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Dear all,
my intention is to use the Brainnetome Atlas parcellation/segmentation in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
Is this the right approach to obtain a high resolution segmentation to run PVC methods?
Thanks, Boris
I don't know what the Brainnetome is, but it looks like you have it in annotation form. I think that command should work. Why are you using --no-xcerseg? This will cause it to not include extracerebral structures. Also note that you cannot use arbitrarily small segments when doing PVC.
On 8/13/19 10:26 AM, Boris Rauchmann wrote:
External Email - Use Caution
Dear all,
my intention is to use the Brainnetome Atlas parcellation/segmentation in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
Is this the right approach to obtain a high resolution segmentation to run PVC methods?
Thanks, Boris
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for your prompt answer - the command worked. This is the atlas mentioned: http://atlas.brainnetome.org/brainnetome.html What is approximately the smallest possible segment when using PVC? Also, does the exclusion of extracerebral structures harm? I used that flag because it complained:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok but you must indicate whether to use what is there (--no-xcerseg) or create a new one and overwrite what is there (--xcerseg) or specify your own headseg (--head)
and did not want to override my apas+head.mgz
Thanks, Boris
On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
I don't know what the Brainnetome is, but it looks like you have it in annotation form. I think that command should work. Why are you using --no-xcerseg? This will cause it to not include extracerebral structures. Also note that you cannot use arbitrarily small segments when doing PVC.
On 8/13/19 10:26 AM, Boris Rauchmann wrote:
External Email - Use CautionDear all,
my intention is to use the Brainnetome Atlas parcellation/segmentation in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
Is this the right approach to obtain a high resolution segmentation to run PVC methods?
Thanks, Boris
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There is no cut off for the minimum size. As it gets smaller, the PVC noise amplification will become bigger (it also depends on the shape as well).
I think the --no-xcerseg is the right way to go now
On 8/13/19 11:00 AM, Boris Rauchmann wrote:
External Email - Use Caution
Thank you for your prompt answer - the command worked. This is the atlas mentioned: http://atlas.brainnetome.org/brainnetome.html What is approximately the smallest possible segment when using PVC? Also, does the exclusion of extracerebral structures harm? I used that flag because it complained:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok but you must indicate whether to use what is there (--no-xcerseg) or create a new one and overwrite what is there (--xcerseg) or specify your own headseg (--head)
and did not want to override my apas+head.mgz
Thanks, Boris
On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I don't know what the Brainnetome is, but it looks like you have it in annotation form. I think that command should work. Why are you using --no-xcerseg? This will cause it to not include extracerebral structures. Also note that you cannot use arbitrarily small segments when doing PVC. On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Dear all, > > my intention is to use the Brainnetome Atlas parcellation/segmentation > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > Is this the right approach to obtain a high resolution segmentation to > run PVC methods? > > Thanks, > Boris > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Alright, thanks!
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
There is no cut off for the minimum size. As it gets smaller, the PVC noise amplification will become bigger (it also depends on the shape as well).
I think the --no-xcerseg is the right way to go now
On 8/13/19 11:00 AM, Boris Rauchmann wrote:
External Email - Use CautionThank you for your prompt answer - the command worked. This is the atlas mentioned: http://atlas.brainnetome.org/brainnetome.html What is approximately the smallest possible segment when using PVC? Also, does the exclusion of extracerebral structures harm? I used that flag because it complained:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok but you must indicate whether to use what is there (--no-xcerseg) or create a new one and overwrite what is there (--xcerseg) or specify your own headseg (--head)
and did not want to override my apas+head.mgz
Thanks, Boris
On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I don't know what the Brainnetome is, but it looks like you have it in annotation form. I think that command should work. Why are you using --no-xcerseg? This will cause it to not include extracerebral structures. Also note that you cannot use arbitrarily small segments when doing PVC. On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Dear all, > > my intention is to use the Brainnetome Atlas parcellation/segmentation > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > Is this the right approach to obtain a high resolution segmentation to > run PVC methods? > > Thanks, > Boris > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I just realized that the above mentioned command (gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives me only the cortical segmentation. Is there any way to also include the subcortical segmentation based on my individual atlas? I also have an Atlas_subcortex.gca file available.
Best, Boris
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
There is no cut off for the minimum size. As it gets smaller, the PVC noise amplification will become bigger (it also depends on the shape as well).
I think the --no-xcerseg is the right way to go now
On 8/13/19 11:00 AM, Boris Rauchmann wrote:
External Email - Use CautionThank you for your prompt answer - the command worked. This is the atlas mentioned: http://atlas.brainnetome.org/brainnetome.html What is approximately the smallest possible segment when using PVC? Also, does the exclusion of extracerebral structures harm? I used that flag because it complained:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok but you must indicate whether to use what is there (--no-xcerseg) or create a new one and overwrite what is there (--xcerseg) or specify your own headseg (--head)
and did not want to override my apas+head.mgz
Thanks, Boris
On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I don't know what the Brainnetome is, but it looks like you have it in annotation form. I think that command should work. Why are you using --no-xcerseg? This will cause it to not include extracerebral structures. Also note that you cannot use arbitrarily small segments when doing PVC. On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Dear all, > > my intention is to use the Brainnetome Atlas parcellation/segmentation > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > Is this the right approach to obtain a high resolution segmentation to > run PVC methods? > > Thanks, > Boris > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject
On 11/5/19 1:06 PM, Boris Rauchmann wrote:
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I just realized that the above mentioned command (gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives me only the cortical segmentation. Is there any way to also include the subcortical segmentation based on my individual atlas? I also have an Atlas_subcortex.gca file available.
