Re: [Freesurfer] Contrast file to be used in mri_glimfit
2020-04-23
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution I tried running mri_glmfit and this error is occurring - WARNING: gdfReadV1: class B, is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 ,,,Gender,Age,AQ_Top_Quart nan nan Class Means of each Continuous Variable 1 B, nan 2 NB, nan INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf/lh.–-glmdir MRISread(/Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf This is probably related to some error in my .mtx file. Thank you, Alex Job On Fri, Apr 24, 2020 at 12:31 AM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < l...@email.gwu.edu> wrote: > Dear Freesurfer experts, > > I am a little bit confused on how I should construct my .mtx file to be > used in mri_glmfit. The following variables are what I have used in my fsgd > file: > GroupDescriptorFile 1 > Title Study > Class B > Class NB > Variables ,,,Gender,Age > Input, Sub_ID,NB,F,71 > Input, Sub_ID, B, F, 80 > > Please let me know if you need more information on my work. Thank you! > > All the best, > Alex Job > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Contrast file to be used in mri_glimfit
2020-04-23
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I am a little bit confused on how I should construct my .mtx file to be used in mri_glmfit. The following variables are what I have used in my fsgd file: GroupDescriptorFile 1 Title Study Class B Class NB Variables ,,,Gender,Age Input, Sub_ID,NB,F,71 Input, Sub_ID, B, F, 80 Please let me know if you need more information on my work. Thank you! All the best, Alex Job ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Generating Surfaces Meshes
Hi Bruce, The issue is that I want the surface mesh itself to reflect the correct (partial volume corrected) volume as I will be simulating the passage of high energy particles through it. Do you think it would suffice to take the (smoothed) mesh and simply scale its volume in an application like blender? My thinking is that the partial volume effects are probably isotropic so a uniform scaling would leave the geometry unchanged. Best, Jonah On Thu, Apr 23, 2020 at 9:53 PM Bruce Fischl wrote: > HI Jonah > > it depends how you compute volume. mris_volume for example will compute > the > volume of the interior without any partial volume correction. > > And yes, I would expect you want to smooth the surface a bit. You might > try > the Taubin smoothing built into freeview as it won't shrink the surface, > but you can also try mris_smooth > > cheers > Bruce > > > On Thu, 23 Apr 2020, Peter, Jonah wrote: > > > Hi Bruce, > > I tried mri_tessellate which worked well in that the surface seems to > follow the aseg projections > > exactly. Does the volume of this mesh account for partial volume > effects? Also, is there a need to run > > mri_pretess or some sort of smoothing procedure? > > > > For reference, what I am trying to do is import these surface meshes > into a Geant4 simulation for proton > > therapy, and want to make sure I'm using as realistic geometry as > possible. Ideally I'd be able to > > generate a mesh for the whole brain as well as individual segmentations. > > > > Thanks again for your help, > > Jonah > > > > On Thu, Apr 23, 2020 at 5:50 PM Bruce Fischl > wrote: > > no, they are definitely not negligible. It depends on structure > geometry, > > but I bet for something like the hippocampus a large fraction of > voxels in > > it are partial volumed. > > > > You can use mri_mc or mri_tessellate to generate a mesh. It will > be closed > > but may not have a simple topology > > > > On Thu, 23 Apr 2020, Peter, Jonah > > wrote: > > > > > Hi all, > > > Thanks for the response. I'm familiar with partial volume > effects within the context of > > PET imaging, but > > > wouldn't you expect these effects to be negligible in MRI for > structures on the order of > > mm? > > > > > > With respect to the mesh type, I'd like to get closed meshes for > each > > segmentation/parcellation. > > > > > > Is there a way to do this in freesurfer? > > > > > > On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl < > fis...