Freesurfer August 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
75 discussions

Re: [Freesurfer] ERROR: cannot find ... /surf/rh.volume
by rafael＠huberworld.ch 28 Aug '07

28 Aug '07

Hy there First i tried to type in the command (load_curv.m) into the matlab shell but it didn't work, so i searched in the /freesurfer/matlab folder, but i didn't found a load_curv.m file there either. Could somebody help me and send me the correct syntax? (i'm using matlab, version 7.4, mac osx) Best regards, Rafael it would be easy enough in matlab using load_curv.m On Mon, 27 Aug 2007 rafael(a)huberworld.ch wrote: Hy Nick, First of all thank you for your quick answer. I understand what you wrote there is to do, but I don't know if there is a function already included to do the step you described. In which way would you multiply the area and thickness measures? Best Regards Rafael Rafael, Creation of the surf/?h.volume surface file by recon-all is a function that did not make it into recon-all into for v4.0, so it is not available yet (but selection of it was mentioned in mris_preproc, as you discovered). ?h.volume will be ?h.area times ?h.thickness at each vertices. Nick On Fri, 2007-08-24 at 11:10 +0200, rafael(a)huberworld.ch wrote: Dear Freesurfer Users Always when i try to do the mri_preproc command with the option "meas volume" i get a error message. (ERROR: cannot find ... /surf/rh.volume). I only get this error message with "volume". All other measures like area, thickness and so on work correctly. Does somebody has a clue how i can solve this problem? _______________________________________________ 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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version question...
by David Perlman 27 Aug '07

27 Aug '07

Is there a way to query an installation of freesurfer to determine what version & platform it came from? Just curious... looking forward to trying out 4.0! -- -dave---------------------------------------------------------------- "Pseudo-colored pictures of a person's brain lighting up are undoubtedly more persuasive than a pattern of squiggles produced by a polygraph. That could be a big problem if the goal is to get to the truth." -Dr. Steven Hyman, Harvard

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preprocessing, eh?
by Jamie Hanson 27 Aug '07

27 Aug '07

Hello Freesurfers- I wondered what the word was on preprocessing before you get into the land of freesurfer and recon-all. I have some Inversion Recovery-T1s, where bias / field inhomogeneity is a slight issue. The standard N3ing that is done autorecon1 really wasn't cutting it (it was fine, but it required additional time in the back end, e.g., correcting skull-strips, adding control points). And for all non-freesurfing, I have been using either: 1) a combo of N3 and MFAST (b/c we have T2 where the same bias isn't present) or 2) a tweaked MFAST routine. I however didn't want to "over-correct" my data, so I wanted to get some feedback before I go down either rabbit-hole. Anyone have some feedback / past experiences? Pics from both routines are at: http://brainimaging.waisman.wisc.edu/~hanson/freesurf1/ Prefix of n3mfast- Combo of N3 and MFAST Prefix of superrestore- Tweaked MFAST routine The superrestores looked cleaner, but I was worried it might be "too much" preprocessing. Thoughts? Thanks much, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 Phone: (608) 262-5148 ***Please note my new email: jamielarshanson(a)gmail.com***

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Ubuntu and freesurfer
by lan lin 27 Aug '07

27 Aug '07

Can freesurfer be installed in Ubuntu? thanks

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Re: [Freesurfer] ERROR: cannot find ... /surf/rh.volume
by rafael＠huberworld.ch 27 Aug '07

27 Aug '07

Hy Nick, First of all thank you for your quick answer. I understand what you wrote there is to do, but I don't know if there is a function already included to do the step you described. In which way would you multiply the area and thickness measures? Best Regards Rafael Rafael, Creation of the surf/?h.volume surface file by recon-all is a function that did not make it into recon-all into for v4.0, so it is not available yet (but selection of it was mentioned in mris_preproc, as you discovered). ?h.volume will be ?h.area times ?h.thickness at each vertices. Nick On Fri, 2007-08-24 at 11:10 +0200, rafael(a)huberworld.ch wrote: Dear Freesurfer Users Always when i try to do the mri_preproc command with the option "meas volume" i get a error message. (ERROR: cannot find ... /surf/rh.volume). I only get this error message with "volume". All other measures like area, thickness and so on work correctly. Does somebody has a clue how i can solve this problem? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Excluded gray matter - pial surface
by Inês Souta 27 Aug '07

27 Aug '07

Hi there, I need to edit the pial surface. It isn't getting out far enough all over the cortex. I'm sure it is not a skull stripping problem. Do I need to add control points everywhere in order to correct this? Isn't there another way? Thanks Ines

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cerebellum WM.
by Jamie Hanson 24 Aug '07

24 Aug '07

Hi Fellow Freesurfers- I am new to the world of FS and just had a quick question re: cerebellar white matter. After some skull-stripping issues (and adjusting the watershed algorithm numerous times), I just edited a bad skull-strip with manual aux vol value cloning. I ran autorecon2 again (and again because of some need for control points). But while double-checking / looking at my wm.mgz, I found massive holes in cerebellar white matter. Pics here: http://brainimaging.waisman.wisc.edu/~hanson/freesurf/ 001.tiff - my brainmask.mgz with some surfaces (just to show nothing wrong with those steps) 002.tiff - brainmask.mgz + aseg.mgz + surfaces 003.tiff- brainmask.mgz + surfaces (at brain-cerebellar "junction") 004.tiff- my wm.mgz + surfaces of the cerebellum in question. My surfaces "seem" to be fine. But I have a few more subjects who show the same patterns in their wm.mgz . Any thoughts? jamie.

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FS version for old data
by Gallo, Antonio (NIH/NINDS) [F] 24 Aug '07

24 Aug '07

Hi All, We have subjects data processed by another person in the lab sometime ago and we were wondering how can we exactly know which version of FS was used at that time for those data. Thanks in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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Re: [Analysis-bugs] Freesurfer v4.0.0 problem??
by Nick Schmansky 24 Aug '07

24 Aug '07

Jonathan, For this error you are encountering with the Linux Centos4 release only: gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file you will either need to install the Fortran compatibility libraries, which can be obtained here: http://rpmfind.net/linux/rpm2html/search.php?query=libg2c or you can download some updated binaries which are built against the static libg2c, from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/cento… copy the file talairach_avi.tar.gz to your FREESURFER_HOME/bin, then type: cd $FREESURFER_HOME/bin tar zxvf talairach_avi.tar.gz chmod a+x * The other Freesurfer releases were built against the static libg2c, but the Centos4 release was inadvertently built against the dynamic lib, which is not available on some platforms (but is on Centos4). This will be fixed by the next release. Nick On Fri, 2007-08-24 at 14:19 -0400, McDaniel, Jonathan (NIH/NIMH) [F] wrote: > Hello, I have recently downloaded and installed Freesurfer v.4.0.0 for Centos onto my Linux machine running Fedora 6. I keep getting the same error message during autorecon1. It is not clear to me if I have set up the package wrong or if possibly there is a problem with this new version of Freesurfer. Any assistance you can provide would be much appreciated. I am attaching the error log file that I receive. > > Thank you, > > Jonathan > > _______________________________________________ > Analysis-bugs mailing list > Analysis-bugs(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/analysis-bugs

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ERROR: cannot find ... /surf/rh.volume
by rafael＠huberworld.ch 24 Aug '07

24 Aug '07

Dear Freesurfer Users Always when i try to do the mri_preproc command with the option "meas volume" i get a error message. (ERROR: cannot find ... /surf/rh.volume). I only get this error message with "volume". All other measures like area, thickness and so on work correctly. Does somebody has a clue how i can solve this problem?

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Freesurfer August 2007