Best, Boris
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
There is no cut off for the minimum size. As it gets smaller, the PVC noise amplification will become bigger (it also depends on the shape as well). I think the --no-xcerseg is the right way to go now On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for your prompt answer - the command worked. This is the > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html > What is approximately the smallest possible segment when using PVC? > Also, does the exclusion of extracerebral structures harm? I used that > flag because it complained: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > but you must indicate whether to use what is there (--no-xcerseg) > or create a new one and overwrite what is there (--xcerseg) > or specify your own headseg (--head) > > and did not want to override my apas+head.mgz > > Thanks, > Boris > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I don't know what the Brainnetome is, but it looks like you have > it in > annotation form. I think that command should work. Why are you using > --no-xcerseg? This will cause it to not include extracerebral > structures. Also note that you cannot use arbitrarily small segments > when doing PVC. > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > my intention is to use the Brainnetome Atlas > parcellation/segmentation > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I > used: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > > > Is this the right approach to obtain a high resolution > segmentation to > > run PVC methods? > > > > Thanks, > > Boris > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats.
For the PET analysis I have the following problem:
If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210).
If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations.
How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg.
Thanks a lot!
On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject
On 11/5/19 1:06 PM, Boris Rauchmann wrote:
External Email - Use CautionI just realized that the above mentioned command (gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives me only the cortical segmentation. Is there any way to also include the subcortical segmentation based on my individual atlas? I also have an Atlas_subcortex.gca file available.
Best, Boris
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
There is no cut off for the minimum size. As it gets smaller, the PVC noise amplification will become bigger (it also depends on the shape as well). I think the --no-xcerseg is the right way to go now On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for your prompt answer - the command worked. This is the > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html > What is approximately the smallest possible segment when using PVC? > Also, does the exclusion of extracerebral structures harm? I used that > flag because it complained: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > but you must indicate whether to use what is there (--no-xcerseg) > or create a new one and overwrite what is there (--xcerseg) > or specify your own headseg (--head) > > and did not want to override my apas+head.mgz > > Thanks, > Boris > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I don't know what the Brainnetome is, but it looks like youhave
> it in > annotation form. I think that command should work. Why are you using > --no-xcerseg? This will cause it to not include extracerebral > structures. Also note that you cannot use arbitrarily small segments > when doing PVC. > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > my intention is to use the Brainnetome Atlas > parcellation/segmentation > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I > used: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > > > Is this the right approach to obtain a high resolution > segmentation to > > run PVC methods? > > > > Thanks, > > Boris > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Can you send the log file for each of the gtmseg runs?
On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
External Email - Use Caution
Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats.
For the PET analysis I have the following problem:
If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210).
If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations.
How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg.
Thanks a lot!
On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject
On 11/5/19 1:06 PM, Boris Rauchmann wrote:
External Email - Use CautionI just realized that the above mentioned command (gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives me only the cortical segmentation. Is there any way to also include the subcortical segmentation based on my individual atlas? I also have an Atlas_subcortex.gca file available.
Best, Boris
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote:
There is no cut off for the minimum size. As it gets smaller, the PVC noise amplification will become bigger (it also depends on the shape as well). I think the --no-xcerseg is the right way to go now On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for your prompt answer - the command worked. This is the > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html > What is approximately the smallest possible segment when using PVC? > Also, does the exclusion of extracerebral structures harm? I used that > flag because it complained: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > but you must indicate whether to use what is there (--no-xcerseg) > or create a new one and overwrite what is there (--xcerseg) > or specify your own headseg (--head) > > and did not want to override my apas+head.mgz > > Thanks, > Boris > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>>> wrote: > > I don't know what the Brainnetome is, but it looks like you have > it in > annotation form. I think that command should work. Why are you using > --no-xcerseg? This will cause it to not include extracerebral > structures. Also note that you cannot use arbitrarily small segments > when doing PVC. > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > my intention is to use the Brainnetome Atlas > parcellation/segmentation > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I > used: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > > > Is this the right approach to obtain a high resolution > segmentation to > > run PVC methods? > > > > Thanks, > > Boris > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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In this example tried it with only the subcortical segmentations from my atlas. Please find the logfile attached. It gives me back: "tissue type is not set" but I set it to 2 in the LUT.txt
In principle look the following commands right to you?
xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
Ideally I would have a gtmseg with both, the subcortical and the cortical structures, but only the subcortical would also be fine as long as I can get mri_gtmpvc running on it.
Thanks, Boris
On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Can you send the log file for each of the gtmseg runs?
On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
External Email - Use CautionThank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats.
For the PET analysis I have the following problem:
If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210).
If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations.
How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg.
Thanks a lot!
On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject
On 11/5/19 1:06 PM, Boris Rauchmann wrote:
External Email - Use CautionI just realized that the above mentioned command (gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives me only the cortical segmentation. Is there any way to also include the subcortical segmentation based on my individual atlas? I also have an Atlas_subcortex.gca file available.
Best, Boris
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
There is no cut off for the minimum size. As it gets smaller, thePVC
noise amplification will become bigger (it also depends on the shape as well). I think the --no-xcerseg is the right way to go now On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for your prompt answer - the command worked. This is the > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html > What is approximately the smallest possible segment when usingPVC?