@nmr.mgh.harvard.edu> wrote: > > > Hi Jonah > > > > > > when we compute volumes we typically use a partial-volume > model, which we > > > have found improves accuracy and repeatability. That may > be the source of > > > your discrepancy > > > > > > cheers > > > Bruce > > > On Wed, 22 Apr 2020, Peter, Jonah wrote: > > > > > > > Hello, > > > > I'm trying to generate surface meshes for different > brain regions that can > > > > be imported into a software like MeshLab or Blender > (i.e. .STL, .PLY, .OBJ, > > > > etc.). I ran recon-all on my T1 images, and the > parcellation/segmentation > > > > looks fine. However, I noticed that when I imported this > data into 3DSlicer, > > > > the volumes of these regions did not match the volumes > in the aseg.stats > > > > file. In some cases, the differences were quite > substantial. I tried > > > > removing all smoothing filters in 3DSlicer but the > outcome was the same. > > > > > > > > Do you know what could be going wrong here? > Alternatively, is there an > > > > easier way to generate surface meshes from the aparc or > aseg atlases? > > > > > > > > I'm using the ICBM 2009c Nonlinear Asymmetric > > > > template (http://nist.mni.mcgill.ca/?p=904) as a > generic brain volume > > > > (though alternative suggestions are welcome). > > > > > > > > Thanks! > > > > Jonah > > > > > > > > -- > > > > Jonah PeterGraduate Student in The Biophysics > ProgramHarvard University > > > > P: 646-306-0848 > > > > E: jonahpe...@g.harvard.edu > > > > > > > >___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > -- > > > Jonah PeterGraduate Student in The Biophysics ProgramHarvard > University > > > P: 646-306-0848 > > > E: jonahpe...@g.harvard.edu > > > > > >___ > > Freesurfer mailing list > >
Re: [Freesurfer] Generating Surfaces Meshes
HI Jonah it depends how you compute volume. mris_volume for example will compute the volume of the interior without any partial volume correction. And yes, I would expect you want to smooth the surface a bit. You might try the Taubin smoothing built into freeview as it won't shrink the surface, but you can also try mris_smooth cheers Bruce On Thu, 23 Apr 2020, Peter, Jonah wrote: Hi Bruce, I tried mri_tessellate which worked well in that the surface seems to follow the aseg projections exactly. Does the volume of this mesh account for partial volume effects? Also, is there a need to run mri_pretess or some sort of smoothing procedure? For reference, what I am trying to do is import these surface meshes into a Geant4 simulation for proton therapy, and want to make sure I'm using as realistic geometry as possible. Ideally I'd be able to generate a mesh for the whole brain as well as individual segmentations. Thanks again for your help, Jonah On Thu, Apr 23, 2020 at 5:50 PM Bruce Fischl wrote: no, they are definitely not negligible. It depends on structure geometry, but I bet for something like the hippocampus a large fraction of voxels in it are partial volumed. You can use mri_mc or mri_tessellate to generate a mesh. It will be closed but may not have a simple topology On Thu, 23 Apr 2020, Peter, Jonah wrote: > Hi all, > Thanks for the response. I'm familiar with partial volume effects within the context of PET imaging, but > wouldn't you expect these effects to be negligible in MRI for structures on the order of mm? > > With respect to the mesh type, I'd like to get closed meshes for each segmentation/parcellation. > > Is there a way to do this in freesurfer? > > On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl wrote: > Hi Jonah > > when we compute volumes we typically use a partial-volume model, which we > have found improves accuracy and repeatability. That may be the source of > your discrepancy > > cheers > Bruce > On Wed, 22 Apr 2020, Peter, Jonah wrote: > > > Hello, > > I'm trying to generate surface meshes for different brain regions that can > > be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ, > > etc.). I ran recon-all on my T1 images, and the parcellation/segmentation > > looks fine. However, I noticed that when I imported this data into 3DSlicer, > > the volumes of these regions did not match the volumes in the aseg.stats > > file. In some cases, the differences were quite substantial. I tried > > removing all smoothing filters in 3DSlicer but the outcome was the same. > > > > Do you know what could be going wrong here? Alternatively, is there an > > easier way to generate surface meshes from the aparc or aseg atlases? > > > > I'm using the ICBM 2009c Nonlinear Asymmetric > > template (http://nist.mni.mcgill.ca/?p=904) as a generic brain volume > > (though alternative suggestions are welcome). > > > > Thanks! > > Jonah > > > > -- > > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University > > P: 646-306-0848 > > E: jonahpe...