Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

post-doc position in cognitive and clinical neuroscience
by walhovd＠nmr.mgh.harvard.edu 20 Jan '08

20 Jan '08

Hi all There is a vacant post-doctoral research fellow position in cognitive and clinical neuroscience at the Department of Psychology, University of Oslo, Norway. If interested, please see the attached announcement. Best wishes, Kristine B Walhovd Professor University of Oslo Center for the Study of Human Cognition Department of Psychology PB 1094 Blindern 0317 Oslo Norway phone (+47) 22845130 e-mail: k.b.walhovd(a)psykologi.uio.no

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RE: [Freesurfer] FreeSurfer on SUN Linux machines
by Pedro Paulo Oliveira Jr 18 Jan '08

18 Jan '08

Solaris is another OS distinct from Linux. Freesurfer 4.0 won't run Pedro Paulo on E61 -- mens. original -- Assunto: RE: [Freesurfer] FreeSurfer on SUN Linux machines De: "Iman Aganj" <Iman(a)umn.edu> Data: 18/01/2008 19:28 Dear Nick, I think it is Solaris. Tcsh is installed, and I am not quite sure about the processor. Thanks, Iman -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2008 9:49 PM To: Iman Aganj Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer on SUN Linux machines Iman, What OS is installed on the system? What processor does it use? Do all the freesurfer commands give that error? Is tcsh installed? Nick > Hello everybody, > > > > I am trying to install FreeSurfer on SUN Linux machines, and I am not sure > which platform to choose. I have already tried CentOS 4, but when I try > for > example "tkmedit bert orig.mgz", I get the Invalid argument error. I will > appreciate any help. > > > > Thanks a lot. > > > > Best, > > Iman > > > > _______________________________________________ > 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

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FreeSurfer on SUN Linux machines
by Iman Aganj 18 Jan '08

18 Jan '08

Hello everybody, I am trying to install FreeSurfer on SUN Linux machines, and I am not sure which platform to choose. I have already tried CentOS 4, but when I try for example "tkmedit bert orig.mgz", I get the Invalid argument error. I will appreciate any help. Thanks a lot. Best, Iman

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Creating one's own average sphere/template
by Graham Wideman 18 Jan '08

18 Jan '08

Folks: I'm trying to get a complete picture of what's entailed in creating our own atlas, including our own average reference sphere, so if there's a doc on this specific subject I'd love to see it. Absent that, below are questions to fill in some gaps: 1. Normal spherical reg: mris_register's command-line params don't include all files it must read, so I'm looking for a list of all the files that it reads under the usual circumstances (ie: registration to ref sphere; registration to opposite hemi), and how it decides *which* files to read. (Amongst other discrepancies, when recon-all runs, mris_register doesn't seem to read ?h.curv, whereas various postings suggest that it does.) 2. Normal labeling with mris_ca_label: Presumably this only works if subjects are registered to the same average sphere mesh as was used to create the chosen GCS file, right? Yet mris_ca_label doesn't need to read that actual ?h.sphere.reg file because equivalent position-on-sphere info is contained in the GCS file... right? 3. Creating one's own average reference sphere: What progam(s) does one use to create the average ?h.sphere(.reg?) file (presumably from each subject's ?h.sphere file)? and average curvature file (ie: the tif file)? FWIW, it looks like mris_make_template is somehow involved here, but it's entire documentation consists of just "This program will add a template into an average surface" (what does that mean?), and the source code looks like it only produces the tif file containing average sulc and curv data. (From which I conclude the here, "template" refers to just that file.) 4. What, if any, is the relationship between .../freesurfer/average and .../freesurfer/subjects/fsaverage Thanks, Graham

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recon-all error
by fpolli＠nmr.mgh.harvard.edu 17 Jan '08

17 Jan '08

hi in /space/nexlin3/3/users/kahn/fpolli, i ran reconall -i RECONS_DIR/pol001/003/001.mgz -all i got the following error: ERROR: wrong talsrcimg.4dfp.ifh orientation ERROR: mpr2mni305 failed, see transforms/talairach_avi.log this is data collected at MIT, so does it have to do with something in the DICOM being different here? thanks, frida

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apple leopard 64 bit
by Kirk, Gregory 17 Jan '08

17 Jan '08

Hi all, Are there plans to release binaries for the Mac Leopard 64 bit Greg.

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Zen of label editing in tksurfer
by Graham Wideman 17 Jan '08

17 Jan '08

Folks: We notice that when we try editing labels in tksurfer (eg: draw an outline, fill with new label value), this results in tksurfer's control panel showing two labels everywhere (even where we didn't edit), with the second one saying "1 additional label" (or something like that... don't have it running at the moment). Further exploration has us puzzled about deletion, saving and so on. What is the model that tksurfer is following here? If you load one label file, and then start editing, is that like tksurfer introduces another "layer" (ie: a second label slot for every vertex?). How do you load a label file and explicitly edit that data instead of creating new data? Thanks, Graham

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error: libexpat.so.0
by Woo Suk, Tae 17 Jan '08

17 Jan '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } How are you?When I run recon-all -s subjid -all with Fressurfer 4.02,the process was terminated with the error message of" mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory"And, when I ran 'qdec' , the same error "qdec.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file:No such file or directory" was occured.But, "libexpat.so.0" was already installed.How can I correct it?Woo Suk, Tae Ph.D

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-autorecon2 FILL
by bell0368＠umn.edu 15 Jan '08

15 Jan '08

Freesurfers, I have a subject that exits with errors from autorecon2 FILL with the following message "mri_fill: could not find any points where lh and rh wm are nbr s" Has anyone come across a similar problem? Thanks Chris Bell

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Custom color scale for overlays in tksurfer
by Hans Johnson 15 Jan '08

15 Jan '08

Hello, Is there a way to apply a custom color scale to overlays in tksurfer. It seems that the the only options are "Green Red; Heat; "Blue Red". I would really like to make my own colors. Any suggestions would be greatly appreciated. Thanks, Hans -- Hans J. Johnson, Ph.D. Hans-johnson(a)uiowa.edu 278 GH The University of Iowa Iowa City, IA 52241 (319) 353 8587

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