> Also, does the exclusion of extracerebral structures harm? I used that > flag because it complained: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > but you must indicate whether to use what is there (--no-xcerseg) > or create a new one and overwrite what is there (--xcerseg) > or specify your own headseg (--head) > > and did not want to override my apas+head.mgz > > Thanks, > Boris > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I don't know what the Brainnetome is, but it looks like youhave
> it in > annotation form. I think that command should work. Why are you using > --no-xcerseg? This will cause it to not include extracerebral > structures. Also note that you cannot use arbitrarily small segments > when doing PVC. > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > my intention is to use the Brainnetome Atlas > parcellation/segmentation > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I > used: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > > > Is this the right approach to obtain a high resolution > segmentation to > > run PVC methods? > > > > Thanks, > > Boris > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Did you already have the time to look at the logfile? Do you have any suggestions how to proceed?
Thank you!
Am 02.12.2019 um 19:18 schrieb Boris Rauchmann boris.rauchmann@gmail.com:
In this example tried it with only the subcortical segmentations from my atlas. Please find the logfile attached. It gives me back: "tissue type is not set" but I set it to 2 in the LUT.txt
In principle look the following commands right to you?
xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
Ideally I would have a gtmseg with both, the subcortical and the cortical structures, but only the subcortical would also be fine as long as I can get mri_gtmpvc running on it.
Thanks, Boris
On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: Can you send the log file for each of the gtmseg runs?
On 11/26/2019 1:09 PM, Boris Rauchmann wrote: External Email - Use Caution
Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats.
For the PET analysis I have the following problem:
If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210).
If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations.
How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg.
Thanks a lot!
On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject
On 11/5/19 1:06 PM, Boris Rauchmann wrote:
External Email - Use CautionI just realized that the above mentioned command (gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives me only the cortical segmentation. Is there any way to also include the subcortical segmentation based on my individual atlas? I also have an Atlas_subcortex.gca file available.
Best, Boris
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
There is no cut off for the minimum size. As it gets smaller, the PVC noise amplification will become bigger (it also depends on the shape as well). I think the --no-xcerseg is the right way to go now On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for your prompt answer - the command worked. This is the > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html > What is approximately the smallest possible segment when using PVC? > Also, does the exclusion of extracerebral structures harm? I used that > flag because it complained: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > but you must indicate whether to use what is there (--no-xcerseg) > or create a new one and overwrite what is there (--xcerseg) > or specify your own headseg (--head) > > and did not want to override my apas+head.mgz > > Thanks, > Boris > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I don't know what the Brainnetome is, but it looks like you have > it in > annotation form. I think that command should work. Why are you using > --no-xcerseg? This will cause it to not include extracerebral > structures. Also note that you cannot use arbitrarily small segments > when doing PVC. > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > my intention is to use the Brainnetome Atlas > parcellation/segmentation > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I > used: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > > > Is this the right approach to obtain a high resolution > segmentation to > > run PVC methods? > > > > Thanks, > > Boris > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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<gtmseg+subcort_BN.mgz.log>
Hi Boris, I'll try to get to it today. Unfortunately, I think this is going to require a fair amount of effort on my part. When I wrote this part of PETsurfer, I just did not make it super flexible. doug
On 12/5/2019 10:17 PM, Boris Rauchmann wrote:
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Did you already have the time to look at the logfile? Do you have any suggestions how to proceed?
Thank you!
Am 02.12.2019 um 19:18 schrieb Boris Rauchmann boris.rauchmann@gmail.commailto:boris.rauchmann@gmail.com:
In this example tried it with only the subcortical segmentations from my atlas. Please find the logfile attached. It gives me back: "tissue type is not set" but I set it to 2 in the LUT.txt
In principle look the following commands right to you?
xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
Ideally I would have a gtmseg with both, the subcortical and the cortical structures, but only the subcortical would also be fine as long as I can get mri_gtmpvc running on it.
Thanks, Boris
On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Can you send the log file for each of the gtmseg runs?
On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
External Email - Use Caution
Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats.
For the PET analysis I have the following problem:
If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210).
If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations.
How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg.
Thanks a lot!
On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject
On 11/5/19 1:06 PM, Boris Rauchmann wrote:
External Email - Use CautionI just realized that the above mentioned command (gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives me only the cortical segmentation. Is there any way to also include the subcortical segmentation based on my individual atlas? I also have an Atlas_subcortex.gca file available.
Best, Boris
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote:
There is no cut off for the minimum size. As it gets smaller, the PVC noise amplification will become bigger (it also depends on the shape as well). I think the --no-xcerseg is the right way to go now On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for your prompt answer - the command worked. This is the > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html > What is approximately the smallest possible segment when using PVC? > Also, does the exclusion of extracerebral structures harm? I used that > flag because it complained: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > but you must indicate whether to use what is there (--no-xcerseg) > or create a new one and overwrite what is there (--xcerseg) > or specify your own headseg (--head) > > and did not want to override my apas+head.mgz > > Thanks, > Boris > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>>> wrote: > > I don't know what the Brainnetome is, but it looks like you have > it in > annotation form. I think that command should work. Why are you using > --no-xcerseg? This will cause it to not include extracerebral > structures. Also note that you cannot use arbitrarily small segments > when doing PVC. > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > my intention is to use the Brainnetome Atlas > parcellation/segmentation > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I > used: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > > > Is this the right approach to obtain a high resolution > segmentation to > > run PVC methods? > > > > Thanks, > > Boris > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Doug,
thank you for your effort. Let me know if you have any updates on this.
Best, Boris
On Fri, Dec 6, 2019 at 5:45 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Hi Boris, I'll try to get to it today. Unfortunately, I think this is going to require a fair amount of effort on my part. When I wrote this part of PETsurfer, I just did not make it super flexible. doug
On 12/5/2019 10:17 PM, Boris Rauchmann wrote:
External Email - Use CautionDid you already have the time to look at the logfile? Do you have any suggestions how to proceed?
Thank you!