@g.harvard.edu > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University > P: 646-306-0848 > E: jonahpe...@g.harvard.edu > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jonah PeterGraduate Student in The Biophysics ProgramHarvard University P: 646-306-0848 E: jonahpe...@g.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Generating Surfaces Meshes
Hi Bruce, I tried mri_tessellate which worked well in that the surface seems to follow the aseg projections exactly. Does the volume of this mesh account for partial volume effects? Also, is there a need to run mri_pretess or some sort of smoothing procedure? For reference, what I am trying to do is import these surface meshes into a Geant4 simulation for proton therapy, and want to make sure I'm using as realistic geometry as possible. Ideally I'd be able to generate a mesh for the whole brain as well as individual segmentations. Thanks again for your help, Jonah On Thu, Apr 23, 2020 at 5:50 PM Bruce Fischl wrote: > no, they are definitely not negligible. It depends on structure geometry, > but I bet for something like the hippocampus a large fraction of voxels in > it are partial volumed. > > You can use mri_mc or mri_tessellate to generate a mesh. It will be closed > but may not have a simple topology > > On Thu, 23 Apr 2020, Peter, Jonah > wrote: > > > Hi all, > > Thanks for the response. I'm familiar with partial volume effects within > the context of PET imaging, but > > wouldn't you expect these effects to be negligible in MRI for structures > on the order of mm? > > > > With respect to the mesh type, I'd like to get closed meshes for each > segmentation/parcellation. > > > > Is there a way to do this in freesurfer? > > > > On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl < > fis...@nmr.mgh.harvard.edu> wrote: > > Hi Jonah > > > > when we compute volumes we typically use a partial-volume model, > which we > > have found improves accuracy and repeatability. That may be the > source of > > your discrepancy > > > > cheers > > Bruce > > On Wed, 22 Apr 2020, Peter, Jonah wrote: > > > > > Hello, > > > I'm trying to generate surface meshes for different brain > regions that can > > > be imported into a software like MeshLab or Blender (i.e. .STL, > .PLY, .OBJ, > > > etc.). I ran recon-all on my T1 images, and the > parcellation/segmentation > > > looks fine. However, I noticed that when I imported this data > into 3DSlicer, > > > the volumes of these regions did not match the volumes in the > aseg.stats > > > file. In some cases, the differences were quite substantial. I > tried > > > removing all smoothing filters in 3DSlicer but the outcome was > the same. > > > > > > Do you know what could be going wrong here? Alternatively, is > there an > > > easier way to generate surface meshes from the aparc or aseg > atlases? > > > > > > I'm using the ICBM 2009c Nonlinear Asymmetric > > > template (http://nist.mni.mcgill.ca/?p=904) as a generic brain > volume > > > (though alternative suggestions are welcome). > > > > > > Thanks! > > > Jonah > > > > > > -- > > > Jonah PeterGraduate Student in The Biophysics ProgramHarvard > University > > > P: 646-306-0848 > > > E: jonahpe...@g.harvard.edu > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University > > P: 646-306-0848 > > E: jonahpe...@g.harvard.edu > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jonah Peter Graduate Student in The Biophysics Program Harvard University P: 646-306-0848 E: jonahpe...@g.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Trac-All NaN
