Freesurfer December 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
128 discussions

--fsl flag in bbregister
by Nasim Maleki 11 Dec '10

11 Dec '10

Hello Doug, I get an error message when using --fsl flag with bbregister: "ERROR: Flag --fsl unrecognized." I'm using: bbregister,v 1.14.2.12 2009/08/07 22:21:00 greve Is this version of the bbregister that I'm using the latest? Thank you, Nasim

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source code for freesurfer
by Alexander Taghva 11 Dec '10

11 Dec '10

Is it possible to get the source code for freesurfer for research purposes? There are mentions of open source distributions but I can't find them. Thanks! -- Alexander Taghva, MD Department of Neurological Surgery Ohio State University

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inaccuracy in surface reconstruction
by Sasa Kivisaari 10 Dec '10

10 Dec '10

Hi all, I have a question about what to me looks like an inaccurate surface reconstruction. I attach here 3 consecutive coronnal slices: in the first and second, the pial surface doesn't seem to follow the whole extent of the collateral sulcus on the right hemisphere (the location of the crosshair). Just eye balling it, it looks like there is a relatively deep sulcus there, but the pial surface doesn't go all the way in. In the third screen shot, 2mm posterior to the first, the sulcus is reconstructed the way I would expect it to. Could you please give me some insights into the reason behind this? Is there a way of fixing it without touching the gray matter voxels? Please let me know if you need any additional information! Thank you in advance, Sasa

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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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Freesurfer December 2010