Freesurfer October 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
110 discussions

Segmentation of pallidum.
by zheng.hui＠singhealth.com.sg 07 Oct '08

07 Oct '08

Hi all, We are doing a test-retest study of FreeSurfer segmentation on our dataset. We found reliable estimations for most of the subcortical structures (1% difference) except palladum(3% to 4% difference) while in Fisch's 2002 Neuron paper, pallidum is one of the best segmented structure using manual tracing as gold standard. Any comment? By looking at the aseg, there is no intensity change from pallidum voxels and neighborhood white matter voxels. Is the definition of boundary purely based on the probabilistic atlas? Thanks, Zheng Hui

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freesurfer on fedora core 6
by dahlia＠nmr.mgh.harvard.edu 06 Oct '08

06 Oct '08

Hi, Does anyone know if FS will work smoothly on Fedora 6? The info on FSwiki went up to core 5. Thanks! Dahlia

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LGI output Q's
by Juranek, Jenifer 06 Oct '08

06 Oct '08

Hi, We've run LGI and have looked at the overlay. 1) Is there a txt-type file containing the actual LGI values as computed across aggregates of vertices? Noticed that the recon-all.log file does contain a quantitative value summarizing an average of each hemisphere. 2) Is there a way to plot the computed LGI info along the rostral-caudal extent of each hemisphere? 3) Best method to compare across subjects (or groups)? Seems like qdec is based on vertex-wise analyses, whereas LGI uses aggregates of vertices. Many Thanks for any assistance anyone can provide Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

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Re: [Freesurfer] difference between aparc+aseg.mgz and aparc.a2005s+aseg.mgz
by Doug Greve 06 Oct '08

06 Oct '08

one uses ?h.aparc.annot and one uses ?h.aparc.a2005s.annot. These are two different parcellations. Hwee Ling Lee wrote: > > > > > Hi! > > > > I hope this finds you well. > > What is the difference between aparc+aseg.mgz and aparc.a2005s+aseg.mgz? > > I tried to extract the label for 1180 but I get nothing from > aparc+aseg.mgz. I was wondering if the difference in these images > affect what kind of label I extract. > > > > Thanks! > > > > Cheers, > > HweeLing > > > >------------------------------------------------------------------------ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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[Fwd: Re: [Freesurfer] Volume processing question]
by Tommaso De Marco 06 Oct '08

06 Oct '08

Dear Doug Greve, I have tried to use mri_surf2vol command, but the results obtained aren't enough detailed. I have found a matlab code to open .mgz files and so I'm working on the brain.finalsurfs.mgz file. Do you know if there is a list explaining how the values of the points in this file are associated to the regions of the head? Regards Tommaso De Marco Doug Greve wrote: > > You can use mri_surf2vol to create a mask. Is that what you mean? > > doug > > > On Tue, 30 Sep 2008, Tommaso De Marco wrote: > >> Hi, >> I'm a freesurfer user beginner. I need to discretize the gray matter >> in a cubic mesh. I have extracted the $h.pial and $h.white surfaces, >> and I would know if it is possible in freesurfer to discretize the >> volume suttended by these surfaces. I have seen that there are some >> files called $h.volume; what kind of information is stored in these >> files? Is it possible to open them in a matlab environment or with >> tksurfer? >> >> Regards >> >> Tommaso De Marco >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >

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difference between aparc+aseg.mgz and aparc.a2005s+aseg.mgz
by Hwee Ling Lee 06 Oct '08

06 Oct '08

Hi! I hope this finds you well. What is the difference between aparc+aseg.mgz and aparc.a2005s+aseg.mgz? I tried to extract the label for 1180 but I get nothing from aparc+aseg.mgz. I was wondering if the difference in these images affect what kind of label I extract. Thanks! Cheers, HweeLing

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[Fwd: Re: [Freesurfer] Volume processing question]
by Tommaso De Marco 06 Oct '08