Those values are at the endpoints of the tracts. As the median tract may be a bit longer or shorter in different subjects, the endpoints don't always have corresponding points in all subjects From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Hua, Jessica Sent: Thursday, April 23, 2020 4:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Trac-All NaN External Email - Use Caution Hi FreeSurfer, I ran the trac-all -stat command on some of my participants, and I noticed that some of the values that were outputted contained NaN. Why are the values coming out as NaN? fmajor_PP.avg33_mni_bbr.AD_Avg.txt S11018a_LGI S11019a_LGI S11021a_LGI NaN NaN 0.00109668 0.00116704 NaN 0.00110631 0.00118262 NaN 0.00113231 0.00119589 NaN 0.00116401 0.00121558 NaN 0.00117549 0.00123733 NaN 0.00119309 0.00126087 NaN 0.00123177 0.00127355 0.00116328 0.00127236 0.00126695 0.00115413 0.00129993 0.00125837 0.00117334 0.00131861 0.00125611 0.00117423 0.00134501 0.00130347 0.00117161 0.00135121 0.00133526 0.00117097 0.00136288 0.00135801 0.00116546 0.00136839 0.00138131 0.0011961 0.00141117 0.00137605 0.00126803 0.00143167 0.00139927 0.00132198 0.00144947 0.00140814 0.00135481 0.00145095 0.00141403 0.00136342 0.00144231 0.00143846 0.00136409 0.0014307 0.00144842 0.00134806 0.00141466 0.00144669 0.00138324 0.00139904 0.00144974 0.00143263 0.00139749 0.00146505 0.00145596 0.00143352 0.00149473 0.0014523 0.00144366 0.00150771 0.0014622 0.00144891 0.00151567 0.00148269 0.00147786 0.0015513 0.00151399 0.00153047 0.00158431 0.00155476 0.00160898 0.00163524 0.00162621 0.00166298 0.00166918 0.0016651 0.0016538 0.00165915 0.00165803 0.00169534 0.00171513 0.00164646 0.00176355 0.00178509 0.00167836 0.00179073 0.00186456 0.00175883 0.00181997 0.00187805 0.00183493 0.00178465 0.00189962 0.00187421 0.00175515 0.00192235 0.00189781 0.00171387 0.0019091 0.00184765 0.00160073 0.00191175 0.00181558 0.00157862 0.00191679 0.00182829 0.00165907 0.00185513 0.00185947 0.0017003 0.00181572 0.00189271 0.00172307 0.00181154 0.0018763 0.00159418 0.0018311 0.0018657 0.00159179 0.00172958 0.00189407 0.00164795 0.00165341 0.00191997 0.00167435 0.00156794 0.00190814 0.00168963 0.00146072 0.001859 0.00172164 0.00138372 0.00178192 0.00175954 0.00136893 0.00170486 0.0018261 0.0013654 0.00164533 0.0018264 0.00135974 0.00155251 0.00176598 0.00137226 0.00149038 0.00166574 0.00133654 0.00146834 0.00152383 0.00134757 0.00148128 0.00138086 0.00136271 0.00147022 0.00132929 0.00136545 0.00144934 0.00127674 0.00137979 0.00145088 0.00125313 0.00137398 0.00151918 0.00125802 0.00137699 0.00151537 0.00126461 0.00136867 0.00146195 0.00126159 0.00136882 0.00140568 0.0012639 0.00134777 0.00138923 0.00126469 0.00127934 0.00138564 0.00127229 0.00122813 0.00138057 0.00128295 0.00118596 0.00138419 0.00129555 0.00117204 0.0013933 0.00131012 0.00114282 0.0013934 0.00129255 0.00114104 0.00141831 0.0012982 0.00116965 0.00141932 0.00128999 0.00118427 0.00139441 0.00128321 0.00117267 0.0013619 0.00127428 0.00117105 0.00133817 0.00124349 0.00114046 0.00131501 0.00121045 NaN 0.0012865 0.00117847 NaN 0.00126657 0.00114993 NaN 0.00123952 0.00113779 NaN NaN 0.00112863 Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Generating Surfaces Meshes
no, they are definitely not negligible. It depends on structure geometry, but I bet for something like the hippocampus a large fraction of voxels in it are partial volumed. You can use mri_mc or mri_tessellate to generate a mesh. It will be closed but may not have a simple topology On Thu, 23 Apr 2020, Peter, Jonah wrote: Hi all, Thanks for the response. I'm familiar with partial volume effects within the context of PET imaging, but wouldn't you expect these effects to be negligible in MRI for structures on the order of mm? With respect to the mesh type, I'd like to get closed meshes for each segmentation/parcellation. Is there a way to do this in freesurfer? On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl wrote: Hi Jonah when we compute volumes we typically use a partial-volume model, which we have found improves accuracy and repeatability. That may be the source of your discrepancy cheers Bruce On Wed, 22 Apr 2020, Peter, Jonah wrote: > Hello, > I'm trying to generate surface meshes for different brain regions that can > be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ, > etc.). I ran recon-all on my T1 images, and the parcellation/segmentation > looks fine. However, I noticed that when I imported this data into 3DSlicer, > the volumes of these regions did not match the volumes in the aseg.stats > file. In some cases, the differences were quite substantial. I tried > removing all smoothing filters in 3DSlicer but the outcome was the same. > > Do you know what could be going wrong here? Alternatively, is there an > easier way to generate surface meshes from the aparc or aseg atlases? > > I'm using the ICBM 2009c Nonlinear Asymmetric > template (http://nist.mni.mcgill.ca/?p=904) as a generic brain volume > (though alternative suggestions are welcome). > > Thanks! > Jonah > > -- > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University > P: 646-306-0848 > E: jonahpe...@g.harvard.edu > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jonah PeterGraduate Student in The Biophysics ProgramHarvard University P: 646-306-0848 E: jonahpe...@g.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Generating Surfaces Meshes
