Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

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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qdec cannot find subjects in qdec.table.dat
by David Qixiang Chen 02 Oct '08

02 Oct '08

Hi, I'm running freesurfer in Ubuntu hardy 2.6.24-19 I've ran into a problem with loading data tables in qdec. I've followed the instructions in tutorial 2a and created associated data tables, but qdec always returned the error: ERROR: QdecProject::VerifySubjects: Couldn't find subject '<sdi>' in SUBJECTS_DIR sh: Syntax error: Bad fd number I've even tried to load the tutorial example files, and had the same errors returned back to me, please assist: Here's the error output: Loading data table /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/qdec.table.dat... Number of columns: 189 fsid column: 1 Number of factors: 188 Number of subjects: 40 Reading discrete factor levels from config file /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/gender.levels...'Male','Female', done. Data table /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/qdec.table.dat loaded. sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '004' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '008' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '017' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '021' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '039' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '040' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '045' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '049' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '067' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '073' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '074' in SUBJECTS_DIR Thanks - David Qixiang Chen

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correction
by Jared Price 02 Oct '08

02 Oct '08

Hi, this is Jared again at the Brigham. Quick correction. The error says "pbsubmit: Command not found." not "psubmit: Command not found." Thanks -Jared Jared Price Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 1249 Boylston Street Boston, MA 02115 617-525-6076 jcp44(a)bwh.harvard.edu The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance Help Line at 800-856-1983 and properly dispose of this information.

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"psubmit: Command not found" error
by Jared Price 02 Oct '08

02 Oct '08

Hi everybody, this is Jared over at the Brigham. Quick question for anyone who knows. I am trying to rebuild a subcortical atlas using the script rebuild_gca_atlas.csh. When calling the script I almost immediately get the error "psubmit: Command not found." I would like to get this working before I leave work today, so if anyone knows something about this error please let me know as soon as possible.

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