Re: [Freesurfer] hippo_subfields atlas
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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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
Re: [Freesurfer] hippo_subfields atlas
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
Re: [Freesurfer] hippo_subfields atlas
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
Re: [Freesurfer] hippo_subfields atlas
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] hippo_subfields atlas
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 mailto: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 mailto: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 mailto: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 list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu mailto:igles...@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
Re: [Freesurfer] hippo_subfields atlas
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.
Re: [Freesurfer] hippo_subfields atlas
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.comwrote: 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
Re: [Freesurfer] hippo_subfields atlas
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] hippo_subfields atlas
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 mailto: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 list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu mailto:igles...@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, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