Hi all, Thanks for the response. I'm familiar with partial volume effects within the context of PET imaging, but wouldn't you expect these effects to be negligible in MRI for structures on the order of mm? With respect to the mesh type, I'd like to get closed meshes for each segmentation/parcellation. Is there a way to do this in freesurfer? On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl wrote: > Hi Jonah > > when we compute volumes we typically use a partial-volume model, which we > have found improves accuracy and repeatability. That may be the source of > your discrepancy > > cheers > Bruce > On Wed, 22 Apr 2020, Peter, Jonah wrote: > > > Hello, > > I'm trying to generate surface meshes for different brain regions that > can > > be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, > .OBJ, > > etc.). I ran recon-all on my T1 images, and the parcellation/segmentation > > looks fine. However, I noticed that when I imported this data into > 3DSlicer, > > the volumes of these regions did not match the volumes in the aseg.stats > > file. In some cases, the differences were quite substantial. I tried > > removing all smoothing filters in 3DSlicer but the outcome was the same. > > > > Do you know what could be going wrong here? Alternatively, is there an > > easier way to generate surface meshes from the aparc or aseg atlases? > > > > I'm using the ICBM 2009c Nonlinear Asymmetric > > template (http://nist.mni.mcgill.ca/?p=904) as a generic brain volume > > (though alternative suggestions are welcome). > > > > Thanks! > > Jonah > > > > -- > > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University > > P: 646-306-0848 > > E: jonahpe...@g.harvard.edu > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jonah Peter Graduate Student in The Biophysics Program Harvard University P: 646-306-0848 E: jonahpe...@g.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Trac-All NaN
External Email - Use Caution Hi FreeSurfer, I ran the trac-all -stat command on some of my participants, and I noticed that some of the values that were outputted contained NaN. Why are the values coming out as NaN? fmajor_PP.avg33_mni_bbr.AD_Avg.txt S11018a_LGI S11019a_LGI S11021a_LGI NaN NaN 0.00109668 0.00116704 NaN 0.00110631 0.00118262 NaN 0.00113231 0.00119589 NaN 0.00116401 0.00121558 NaN 0.00117549 0.00123733 NaN 0.00119309 0.00126087 NaN 0.00123177 0.00127355 0.00116328 0.00127236 0.00126695 0.00115413 0.00129993 0.00125837 0.00117334 0.00131861 0.00125611 0.00117423 0.00134501 0.00130347 0.00117161 0.00135121 0.00133526 0.00117097 0.00136288 0.00135801 0.00116546 0.00136839 0.00138131 0.0011961 0.00141117 0.00137605 0.00126803 0.00143167 0.00139927 0.00132198 0.00144947 0.00140814 0.00135481 0.00145095 0.00141403 0.00136342 0.00144231 0.00143846 0.00136409 0.0014307 0.00144842 0.00134806 0.00141466 0.00144669 0.00138324 0.00139904 0.00144974 0.00143263 0.00139749 0.00146505 0.00145596 0.00143352 0.00149473 0.0014523 0.00144366 0.00150771 0.0014622 0.00144891 0.00151567 0.00148269 0.00147786 0.0015513 0.00151399 0.00153047 0.00158431 0.00155476 0.00160898 0.00163524 0.00162621 0.00166298 0.00166918 0.0016651 0.0016538 0.00165915 0.00165803 0.00169534 0.00171513 0.00164646 0.00176355 0.00178509 0.00167836 0.00179073 0.00186456 0.00175883 0.00181997 0.00187805 0.00183493 0.00178465 0.00189962 0.00187421 0.00175515 0.00192235 0.00189781 0.00171387 0.0019091 0.00184765 0.00160073 0.00191175 0.00181558 0.00157862 0.00191679 0.00182829 0.00165907 0.00185513 0.00185947 0.0017003 0.00181572 0.00189271 0.00172307 0.00181154 0.0018763 0.00159418 0.0018311 0.0018657 0.00159179 0.00172958 0.00189407 0.00164795 0.00165341 0.00191997 0.00167435 0.00156794 0.00190814 0.00168963 0.00146072 0.001859 0.00172164 0.00138372 0.00178192 0.00175954 0.00136893 