Am 02.12.2019 um 19:18 schrieb Boris Rauchmann boris.rauchmann@gmail.com boris.rauchmann@gmail.com:
In this example tried it with only the subcortical segmentations from my atlas. Please find the logfile attached. It gives me back: "tissue type is not set" but I set it to 2 in the LUT.txt
In principle look the following commands right to you?
xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
Ideally I would have a gtmseg with both, the subcortical and the cortical structures, but only the subcortical would also be fine as long as I can get mri_gtmpvc running on it.
Thanks, Boris
On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Can you send the log file for each of the gtmseg runs?
On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
External Email - Use CautionThank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats.
For the PET analysis I have the following problem:
If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210).
If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations.
How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg.
Thanks a lot!
On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject
On 11/5/19 1:06 PM, Boris Rauchmann wrote:
External Email - Use CautionI just realized that the above mentioned command (gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives me only the cortical segmentation. Is there any way to also include the subcortical segmentation based on my individual atlas? I also have an Atlas_subcortex.gca file available.
Best, Boris
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
There is no cut off for the minimum size. As it gets smaller, thePVC
noise amplification will become bigger (it also depends on the shape as well). I think the --no-xcerseg is the right way to go now On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for your prompt answer - the command worked. This isthe
> atlas mentioned: http://atlas.brainnetome.org/brainnetome.html > What is approximately the smallest possible segment when usingPVC?
> Also, does the exclusion of extracerebral structures harm? I used that > flag because it complained: > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot--ctab
> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > but you must indicate whether to use what is there (--no-xcerseg) > or create a new one and overwrite what is there (--xcerseg) > or specify your own headseg (--head) > > and did not want to override my apas+head.mgz > > Thanks, > Boris > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I don't know what the Brainnetome is, but it looks like youhave
> it in > annotation form. I think that command should work. Why are you using > --no-xcerseg? This will cause it to not include extracerebral > structures. Also note that you cannot use arbitrarily small segments > when doing PVC. > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > my intention is to use the Brainnetome Atlas > parcellation/segmentation > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I > used: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg > > > > Is this the right approach to obtain a high resolution > segmentation to > > run PVC methods? > > > > Thanks, > > Boris > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below.
Let me know if that works doug
On 12/2/19 1:18 PM, Boris Rauchmann wrote:
External Email - Use Caution
In this example tried it with only the subcortical segmentations from my atlas. Please find the logfile attached. It gives me back: "tissue type is not set" but I set it to 2 in the LUT.txt
In principle look the following commands right to you?
xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
Ideally I would have a gtmseg with both, the subcortical and the cortical structures, but only the subcortical would also be fine as long as I can get mri_gtmpvc running on it.
Thanks, Boris
On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Can you send the log file for each of the gtmseg runs? On 11/26/2019 1:09 PM, Boris Rauchmann wrote:External Email - Use Caution Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats. For the PET analysis I have the following problem: If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210). If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations. How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg. Thanks a lot! On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject On 11/5/19 1:06 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > I just realized that the above mentioned command (gtmseg --s XYZ --o > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) > gives me only the cortical segmentation. Is there any way to also > include the subcortical segmentation based on my individual atlas? I > also have an Atlas_subcortex.gca file available. > > Best, > Boris > > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > There is no cut off for the minimum size. As it gets smaller, the PVC > noise amplification will become bigger (it also depends on the > shape as > well). > > I think the --no-xcerseg is the right way to go now > > On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Thank you for your prompt answer - the command worked. This is the > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html <http://atlas.brainnetome.org/brainnetome.html> > > What is approximately the smallest possible segment when using PVC? > > Also, does the exclusion of extracerebral structures harm? I > used that > > flag because it complained: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > > but you must indicate whether to use what is there (--no-xcerseg) > > or create a new one and overwrite what is there (--xcerseg) > > or specify your own headseg (--head) > > > > and did not want to override my apas+head.mgz > > > > Thanks, > > Boris > > > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > I don't know what the Brainnetome is, but it looks like you have > > it in > > annotation form. I think that command should work. Why are > you using > > --no-xcerseg? This will cause it to not include extracerebral > > structures. Also note that you cannot use arbitrarily small > segments > > when doing PVC. > > > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > > > External Email - Use Caution > > > > > > Dear all, > > > > > > my intention is to use the Brainnetome Atlas > > parcellation/segmentation > > > in PETSurfer to obtain PVC corrected SUVRs for the atlas > ROIs. I > > used: > > > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot > BN_Atlas.annot --ctab > > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > --no-xcerseg > > > > > > Is this the right approach to obtain a high resolution > > segmentation to > > > run PVC methods? > > > > > > Thanks, > > > Boris > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz
The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
Best, Boris
On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below.
Let me know if that works doug
On 12/2/19 1:18 PM, Boris Rauchmann wrote:
External Email - Use CautionIn this example tried it with only the subcortical segmentations from my atlas. Please find the logfile attached. It gives me back: "tissue type is not set" but I set it to 2 in the LUT.txt
In principle look the following commands right to you?
xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
Ideally I would have a gtmseg with both, the subcortical and the cortical structures, but only the subcortical would also be fine as long as I can get mri_gtmpvc running on it.
