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. > >
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