Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

?h.volume vertex-wise
by Juergen Haenggi 30 Aug '07

30 Aug '07

Dear Freesurfer users We would like to analyze cortical volumes vertex-wise. We recognized that ?h.volume are not produced by the recon-all command. I have read the questions posted some days ago by Rafael Huber concerning the same problem. One proposed solution was to multiply ?h.area times ?h.thickness at each vertices. To do this read_curv.m and the write_curv.m functions in MATLAB were suggested. We tried it but failed maybe due to our insufficient knowledge in MATLAB programming. The first step (read_curv.m) works and produced a vector of curvature (small negative values) instead a vector of thickness (positive values between 1.5 and 3.5 mm) as we expected. What happens here? The command write_curv.m does not work at all. Is there any short documentation about multiplying images in MATLAB? We appreciate any suggestions about that issue. Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

xform avesurf-> subject
by Kirk, Gregory 29 Aug '07

29 Aug '07

Hi All, I want to click on a point on my average surface for my group and ' save point' load a T1 or orig subject in the group with tkmedit and 'goto saved point' i.e. map by the inverse of the transform that embeded the subject surface into the average surface and see the point on the structural that mapped to it. Seems I remember this can be done, I have to load a transform I think. looked through the docs and mail archive but perhaps I was not thinking of the best key to search the archive. thankx Greg.

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resampling thickness
by Goldman, Aaron (NIH/NIMH) [C] 29 Aug '07

29 Aug '07

Hi, for a group of subjects, I was interested in getting ascii files for each subjects' thickness, resampled to an average subject. I know how to do the resampling using something like: mris_preproc --fsgd fsgd.txt --target average --hemi lh --meas thickness --out file.mgh but was wondering what I'd need to do to get individual files that can be read by a text editor, rather than the one big mgh file. Is there some kind of flag or subsequent command I can add to do that? Thanks, -Aaron-

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ReconAllDevTable Q.
by Jamie Hanson 28 Aug '07

28 Aug '07

Which version of Freesurfer is the ReconAllDevTable on the wiki for? Is it for v.3.0x or v.4.0? ... has anything changed in that regard for v.4.0? 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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Standard deviation map
by Inês Souta 28 Aug '07

28 Aug '07

Hello, After computing the average thickness of an average subject (prior to Qdec), how can I estimate and get a map of standard deviations of the thickness measures across the subjects I've averaged. Thanks, Ines

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TICV references of Freesurfer
by Woo Suk, Tae 28 Aug '07

28 Aug '07

Dear Freesurfer developers. I'd like to know the detail process of total intracrainal volume (TICV) measurement by Freesurfer. Would you recommend the directly or indirectly related articles on TICV measurement? Woo Suk, Tae Seoul, Korea

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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

2 1

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

1 1

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***

2 3

Ubuntu and freesurfer
by lan lin 27 Aug '07

27 Aug '07

Can freesurfer be installed in Ubuntu? thanks

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