work seamlessly with Freesurfer, equivalent to CentOS. Is this correct? > > > > Thanks, > > Dahlia. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > --------------------------------------------------------------- > Paul Raines email: raines at nmr.mgh.harvard.edu > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > 149 (2301) 13th Street Charlestown, MA 02129 USA > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2010080 9/ed5e991a/attachment-0001.html ------------------------------ Message: 4 Date: Mon, 9 Aug 2010 18:00:52 -0400 From: Glen Lee <glen.le...@gmail.com> Subject: [Freesurfer] [freesurfer] a puzzling installation error To: freesurfer@nmr.mgh.harvard.edu Message-ID: <aanlktin9m8h64a3kul_-x2q5qpuaqnh3srkmstsh9...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear freesurfer experts, I'm running into installation failure and can't quite figure this out (I'm a novice Linux user too). It complains there is no such file or directory although I've downloaded the file and move that to the usr/local directory, so there clearly is the file. Would anybody help me how to resolve this issue? Below is the error message and platform info. Many thanks! -GL ------------------------------------------------------------------------ ------- g...@ubuntu:/usr/local$ uname -a Linux ubuntu 2.6.32-24-generic-pae #39-Ubuntu SMP Wed Jul 28 07:39:26 UTC 2010 i686 GNU/Linux. tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/surf/ tar: freesurfer/average/surf: Cannot mkdir: No such file or directory freesurfer/average/surf/lh.sphere.reg tar: freesurfer/average/surf/lh.sphere.reg: Cannot open: No such file or directory freesurfer/average/surf/rh.sphere.reg tar: freesurfer/average/surf/rh.sphere.reg: C -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2010080 9/fc688d77/attachment-0001.html ------------------------------ Message: 5 Date: Mon, 9 Aug 2010 15:44:50 -0700 From: "Eriksen, Jeffrey (Portland)" <kjeffrey.eriks...@va.gov> Subject: [Freesurfer] region seeding and growing To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <880fcf20f1ad724c995aa1865750cc1404fed...@vhav20msga3.v20.med.va.gov> Content-Type: text/plain; charset="us-ascii" I have looked at the web site and gone through much of the available documentation (without downloading the installer yet) and cannot find if FreeSurfer offers low-level region seeding and growing capabilities. Anyone able to confirm or deny such a feature? Thanks, Jeff Eriksen, PhD Senior Research Associate Oregon Brain Imaging Research Lab (OBIRL) Portland VA Research Foundation kjeffrey.eriks...@va.gov 503-220-8262, x54117 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2010080 9/48b207c9/attachment-0001.html ------------------------------ Message: 6 Date: Mon, 9 Aug 2010 21:08:54 -0400 (EDT) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] region seeding and growing To: "Eriksen, Jeffrey (Portland)" <kjeffrey.eriks...@va.gov> Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <pine.lnx.4.62.1008092108240.21...@gate.nmr.mgh.harvard.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed can you give us an idea as to what you are trying to achieve. We certainly do different kinds of region growing, but they may not meet your needs. cheers Bruce On Mon, 9 Aug 2010, Eriksen, Jeffrey (Portland) wrote: > I have looked at the web site and gone through much of the available > documentation (without downloading the installer yet) and cannot find if > FreeSurfer offers low-level region seeding and growing capabilities. > Anyone able to confirm or deny such a feature? > > Thanks, > > Jeff Eriksen, PhD > Senior Research Associate > Oregon Brain Imaging Research Lab (OBIRL) > Portland VA Research Foundation > kjeffrey.eriks...@va.gov > 503-220-8262, x54117 > > ------------------------------ Message: 7 Date: Tue, 10 Aug 2010 15:00:06 +0800 (CST) From: Zhangyuanchao <woshizhan...@yahoo.cn> Subject: [Freesurfer] surface-based aal template To: freesurfer@nmr.mgh.harvard.edu Message-ID: <712345.14232...@web92413.mail.cnh.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" hi, expert ? I?need a surface-based aal template which is compatible with freesurfer surface files. ? Is there any way I can obtain such a surface-based?aal template? ? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2010081 0/76ec73a3/attachment-0001.html ------------------------------ Message: 8 Date: Tue, 10 Aug 2010 20:34:21 +0800 From: Soon Hock Wei <bie...@nus.edu.sg> Subject: [Freesurfer] File Format for talairach.m3z To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <a0294b392100784a9ae45afa761e8e57746c2...@mbx07.stf.nus.edu.sg> Content-Type: text/plain; charset="us-ascii" Dear All: I am a new user of FreeSurfer and I am wondering what is the file format for talairach.m3z (i.e. the output of mri_ca_register)? I couldn't find this information in FreeSurfer Wiki. In addition, I would like to know how can I use this talairach.m3z to check the accuracy of non-linear mapping to the atlas space? And if I wanted to replace this non-linear transform (i.e. talairach.m3z) by another non-linear transform (without affecting the other process flow), how should I do that? Appreciate if anyone could kindly show me some guidance. Thanks! Best Regards, Soon National University of Singapore ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 78, Issue 18 ****************************************** _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