Thanks, Boris
On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Can you send the log file for each of the gtmseg runs? On 11/26/2019 1:09 PM, Boris Rauchmann wrote:External Email - Use Caution Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats. For the PET analysis I have the following problem: If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210). If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations. How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg. Thanks a lot! On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for the given subject On 11/5/19 1:06 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > I just realized that the above mentioned command (gtmseg --s XYZ --o > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) > gives me only the cortical segmentation. Is there any way to also > include the subcortical segmentation based on my individual atlas? I > also have an Atlas_subcortex.gca file available. > > Best, > Boris > > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > There is no cut off for the minimum size. As it gets smaller, the PVC > noise amplification will become bigger (it also depends on the > shape as > well). > > I think the --no-xcerseg is the right way to go now > > On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Thank you for your prompt answer - the command worked. This is the > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html <http://atlas.brainnetome.org/brainnetome.html> > > What is approximately the smallest possible segment when using PVC? > > Also, does the exclusion of extracerebral structures harm? I > used that > > flag because it complained: > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok > > but you must indicate whether to use what is there (--no-xcerseg) > > or create a new one and overwrite what is there (--xcerseg) > > or specify your own headseg (--head) > > > > and did not want to override my apas+head.mgz > > > > Thanks, > > Boris > > > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> wrote: > > > > I don't know what the Brainnetome is, but it looks like you have > > it in > > annotation form. I think that command should work. Why are > you using > > --no-xcerseg? This will cause it to not include extracerebral > > structures. Also note that you cannot use arbitrarily small > segments > > when doing PVC. > > > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: > > > > > > External Email - Use Caution > > > > > > Dear all, > > > > > > my intention is to use the Brainnetome Atlas > > parcellation/segmentation > > > in PETSurfer to obtain PVC corrected SUVRs for the atlas > ROIs. I > > used: > > > > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot > BN_Atlas.annot --ctab > > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > --no-xcerseg > > > > > > Is this the right approach to obtain a high resolution > > segmentation to > > > run PVC methods? > > > > > > Thanks, > > > Boris > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Hi Boris
can you send us the full command line and screen output of the commands that are failing?
cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use Caution
Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz
The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris
On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below. Let me know if that works doug On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcortical segmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but the >> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu>>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html >> <http://atlas.brainnetome.org/brainnetome.html> >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >> > <mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but it >> looks like you have >> > > it in >> > > annotation form. I think that command should >> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to not include >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg
I get the same result using aseg.mgz
Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Boris
can you send us the full command line and screen output of the commands that are failing?
cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use CautionThanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below. Let me know if that works doug On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcortical segmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but the >> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu>>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html >> <http://atlas.brainnetome.org/brainnetome.html> >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >> > <mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but it >> looks like you have >> > > it in >> > > annotation form. I think that command should >> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to not include >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that folder?
On 12/12/19 12:57 PM, Boris Rauchmann wrote:
External Email - Use Caution
My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg
I get the same result using aseg.mgz
Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
Hi Boris
can you send us the full command line and screen output of the commands that are failing?
cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use Caution Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below.
Let me know if that works doug
On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcortical segmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but the >> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html >> http://atlas.brainnetome.org/brainnetome.html >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >> > mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but it >> looks like you have >> > > it in >> > > annotation form. I think that command should >> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to not include >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
yes to both. I always get the error ERROR: cannot find aseg...
On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that folder?
On 12/12/19 12:57 PM, Boris Rauchmann wrote:
External Email - Use CautionMy-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg
I get the same result using aseg.mgz
Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
Hi Boris
can you send us the full command line and screen output of the commands that are failing?
cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use CautionThanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --asegBN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg,and then run gtmseg as you have done below.
Let me know if that works doug On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcorticalsegmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but
the
>> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I canproceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html >> http://atlas.brainnetome.org/brainnetome.html >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >> > <mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but
it
>> looks like you have >> > > it in >> > > annotation form. I think that commandshould
>> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to notinclude >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > >
>> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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ok, this is very strange to me. Can you send the result of these two commands pwd and ls -l BN_Atlas_subcotex.mgz
On 12/13/2019 2:22 AM, Boris Rauchmann wrote:
External Email - Use Caution
yes to both. I always get the error ERROR: cannot find aseg...
On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that folder?
On 12/12/19 12:57 PM, Boris Rauchmann wrote:
External Email - Use CautionMy-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg
I get the same result using aseg.mgz
Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu>>:
Hi Boris
can you send us the full command line and screen output of the commands that are failing?
cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use CautionThanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --asegBN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg,and then run gtmseg as you have done below.
Let me know if that works doug On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcorticalsegmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but the >> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html >> http://atlas.brainnetome.org/brainnetome.html >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> >> > <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but it >> looks like you have >> > > it in >> > > annotation form. I think that command should >> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to not include >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Here the results:
pwd: /Users/boris/Desktop/MirLIND_test/1122/mri
ls -l BN_Atlas_subcotex.mgz: -rwxrwxrwx 1 boris staff 37013 13 Aug 23:30 BN_Atlas_subcotex.mgz
Best, Boris
Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu:
pwd
OK, now I'm really confused. Try this mri_info N_Atlas_subcotex.mgz
On 12/14/19 3:04 AM, Boris Rauchmann wrote:
External Email - Use Caution
Here the results:
pwd: /Users/boris/Desktop/MirLIND_test/1122/mri
ls -l BN_Atlas_subcotex.mgz: -rwxrwxrwx 1 boris staff 37013 13 Aug 23:30 BN_Atlas_subcotex.mgz
Best, Boris
Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>:
pwd
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file
Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu:
mri_info N_Atlas_subcotex.mgz
There is something weird about that file. How was it created? doug ps. Please include previous correspondence in the email
On 12/16/19 1:12 PM, Boris Rauchmann wrote:
External Email - Use Caution
Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file
Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>:
mri_info N_Atlas_subcotex.mgz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks, it was created using:
mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
Best, Boris
Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu:
There is something weird about that file. How was it created? doug ps. Please include previous correspondence in the email
On 12/16/19 1:12 PM, Boris Rauchmann wrote:
External Email - Use CautionBoriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file
Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>:
mri_info N_Atlas_subcotex.mgz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
This is the log when I´m creating this file:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz sysname Darwin hostname MacBook.local machine x86_64
setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
== Number of threads available to mri_ca_label for OpenMP = 1 == reading 1 input volumes reading classifier array from /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz reading transform from /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z setting orig areas to linear transform determinant scaled 4.97 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 10.8 using min determinant for regularization = 11.7 0 singular and 129 ill-conditioned covariance matrices regularized labeling volume... 0 gm and wm labels changed (%nan to gray, %nan to white out of all changed labels) 0 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 9576 changed. pass 2: 3286 changed. MRItoUCHAR: min=0, max=246 MRItoUCHAR: converting to UCHAR writing labeled volume to /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz mri_ca_label utimesec 146.184667 mri_ca_label stimesec 1.040963 mri_ca_label ru_maxrss 1436573696 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 609288 mri_ca_label ru_majflt 112 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 4 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 3 mri_ca_label ru_nivcsw 36417 auto-labeling took 2 minutes and 28 seconds.