0.00170486 0.0018261 0.0013654 0.00164533 0.0018264 0.00135974 0.00155251 0.00176598 0.00137226 0.00149038 0.00166574 0.00133654 0.00146834 0.00152383 0.00134757 0.00148128 0.00138086 0.00136271 0.00147022 0.00132929 0.00136545 0.00144934 0.00127674 0.00137979 0.00145088 0.00125313 0.00137398 0.00151918 0.00125802 0.00137699 0.00151537 0.00126461 0.00136867 0.00146195 0.00126159 0.00136882 0.00140568 0.0012639 0.00134777 0.00138923 0.00126469 0.00127934 0.00138564 0.00127229 0.00122813 0.00138057 0.00128295 0.00118596 0.00138419 0.00129555 0.00117204 0.0013933 0.00131012 0.00114282 0.0013934 0.00129255 0.00114104 0.00141831 0.0012982 0.00116965 0.00141932 0.00128999 0.00118427 0.00139441 0.00128321 0.00117267 0.0013619 0.00127428 0.00117105 0.00133817 0.00124349 0.00114046 0.00131501 0.00121045 NaN 0.0012865 0.00117847 NaN 0.00126657 0.00114993 NaN 0.00123952 0.00113779 NaN NaN 0.00112863 Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Overlapping Treatments and fsgd files
External Email - Use Caution Hello all, I hope everyone is staying safe and sane out there. I'm running an analysis looking at brain structure differences associated with two separate environmental exposures in children (both dichotomous variables). I am controlling for sex and age, and I'm not interested in interaction effects. My go-to strategy does not match the documentation, but I'm not sure the documented solution using fsgd files will meet my needs. I was hoping I could check with the list about best practices. Because some participants have both exposures, my intuition was to use dummy coded variables so that the design matrix looks like this: +1.0 +3.11124 -0.48322 -0.51007 -0.53020 +1.0 -0.20820 +0.51678 -0.51007 -0.53020 +1.0 -2.06654 -0.48322 -0.51007 -0.53020 ... Where the columns are (mean, mean centered age, mean centered sex, mean centered exposure 1, mean centered exposure 2). A contrast for exposure 1 - exposure 2 would then look like this: [0, 0, 0, 1, -1] However, it's clear from the documentation that, given 3, 2 level factors, the recommended approach is to specify 8 classes (one for every combination of factors) and the covariate in an fsgd file. I can remove the interaction terms from the resulting matrix, but even so it looks very different than what I had above: +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +3.11124 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 -2.06654 ... With a contrast with all classes with exposure 1 set to '1', and all classes with exposure 2 set to '-1' - with the order of the classes in the fsgd file it comes out as [-1 -1 1 1 1 1 -1 -1 0]. I'm not positive that this is the right way to model differences associated with each exposure given unequal #s of participants with neither/both/just one exposure, but I certainly don't have the expertise to be certain. Could someone give me some guidance on the best approach here? Thank you, -Matt -- Matthew Peverill 857-277-9083 mrpever...@gmail.com (preferred) pronouns: he/his ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ROIs to surface overlays / Arithmetic on surface overlays
Hi Quentin if you import it as a surface label you should be able to use morphological operations to smooth it (open, close, dilate, erode) cheers Bruce On Thu, 23 Apr 2020, Funk, Quentin wrote: External Email - Use Caution Freesurfer experts, I have a volumetric ROI (integer valued) in MNI space. I'd really like to display them on the fsaverage brain as a surface overlay so that it's clear what regions I'm looking at. Using something like this, I get pretty good results: mri_vol2surf --mov ROI_integers.nii --regheader fsaverage --hemi lh --out left_overlay.mgh --projfrac-max 0.15 .17 .01 but the edges are kind of a mess, see: https://imgur.com/a/53RVGCM Is there any way to smooth these edges while maintaining the "lookup table' nature of the surface overlay? Any kind of interpolation ruins that, so it's a bit hard (you can't see in that image, but there are multiple regions shown). Alternatively, is there any way I can do arithmetic with surfaces? If there were a tool like fslmaths for surface overlays, solving this problem would be relatively straightforward. Thanks for any help you can provide! -quentin funk Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical thickness measure for external analysis.
