Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

problem on autorecon2
by Xiaoying Tang 10 Dec '10

10 Dec '10

Hi All, When use tkemedit to view my results of autorecon2, I got the attached image. I think this is not correct(I am not very sure). Is there any one know why this happens and any way to solve this? Thanks a lot. Best, Xiaoying

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beta.nii vs h.nii for beta value extraction
by Emily Ward 10 Dec '10

10 Dec '10

I want to look at the beta values for all my conditions, voxel-by-voxel (in a specific ROI). I have 180 conditions, and am not looking at a specific contrast. When I open the beta.nii file produced by selxavg3-sess, and look at configure functional overlay, there are 215 "timepoints" listed (and 0 "conditions). It appears that the beta values for the 180 conditions appear first, and there are 35 other regressors tacked on the end. When I open the h.nii file, there are 180 "conditions" and no timepoints. However, when I read these into matlab using MRIread (to get the voxel-by-voxel values), there are 362 timepoints for h.nii and 216 timepoints for beta.nii. Can someone point me to the specific documentation about the beta.nii and h.nii file, so I can know what these extra regressors are? Or alternatively, point me to a different file for extracting voxel-by-voxel beta values? Thanks, Emily Ward

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report with mri_segstats
by Sghedoni Roberto 10 Dec '10

10 Dec '10

Hi, I have a very stupid problem. I try to generate a report by means of mri_segstats. The problem is that when I open it in a spreadsheet (like in Excel), I cannot visualize correctly the columns. I had the same problem with asegstats2table, but there the option -delimiter helped me to set a character that I can use as a delimiter for "text to columns". In mri_segstats an option such that seems not to exist. Did anyone have my same problem? How did you solve it? Thanks Per favore, pensa all'ambiente prima di stampare questo messaggio.

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guidelines for spatial smoothing
by Joakim Vinberg 09 Dec '10

09 Dec '10

Hi FreeSurfer community: I wanted to ask for general thoughts on spatial smoothing of data. In particular, some searching of the archives reveals that a bit of smoothing can help the quality of the data, as well as the inter-subject registration of significance volumes. FreeSurfer can perform both volume-based smoothing and surface-based smoothing. Theoretical concerns and some testing seem to indicate that smoothing along the surface yields more robust results and more consistent results on the data in practice-is this correct? Secondly, I have read some of the general thoughts about smoothing (more localized region, less smoothing; more subjects, less smoothing). Does anybody have some more practical insight into appropriate smoothing kernels for anatomical data (e.g. thickness), and functional data (typically BOLD, typically recorded at 3 x 3 x 4mm)? I'm interested in subject pool sizes between 10 and 50. Thanks very much in advance for all of the help and thoughts- Joakim

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Best way to detect file type
by Michael Waskom 09 Dec '10

09 Dec '10

Hi there, Are there any Freesurfer utilities that I can use to query the file type of an image directly? i.e., more directly than mri(s)_info. The problem is that mris_info barfs when it gets an image that isn't a proper "surface" file, and I'd like something that is maximally flexible. Ideally, there would be a program I could run that will just return the file type for surface, volume, or curv files. Thanks! Best, Mike

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freesurfer shows different results using different systems
by Jamaan Alghamdi 09 Dec '10

09 Dec '10

Hello, I ran freesurfer ReconAll process on 27 subjects using linux opensuse 11.3. freesurfer version is 5.0.0 (freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz). Then I ran the same process on some of those subjects using same version of freesurfer (freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0.dmg) on mac machine (snow leopard 10.6.5). Surprisingly, result that saved in stats folder are not the same even surface and volume images seem to be the same. I attached resulted files from both systems for the same subject, which issue do you think caused that difference and will it affect my overall results as I am going to use gdec with same data. In addition, what do you think is more correct, mac or linux version. Best wishes, Jamaan -- Jamaan Alghamdi 07779801950 0151 795 4627 Magnetic Resonance & Image Analysis Research Centre (MARIARC) University of Liverpool Pembroke place Liverpool L69 3GE http://web.mac.com/jamaan/Jamaan/Welcome.html http://jalghamdi.kau.edu.sa/Default.aspx?Site_ID=0005294&lng=EN

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Partition a surface
by Andrew Dumas 09 Dec '10

09 Dec '10

Hi! I'm trying to partition a surface into a number of random but roughly-equally sized areas, and I've been using the "mris_make_face_parcellation" function to do this. Is it possible to have a finer control over the sizes of each label it generates? I only see 7 options in: $FREESURFER_HOME/lib/bem/ic[1-7].tri (as per the program usage). Can I specify custom ic*.tri files (and also, how would those be generated)? I've tried mris_divide_parcellation, but that only makes strips which aren't necessarily the same area. Thank you! Best Regards, Andrew

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Rerunning recon-all after editing aseg
by Jennifer Addicks 09 Dec '10

09 Dec '10

Hello, I manually edited the aseg.mgz file for one of my participants, I was wondering if someone could tell me how to rerun the recon-all to ensure that these changes are incorporated in future steps and statistics files. Many thanks, Jennifer

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Re: [Freesurfer] preproc-sess error in version 5.0
by Douglas N Greve 09 Dec '10

