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 < iglesias@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 < iglesias@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 < iglesias@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@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.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
I don't think this is possible with the tools in FreeSurfer. Koen?
On Wed, August 7, 2013 1:30 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 < iglesias@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 < iglesias@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 < iglesias@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@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.comiglesias@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
------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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 <iglesias@nmr.mgh.harvard.edu mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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.gzAlso, 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 trapWhat 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, /EugenioThanks 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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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
Thanks very much!
On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < iglesias@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 < iglesias@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 < iglesias@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 < iglesias@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@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.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.pillai@gmail.comwrote:
Thanks very much!
On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < iglesias@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 < iglesias@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 < iglesias@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 < iglesias@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@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.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.pillai@gmail.com mailto:raja.i.pillai@gmail.com> wrote:
Thanks very much! On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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.gzAlso, 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 trapWhat 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, /EugenioThanks 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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@nmr.mgh.harvard.edu> Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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 < iglesias@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.pillai@gmail.com
wrote:
Thanks very much!
On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < iglesias@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 < iglesias@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 < iglesias@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 < iglesias@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@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.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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 <iglesias@nmr.mgh.harvard.edu mailto:iglesias@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.pillai@gmail.com <mailto:raja.i.pillai@gmail.com>> wrote: Thanks very much! On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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.gzAlso, 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 trapWhat 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, /EugenioThanks 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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@nmr.mgh.harvard.edu> Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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 < iglesias@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 < iglesias@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.pillai@gmail.com> wrote:
Thanks very much!
On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < iglesias@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 < iglesias@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 < iglesias@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 < iglesias@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@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.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@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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Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
Hi Raja,
I think there was a misunderstanding here... Let's go back to the very beginning: a mesh collection file has N meshes, indexed from -1 (the reference) to N-2. These meshes have corresponding vertices, i.e., same number and topology, though different locations. Now, for each vertex, there is a vector of L label probabilities associated to it. This vectors are shared by all the meshes in the collection. So, if I look at the probability of vertex 328 of being CSF, it will be the same for all N meshes in the collection.
So, there is NO correspondance between mesh index and labels. Each mesh has all possible labels. That's why kvlRasterizeAtlasMesh requires two indices: one for the mesh, and another for the label.
The atlas only describes the probabilities of observing the subfields in a bounding box around the hippocampus. If you want to register this to a new image... well, that's what recon-all -hippo-subfields does ;-)
Cheers,
/Eugenio
On 08/08/2013 04:35 PM, Rajapillai Pillai wrote:
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 <iglesias@nmr.mgh.harvard.edu mailto:iglesias@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 <tel:205%2062%2078%20255> 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 <tel:204%2068%2034%20255> 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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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.pillai@gmail.com <mailto:raja.i.pillai@gmail.com>> wrote: Thanks very much! On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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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Rajapillai Pillai