06 Oct '08

Ok. I need of the entire gray matter discretized in small volumes (cubic for example), because I must to identify every point of the gray matter (surface and internal). Pratically I want to have the coordinates of every points included in this volume, and use them for my elaboration. At the beginning I was using the $h.pial meshes; I had loaded the mesh in a matlab environment, trying to discretize the volume suttended by this in small cubic volumes ( with the coordinates of the center of each ones as reference), but the computational cost of this process was too high and the results not enough accurate. Now I' m trying to use directly the brain.finalsurfs.mgz; I have loaded this file in a matlab environment and I'm trying to identify the gray matter voxels according to the associated value in the grid of each slices ( I see that these voxels are binarized at 80, more or less). What I want ask you if the brain.finalsurfs.mgz is the more detailed file in which there are the coordinates of all the internal points of the gray matter and if there is a list explaining how the values of the points of every slices are associated to the regions of the head. Moreover I see that freesurfer generates some files called $h.volume during the step -surfvolume; do you know what kind of information is stored in these files and how to open it? I'm searching in freesurfer site for a code ables to read .volume files, but I haven't found nothing; at least I can write a matlab code to read them, but I don't know how (and what kind of) informations are stored. Regards Tommaso De Marco Doug Greve wrote: > Can you give more details as to what you are trying to do? > > Tommaso De Marco wrote: > >> Dear Doug Greve, >> I have tried to use mri_surf2vol command, but the results obtained >> aren't enough detailed. I have found a matlab code to open .mgz files >> and so I'm working on the brain.finalsurfs.mgz file. Do you know if >> there is a list explaining how the values of the points in this file >> are associated to the regions of the head? >> >> Regards >> >> Tommaso De Marco >> >> >> >> Doug Greve wrote: >> >>> >>> You can use mri_surf2vol to create a mask. Is that what you mean? >>> >>> doug >>> >>> >>> On Tue, 30 Sep 2008, Tommaso De Marco wrote: >>> >>>> Hi, >>>> I'm a freesurfer user beginner. I need to discretize the gray >>>> matter in a cubic mesh. I have extracted the $h.pial and $h.white >>>> surfaces, and I would know if it is possible in freesurfer to >>>> discretize the volume suttended by these surfaces. I have seen that >>>> there are some files called $h.volume; what kind of information is >>>> stored in these files? Is it possible to open them in a matlab >>>> environment or with tksurfer? >>>> >>>> Regards >>>> >>>> Tommaso De Marco >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >> >> >

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importing surfaces into neurolens
by Fenoglio, Angela J 05 Oct '08

05 Oct '08

Hi! We're attempting to overlay group results (generated in neurolens) on a freesurfer-generated inflated brain (and pial surface) in neurolens. The neurolens administrators previously posted instructions on how to do so, but they have not been updated since freesurfer switched from the cor to mgz file format. The old instructions say to open the statistical map and the freesurfer-generated surface in neurolens, and then use the info-.COR file generated by freesurfer to convert the surface vertex coordinates to scanner coordinates. Is there an equivalent to that COR file now?? Thanks -Angela

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A methodological question
by Pedro Paulo de Magalhães Oliveira Junior 03 Oct '08

03 Oct '08

Some weeks ago,I have posted here a compilation of the main papers that describe FreeSurfer implementation. I was wondering if someone has researched in comparison between FreeSurfer methodology and other ones. (For instance: doi:10.1016/j.neuroimage.2004.12.056) Best Regards PPJ -- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom

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labels to surface
by j janssen 03 Oct '08

03 Oct '08

Hi, using version 4.0.5. i want to convert the lh.Medial_wall.label found in the fsaverage label subdir into a mask which consists of 1 x v vector, with value 1 inside the mask, 0 outside the mask and v=#vertices. should i follow mri_label2vol and thereafter mri_vol2surf? i guess i am looking for a way to put binary masks on surface data. thanks, -joost

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Freesurfer October 2008