09 Dec '10

OK, I've tracked down and fixed the error. You can get a new version from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist let me know if that works. doug Katherine Sledge Moore wrote: > Hi, > > I was wondering whether there was any progress on this issue (copied > below)? I have had the same experience as "yuko YY," except that I do > not have access to version 4.5 so I never installed a version of > getrunlist that worked for me. > > To recap, when I try to run a preprocess session, I get output similar > to yuko's. The same is true of "getrunlist." But I can cd into the > folder where my bold runs are, of course. And when I run "find . > -maxdepth 1 -name "[0-9][0-9][0-9]" I get a list of my runs for that > directory (as did yuko). My file structure is essentially the same as > yuko's. > > --Katherine > > Yes, that will solve the problem, I just don't know why it's a problem > to start with. If you cd into that bold dir, can you run: > > find . -maxdepth 1 -name "[0-9][0-9][0-9]" > > doug > > > > > > yuko YY wrote: > > Hi Doug, > > > > "getrunlist /Users/yuko/.../bold" failed, and cd to bold didn't work > > either (error message pasted below). > > Then, Mark suggested me to replace /fsfast/bin/getrunlist with the one > > from v4.5.0., which solved the problem. > > > > Thank you Doug & Mark! > > Yuko Yotsumoto > > > > %------- > > getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM00/bold/ > > find: illegal option -- m > > find: illegal option -- a > > find: illegal option -- e > > find: illegal option -- p > > find: illegal option -- t > > find: illegal option -- h > > find: 1: No such file or directory > > ERROR: no run directories found > > %-------- > > > > On Wed, Nov 24, 2010 at 1:29 AM, Douglas N Greve > > <gr...(a)nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > Hi Yuko, can you try running: > > > > getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold > > > > If that fails, try this: > > > > cd /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold > > > > > > doug > > > > yuko YY wrote: > > > Hello, > > > > > > I recently switch to version 5, and am having a problem with > > > preproc-sess in version 5.0. > > > version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 > > > OS : Mac 10.6.5 > > > > > > When I ran: > > > preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df > > > sessdirfile -s VM20 -fsd bold > > > > > > I got the following error: > > > > > > > %-------------------------------------------------------------------------------------------------------------------------------------------- > > > [Yukos-iMac:sessions/VM/VMan] yuko% preproc-sess -per-session > > -fwhm 5 > > > -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold > > > -------------------------------------------------------------- > > > preproc-sess logfile is log/preproc-sess.log > > > -------------------------------------------------------------- > > > $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ > > > yuko > > > setenv FREESURFER_HOME /Applications/freesurfer/freesurfer > > > setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects > > > Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov > > > 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 > > > /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan > > > /Applications/freesurfer/freesurfer/fsfast/bin/preproc-sess > > > -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile > > -s VM20 > > > -fsd bold > > > Tue Nov 23 19:46:29 JST 2010 > > > instem f > > > mc 1 f fmcpr > > > stc 0 fmcpr > > > sm 0 > > > mask 1 brain > > > VM20 Template ----------------------------- > > > mktemplate-sess -s VM20 -d > > > /Users/yuko/Documents/FreeSurfer/sessions/VM -fsd bold > > > > > > Session: /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 > > > ---------------- > > > Tue Nov 23 19:46:29 JST 2010 > > > find: illegal option -- m > > > find: illegal option -- a > > > find: illegal option -- e > > > find: illegal option -- p > > > find: illegal option -- t > > > find: illegal option -- h > > > find: 1: No such file or directory > > > ERROR: no run directories found > > > > > > > %-------------------------------------------------------------------------------------------------------------------------------------------- > > > > > > I found the same error reported in msg14982, but couldn't find a > > solution. > > > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14982.html > > > > > > Can anyone tell me what I need to do to make this work? > > > Yuko Yotsumoto > > > > > > > > > % additional info > > > > > > > -------------------------------------------------------------------------------------------------------------------------------------------- > > > My data are at: > > > sessions/VM/VM20/bold/001/f.nii > > > sessions/VM/VM20/bold/002/f.nii > > > .. > > > sessions/VM/VM20/bold/009/f.nii > > > > > > and my study directory is at: > > > sessions/VM/VMan/ > > > > > > subject is at: > > > subjects/VM20 > > > > > > > %-------------------------------------------------------------------------------------------------------------------------------------------- > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...(a)nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > Katherine Sledge Moore > Postdoctoral Associate > Visual Cognitive Neuroscience Laboratory > Yale University > http://camplab.psych.yale.edu/ > http://pantheon.yale.edu/~khs8 <http://pantheon.yale.edu/%7Ekhs8> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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CSF masks
by raij＠nmr.mgh.harvard.edu 09 Dec '10

09 Dec '10

Hi, We are trying to create a CSF volume mask from structural MEMPRAGE T1 data (we also have ME FLASH 5/30 ->PD if needed). We are interested in two CSF compartments: - "superficial" CSF outside grey matter and inside inner skull - "deep" CSF inside ventricles Is there a way to simply extract these from aseg.mgz or how should we go about this? Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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