V ery funny indeed...so, just for absolute clarification is there a one-to-one correspondence between the order listed in the mesh collection and the order in the lookup tables? i.e. does label 2 (CSF) correspond to position -1 (reference)? Does label 8 (left subiculum) correspond to position 9?
Also, when I open a given rasterized file, it shows me a subfield view of a particular area. If we wanted to register this with another image, how would we do it--could we find bounding box coordinates? Or can we access the entire t1 weighted image? Best regards, Raja On Thu, Aug 8, 2013 at 4:23 PM, Juan Eugenio Iglesias < igles...@nmr.mgh.harvard.edu> wrote: > It's a funny coincidence that the number of meshes is equal to the number > of labels... For each mesh, you can rasterize all labels, indexed as in the > table. > Cheers, > /Eugenio > > > > On 08/08/2013 04:21 PM, Rajapillai Pillai wrote: > > Okay. I'm still a little unclear. So I'm looking at the compression > lookup file (left in this case) and seeing this: > > 24 2 CSF 60 60 60 255 > 2 0 Left-Cerebral-White-Matter 0 225 0 255 > 3 1 Left-Cerebral-Cortex 205 62 78 255 > 17 3 Left-Hippocampus 220 216 20 255 > 550 5 left_CA2_3 17 85 136 255 > 552 9 left_CA1 204 68 34 255 > 553 4 left_fimbria 204 0 255 255 > 554 7 left_presubiculum 221 187 17 255 > 555 10 left_hippocampal_fissure 153 221 238 255 > 556 6 left_CA4_DG 51 17 17 255 > 557 8 left_subiculum 0 119 85 255 > > Then when I look at the CurrentMeshCollection, I am seeing Positions > 0-9, and the reference position, which as you said is -1. What is the > correspondence between these labels and meshes? Sorry if I'm being > obtuse--I'm just having trouble piecing it all together. > > Best regards, > Raja > > > On Thu, Aug 8, 2013 at 1:49 PM, Juan Eugenio Iglesias < > igles...@nmr.mgh.harvard.edu> wrote: > >> Hi again, Raja. >> Which labels and meshes to use depends on what you want to do. If you >> extract all the priors corresponding to all the labels in the atlas (the >> list is in $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt), you >> would have a volumetric version of the atlas (rather than a mesh). >> Cheers, >> /Eugenio >> >> >> >> On 08/07/2013 06:04 PM, Rajapillai Pillai wrote: >> >> Final question regarding this: what combinations of labels and meshes >> should I use? Should I do all combinations between labels and positions, >> matching labels/positions only, etc? How can I tell which meshes correspond >> to what labels/areas? >> >> Thanks for your time, >> Raja >> >> >> On Wed, Aug 7, 2013 at 4:26 PM, Rajapillai Pillai < >> raja.i.pil...@gmail.com> wrote: >> >>> Thanks very much! >>> >>> >>> On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < >>> igles...@nmr.mgh.harvard.edu> wrote: >>> >>>> Shame on me; there's a way of doing this. You need a reference volume; >>>> for the hippocampal subfield atlas: >>>> $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz >>>> the reference volume would be: >>>> $FREESURFER_HOME/data/GEMS/imageDump.mgz >>>> >>>> The command would be: >>>> >>>> kvlRasterizeAtlasMesh CurrentMeshCollection30.gz imageDump.mgz >>>> [labelNumber] [meshNumber] >>>> >>>> "meshNumber" is the index of the mesh to extract in the collection; use >>>> -1 for the reference position. >>>> labelNumber is the label whose probability map you want to rasterize ( >>>> 0 = white matter, 1 = gray matter, 2 = CSF, 9 = CA1, etc; see >>>> $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt). >>>> >>>> From the volumetric rasterized prior probability map, you can easily >>>> compute volumes, if you want. >>>> >>>> Cheers, and sorry again for the original wrong answer, >>>> >>>> /Eugenio >>>> >>>> >>>> >>>> >>>> >>>> On 08/07/2013 01:30 PM, Rajapillai Pillai wrote: >>>> >>>> Hi again! >>>> >>>> I have another question about the hippocampal subfields atlas--might >>>> be a silly one. Is there a way to extract volumes from the mesh collection? >>>> >>>> Thanks a lot, >>>> Raja >>>> >>>> >>>> On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias < >>>> igles...@nmr.mgh.harvard.edu> wrote: >>>> >>>>> Sounds good, but please email the list, rather than only me ;-) >>>>> /E >>>>> >>>>> >>>>> On 07/31/2013 05:03 PM, Rajapillai Pillai wrote: >>>>> >>>>> Thanks a lot. I'll let you know if I have any more issues. >>>>> >>>>> Best regards, >>>>> Raja >>>>> >>>>> >>>>> On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias < >>>>> igles...