you should be fine with the subject metrics we generate. Typically thickness doesn't need much if any eTIV correction On Thu, 23 Apr 2020, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Dear Freesurfer experts, We are interested in running external analysis with thickness measurements of two brain regions. Can we use safely the metrics exported or by contrary a previous transformation is required before export the stats of each subject? Thanks for your time. Best regards, -- Miguel Ángel Rivas Fernández ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ROIs to surface overlays / Arithmetic on surface overlays
External Email - Use Caution Freesurfer experts, I have a volumetric ROI (integer valued) in MNI space. I'd really like to display them on the fsaverage brain as a surface overlay so that it's clear what regions I'm looking at. Using something like this, I get pretty good results: mri_vol2surf --mov ROI_integers.nii --regheader fsaverage --hemi lh --out left_overlay.mgh --projfrac-max 0.15 .17 .01 but the edges are kind of a mess, see: https://imgur.com/a/53RVGCM Is there any way to smooth these edges while maintaining the "lookup table' nature of the surface overlay? Any kind of interpolation ruins that, so it's a bit hard (you can't see in that image, but there are multiple regions shown). Alternatively, is there any way I can do arithmetic with surfaces? If there were a tool like fslmaths for surface overlays, solving this problem would be relatively straightforward. Thanks for any help you can provide! -quentin funk Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Generating Surfaces Meshes
Hi Jonah when we compute volumes we typically use a partial-volume model, which we have found improves accuracy and repeatability. That may be the source of your discrepancy cheers Bruce On Wed, 22 Apr 2020, Peter, Jonah wrote: Hello, I'm trying to generate surface meshes for different brain regions that can be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ, etc.). I ran recon-all on my T1 images, and the parcellation/segmentation looks fine. However, I noticed that when I imported this data into 3DSlicer, the volumes of these regions did not match the volumes in the aseg.stats file. In some cases, the differences were quite substantial. I tried removing all smoothing filters in 3DSlicer but the outcome was the same. Do you know what could be going wrong here? Alternatively, is there an easier way to generate surface meshes from the aparc or aseg atlases? I'm using the ICBM 2009c Nonlinear Asymmetric template (http://nist.mni.mcgill.ca/?p=904) as a generic brain volume (though alternative suggestions are welcome). Thanks! Jonah -- Jonah PeterGraduate Student in The Biophysics ProgramHarvard University P: 646-306-0848 E: jonahpe...@g.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness measure for external analysis.
External Email - Use Caution Dear Freesurfer experts, We are interested in running external analysis with thickness measurements of two brain regions. Can we use safely the metrics exported or by contrary a previous transformation is required before export the stats of each subject? Thanks for your time. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Generating Surfaces Meshes
External Email - Use Caution Could you clarify what kind of meshes you are working with? Are the meshes you are working with plane-like (parts of the pial surface), or are they closed (e.g., generating from running marching cubes on a set of cortex voxels)? Also what is your intention, i.e., what do you want to do with the meshes? The exact volume inside the mesh will always depend on the parameters of the mesh generation algorithm. Best, Tim > On April 23, 2020 at 1:14 AM "Peter, Jonah" wrote: > > > Hello, > > I'm trying to generate surface meshes for different brain regions that can > be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ, > etc.). I ran recon-all on my T1 images, and the parcellation/segmentation > looks fine. However, I noticed that when I imported this data into > 3DSlicer, the volumes of these regions did not match the volumes in the > aseg.stats file. In some cases, the differences were quite substantial. I > tried removing all smoothing filters in 3DSlicer but the outcome was the > same. > > Do you know what could be going wrong here? Alternatively, is there an > easier way to generate surface meshes from the aparc or aseg atlases? > > I'm using the ICBM 2009c Nonlinear Asymmetric template ( > http://nist.mni.mcgill.ca/?p=904) as a generic brain volume (though > alternative suggestions are welcome). > > Thanks! > Jonah > > -- > Jonah Peter > Graduate Student in The Biophysics Program > Harvard University > P: 646-306-0848 > E: jonahpe...@g.harvard.edu > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