This is what I get when I do mrs_info on the gas:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca reading frame -1 of gca Volume information for /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca type: GCA dimensions: 256 x 256 x 256 x 3 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 3 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000
Am 16.12.2019 um 21:21 schrieb Boris Rauchmann boris.rauchmann@gmail.com:
Thanks, it was created using:
mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
Best, Boris
Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>:
There is something weird about that file. How was it created? doug ps. Please include previous correspondence in the email
On 12/16/19 1:12 PM, Boris Rauchmann wrote:
External Email - Use CautionBoriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file
Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>>:
mri_info N_Atlas_subcotex.mgz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
to summarize, I want a warp that:
foreach subject
compute warp based on curvature apply warp to a functional overlay add that functional overlay to avg
return (tf.reduce_mean(tf.square(avg)))
make sense? So maximizing the mean squared average acivation
On Mon, 16 Dec 2019, Boris Rauchmann wrote:
External Email - Use Caution
This is the log when I´m creating this file:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz sysname Darwin hostname MacBook.local machine x86_64
setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
== Number of threads available to mri_ca_label for OpenMP = 1 == reading 1 input volumes reading classifier array from /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz reading transform from /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z setting orig areas to linear transform determinant scaled 4.97 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 10.8 using min determinant for regularization = 11.7 0 singular and 129 ill-conditioned covariance matrices regularized labeling volume... 0 gm and wm labels changed (%nan to gray, %nan to white out of all changed labels) 0 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 9576 changed. pass 2: 3286 changed. MRItoUCHAR: min=0, max=246 MRItoUCHAR: converting to UCHAR writing labeled volume to /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz mri_ca_label utimesec 146.184667 mri_ca_label stimesec 1.040963 mri_ca_label ru_maxrss 1436573696 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 609288 mri_ca_label ru_majflt 112 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 4 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 3 mri_ca_label ru_nivcsw 36417 auto-labeling took 2 minutes and 28 seconds.
This is what I get when I do mrs_info on the gas:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc a reading frame -1 of gca Volume information for/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc a type: GCA dimensions: 256 x 256 x 256 x 3 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 3 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000
Am 16.12.2019 um 21:21 schrieb Boris Rauchmann <boris.rauchmann@gmail.com>:Thanks, it was created using: mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
Best, Boris
Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:There is something weird about that file. How was it created? doug ps. Please include previous correspondence in the email
On 12/16/19 1:12 PM, Boris Rauchmann wrote:
External Email - Use Caution Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>: mri_info N_Atlas_subcotex.mgz _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry, my fault. That was for someone else On Mon, 16 Dec 2019, Boris Rauchmann wrote:
External Email - Use Caution
This is the log when I´m creating this file:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz sysname Darwin hostname MacBook.local machine x86_64
setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
== Number of threads available to mri_ca_label for OpenMP = 1 == reading 1 input volumes reading classifier array from /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz reading transform from /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z setting orig areas to linear transform determinant scaled 4.97 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 10.8 using min determinant for regularization = 11.7 0 singular and 129 ill-conditioned covariance matrices regularized labeling volume... 0 gm and wm labels changed (%nan to gray, %nan to white out of all changed labels) 0 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 9576 changed. pass 2: 3286 changed. MRItoUCHAR: min=0, max=246 MRItoUCHAR: converting to UCHAR writing labeled volume to /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz mri_ca_label utimesec 146.184667 mri_ca_label stimesec 1.040963 mri_ca_label ru_maxrss 1436573696 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 609288 mri_ca_label ru_majflt 112 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 4 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 3 mri_ca_label ru_nivcsw 36417 auto-labeling took 2 minutes and 28 seconds.
This is what I get when I do mrs_info on the gas:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc a reading frame -1 of gca Volume information for/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc a type: GCA dimensions: 256 x 256 x 256 x 3 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 3 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000
Am 16.12.2019 um 21:21 schrieb Boris Rauchmann <boris.rauchmann@gmail.com>:Thanks, it was created using: mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
Best, Boris
Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:There is something weird about that file. How was it created? doug ps. Please include previous correspondence in the email
On 12/16/19 1:12 PM, Boris Rauchmann wrote:
External Email - Use Caution Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>: mri_info N_Atlas_subcotex.mgz _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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OK, I'm still at a loss. The one suspicious thing is that it only took a few min to run. So you have never looked at that volume? What is in the atlas?