@nmr.mgh.harvard.edu> wrote: >>>>> >>>>>> Did you run recon-all -subjid bert -hippo-subfields? If so, there >>>>>> should be a log file with the output from the hippo-subfield code in >>>>>> $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it >>>>>> to get an idea of what happened. >>>>>> Kind regards, >>>>>> /Eugenio >>>>>> >>>>>> >>>>>> On 07/31/2013 04:38 PM, Rajapillai Pillai wrote: >>>>>> >>>>>> Thanks very much for the prompt response. The command I ran was >>>>>> >>>>>> $ kvlQuantifyPosteriorProbabilityImages >>>>>> /Applications/freesurfer/data/GEMS/compressionLookupTable.txt >>>>>> posterior_right_* posterior_Right-Hippocampus.mgz >>>>>> >>>>>> in $SUBJECTS_DIR/bert/mri >>>>>> >>>>>> And yeah, it's not in the mri directory. Any idea what might have >>>>>> gone wrong and how I can try and fix it? >>>>>> >>>>>> Thanks, >>>>>> Raja >>>>>> >>>>>> >>>>>> On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias < >>>>>> igles...@nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>>> Hi Raja, >>>>>>> >>>>>>> >>>>>>> >>>>>>> I'm have a question regarding the GEMS hippocampal segmentation. I >>>>>>> saw on the wiki how to run -hippo_subfields, but how do I access the >>>>>>> atlas >>>>>>> itself? What file is it under. >>>>>>> >>>>>>> >>>>>>> That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz >>>>>>> >>>>>>> >>>>>>> >>>>>>> Also, I'm not sure if I'm missing some files: whenever I try to do >>>>>>> one of the individual commands using, for example, >>>>>>> posterior_Right_Hippocampus.mgz, it gives the following error: >>>>>>> >>>>>>> volumeInVoxels: >>>>>>> terminate called after throwing an instance of >>>>>>> 'itk::ExceptionObject' >>>>>>> what(): itkMGHImageIO.cxx:216: >>>>>>> itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: >>>>>>> posterior_Right-Hippocampus.mgz >>>>>>> Abort trap >>>>>>> >>>>>>> >>>>>>> What command is this? In any case, it's pretty clear that the file >>>>>>> is missing.... >>>>>>> >>>>>>> >>>>>>> Also, upon searching through my freesurfer directory, I cannot >>>>>>> find any posterior_Right-Hippocamus.mgz or >>>>>>> posterior_Left-Hippocampus.mgz >>>>>>> files. >>>>>>> >>>>>>> It should be under the "mri" directory. If it isn't, there was some >>>>>>> problem running the algorithms. >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> /Eugenio >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Thanks very much for your time, >>>>>>> Raja >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing >>>>>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ------------------------------------------------------------------------------------- >>>>>>> Juan Eugenio Iglesias, >>>>>>> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu >>>>>>> Athinoula A. Martinos Center for Biomedical Imaging >>>>>>> 149 Thirteenth Street, Suite 2301 >>>>>>> Charlestown, Massachusetts 2129 >>>>>>> U.S.A. >>>>>>> >>>>>>> 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. >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ------------------------------------------------------------------------------------- >>>>>> Juan Eugenio Iglesias, >>>>>> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu >>>>>> Athinoula A. Martinos Center for Biomedical Imaging >>>>>> 149 Thirteenth Street, Suite 2301 >>>>>> Charlestown, Massachusetts 2129 >>>>>> U.S.A. >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------------------------------- >>>>> Juan Eugenio Iglesias, >>>>> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu >>>>> Athinoula A. Martinos Center for Biomedical Imaging >>>>> 149 Thirteenth Street, Suite 2301 >>>>> Charlestown, Massachusetts 2129 >>>>> U.S.A. >>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing >>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------------------- >>>> Juan Eugenio Iglesias, >>>> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu >>>> Athinoula A. Martinos Center for Biomedical Imaging >>>> 149 Thirteenth Street, Suite 2301 >>>> Charlestown, Massachusetts 2129 >>>> U.S.A. >>>> >>>> >>> >> >> -- >> ------------------------------------------------------------------------------------- >> Juan Eugenio Iglesias, >> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu >> Athinoula A. Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> >> > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, > PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > >
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