On 12/16/2019 3:42 PM, Boris Rauchmann wrote:
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This is the log when I´m creating this file:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz sysname Darwin hostname MacBook.local machine x86_64
setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
== Number of threads available to mri_ca_label for OpenMP = 1 == reading 1 input volumes reading classifier array from /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz reading transform from /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z setting orig areas to linear transform determinant scaled 4.97 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 10.8 using min determinant for regularization = 11.7 0 singular and 129 ill-conditioned covariance matrices regularized labeling volume... 0 gm and wm labels changed (%nan to gray, %nan to white out of all changed labels) 0 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 9576 changed. pass 2: 3286 changed. MRItoUCHAR: min=0, max=246 MRItoUCHAR: converting to UCHAR writing labeled volume to /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz mri_ca_label utimesec 146.184667 mri_ca_label stimesec 1.040963 mri_ca_label ru_maxrss 1436573696 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 609288 mri_ca_label ru_majflt 112 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 4 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 3 mri_ca_label ru_nivcsw 36417 auto-labeling took 2 minutes and 28 seconds.
This is what I get when I do mrs_info on the gas:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca reading frame -1 of gca Volume information for /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca type: GCA dimensions: 256 x 256 x 256 x 3 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 3 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000
Am 16.12.2019 um 21:21 schrieb Boris Rauchmann <boris.rauchmann@gmail.commailto:boris.rauchmann@gmail.com>:
Thanks, it was created using:
mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
Best, Boris
Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>:
There is something weird about that file. How was it created? doug ps. Please include previous correspondence in the email
On 12/16/19 1:12 PM, Boris Rauchmann wrote:
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Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file
Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>:
mri_info N_Atlas_subcotex.mgz
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OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again?
On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
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My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg
I get the same result using aseg.mgz
Thanks, Boris Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu>:
Hi Boris
can you send us the full command line and screen output of the commands that are failing?
cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use Caution Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below.
Let me know if that works doug
On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcortical segmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but the >> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html >> http://atlas.brainnetome.org/brainnetome.html >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >> > <mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but it >> looks like you have >> > > it in >> > > annotation form. I think that command should >> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to not include >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here?
Best, Boris
MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg MacBook-Pro:mri boris$
Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu:
OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again?
On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
External Email - Use CautionMy-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg
I get the same result using aseg.mgz
Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
Hi Boris
can you send us the full command line and screen output of the commands that are failing?
cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use CautionThanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below. Let me know if that works doug On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcortical segmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but the >> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html <http://atlas.brainnetome.org/brainnetome.html> >> <http://atlas.brainnetome.org/brainnetome.html <http://atlas.brainnetome.org/brainnetome.html>> >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> >> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but it >> looks like you have >> > > it in >> > > annotation form. I think that command should >> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to not include >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder?
On 1/3/20 3:07 PM, Boris Rauchmann wrote:
External Email - Use Caution
Thank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here?
Best, Boris
MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg MacBook-Pro:mri boris$
Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>:
OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again?
On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
External Email - Use Caution
My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg
I get the same result using aseg.mgz
Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
Hi Boris
can you send us the full command line and screen output of the commands that are failing?
cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use Caution Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below.
Let me know if that works doug
On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcortical segmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but the >> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html >> http://atlas.brainnetome.org/brainnetome.html >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >> > mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but it >> looks like you have >> > > it in >> > > annotation form. I think that command should >> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to not include >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
I’m sure just double checked it. I don’t know what’s wrong here.
Von meinem iPhone gesendet
Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu:
This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder?
On 1/3/20 3:07 PM, Boris Rauchmann wrote:
External Email - Use CautionThank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here?
Best, Boris
MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg MacBook-Pro:mri boris$
Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>: OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again? On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
External Email - Use CautionMy-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial ERROR: cannot find aseg I get the same result using aseg.mgz Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>: Hi Boris can you send us the full command line and screen output of the commands that are failing? cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote:
External Email - Use CautionThanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was created using: mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz Best, Boris On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg, mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below. Let me know if that works doug On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > In this example tried it with only the subcortical segmentations from > my atlas. Please find the logfile attached. It gives me back: "tissue > type is not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the > cortical structures, but only the subcortical would also be fine as > long as I can get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for >> cortical structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label >> and mri_ca_label for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it >> looks like it uses the standard FS parcellation with my labels >> for the cortical parcellations (only 93 cortical regions instead >> of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> --no-xcerseg I get all my 210 cortical parcellations but the >> standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it >> doing my PET analysis in PETSurfer? It is not totally clear for >> me what to merge using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: >> >> It gets the subcortical from apas+head.mgz which gets created >> along the >> way by xcerebralseg. You can create your own with >> xcerebralseg by >> specifying your volume as the mergevol. I think this will >> work, but I'm >> not sure. I'm assuming you've used the GCA to create your own >> subcortical seg for the given subject >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > I just realized that the above mentioned command (gtmseg >> --s XYZ --o >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> --no-xcerseg) >> > gives me only the cortical segmentation. Is there any way >> to also >> > include the subcortical segmentation based on my individual >> atlas? I >> > also have an Atlas_subcortex.gca file available. >> > >> > Best, >> > Boris >> > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu>> wrote: >> > >> > There is no cut off for the minimum size. As it gets >> smaller, the PVC >> > noise amplification will become bigger (it also depends >> on the >> > shape as >> > well). >> > >> > I think the --no-xcerseg is the right way to go now >> > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Thank you for your prompt answer - the command >> worked. This is the >> > > atlas mentioned: >> http://atlas.brainnetome.org/brainnetome.html >> http://atlas.brainnetome.org/brainnetome.html >> > > What is approximately the smallest possible segment >> when using PVC? >> > > Also, does the exclusion of extracerebral structures >> harm? I >> > used that >> > > flag because it complained: >> > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> BN_Atlas.annot --ctab >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. >> This is ok >> > > but you must indicate whether to use what is there >> (--no-xcerseg) >> > > or create a new one and overwrite what is there >> (--xcerseg) >> > > or specify your own headseg (--head) >> > > >> > > and did not want to override my apas+head.mgz >> > > >> > > Thanks, >> > > Boris >> > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. >> > > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >> > <mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>>> >> > wrote: >> > > >> > > I don't know what the Brainnetome is, but it >> looks like you have >> > > it in >> > > annotation form. I think that command should >> work. Why are >> > you using >> > > --no-xcerseg? This will cause it to not include >> extracerebral >> > > structures. Also note that you cannot use >> arbitrarily small >> > segments >> > > when doing PVC. >> > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Dear all, >> > > > >> > > > my intention is to use the Brainnetome Atlas >> > > parcellation/segmentation >> > > > in PETSurfer to obtain PVC corrected SUVRs for >> the atlas >> > ROIs. I >> > > used: >> > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot >> > BN_Atlas.annot --ctab >> > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> > --no-xcerseg >> > > > >> > > > Is this the right approach to obtain a high >> resolution >> > > segmentation to >> > > > run PVC methods? >> > > > >> > > > Thanks, >> > > > Boris >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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On 1/6/20 5:01 PM, Boris Rauchmann wrote:
External Email - Use CautionI’m sure just double checked it. I don’t know what’s wrong here.
Von meinem iPhone gesendet
Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu:
This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder?
On 1/3/20 3:07 PM, Boris Rauchmann wrote:
External Email - Use CautionThank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here?
Best, Boris
MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg MacBook-Pro:mri boris$
Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>: OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again? On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
External Email - Use CautionMy-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial ERROR: cannot find aseg I get the same result using aseg.mgz Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>: Hi Boris can you send us the full command line and screen output of the commands that are failing? cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote: > External Email - Use Caution > Thanks. unfortunately I get an error message when I use the --aseg > flag for BN_Atlas_subcotex.mgz but > even, if I'm using the original aseg.mgz I get: ERROR: cannot find > aseg > .../fs_all_subjects/xyz/mri/aseg.mgz > The file BN_Atlas_subcotex.mgz was created using: > mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz > $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z > $SUBJECTS_DIR/BN_Atlas_subcortex.gca > $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz > Best, > Boris > On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: > What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but > with your > subcortical ROIs added? If so, you can try merging it with > the aparc, eg, > mri_aparc2aseg --s subject --volmask --aseg > BN_Atlas_subcotex.mgz --o > aparc+BN_Atlas_subcotex.mgz > Then use aparc+BN_Atlas_subcotex.mgz as input to > xcerebralseg, and then > run gtmseg as you have done below. > Let me know if that works > doug > On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > In this example tried it with only the subcortical > segmentations from > > my atlas. Please find the logfile attached. It gives me > back: "tissue > > type is not set" but I set it to 2 in the LUT.txt > > > > In principle look the following commands right to you? > > > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > > > Ideally I would have a gtmseg with both, the subcortical > and the > > cortical structures, but only the subcortical would also be > fine as > > long as I can get mri_gtmpvc running on it. > > > > Thanks, > > Boris > > > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu> wrote: > > > > Can you send the log file for each of the gtmseg runs? > > > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: > >> > >> External Email - Use Caution > >> > >> Thank you! I have a gca for subcortical and two gcs > (lh/rh) for > >> cortical structures. > >> I created an annot (rh/lh) and a mgz using mris_ca_label > >> and mri_ca_label for parcellation/segmentation stats. > >> > >> For the PET analysis I have the following problem: > >> > >> If I use this command: gtmseg --s test --o test.mgz --ctab > >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz > >> --ctx-annot BN_Atlas.annot --ctab > '/xyz/BN_Atlas_246_LUT.txt' > >> > >> It gives me the right regions for subcortical > structures but it > >> looks like it uses the standard FS parcellation with > my labels > >> for the cortical parcellations (only 93 cortical > regions instead > >> of 210). > >> > >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz > >> --ctx-annot BN_Atlas.annot --ctab > '/xyz/BN_Atlas_246_LUT.txt' > >> --no-xcerseg I get all my 210 cortical parcellations > but the > >> standard FS subcortical segmentations. > >> > >> How can I use both in one gtmseg so that I can > proceed with it > >> doing my PET analysis in PETSurfer? It is not totally > clear for > >> me what to merge using xcerebralseg. > >> > >> Thanks a lot! > >> > >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. > >> <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> > wrote: > >> > >> It gets the subcortical from apas+head.mgz which > gets created > >> along the > >> way by xcerebralseg. You can create your own with > >> xcerebralseg by > >> specifying your volume as the mergevol. I think > this will > >> work, but I'm > >> not sure. I'm assuming you've used the GCA to > create your own > >> subcortical seg for the given subject > >> > >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: > >> > > >> > External Email - Use Caution > >> > > >> > I just realized that the above mentioned command > (gtmseg > >> --s XYZ --o > >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > >> --no-xcerseg) > >> > gives me only the cortical segmentation. Is > there any way > >> to also > >> > include the subcortical segmentation based on my > individual > >> atlas? I > >> > also have an Atlas_subcortex.gca file available. > >> > > >> > Best, > >> > Boris > >> > > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas > N.,Ph.D. > >> > <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu>> wrote: > >> > > >> > There is no cut off for the minimum size. As > it gets > >> smaller, the PVC > >> > noise amplification will become bigger (it > also depends > >> on the > >> > shape as > >> > well). > >> > > >> > I think the --no-xcerseg is the right way to > go now > >> > > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: > >> > > > >> > > External Email - Use Caution > >> > > > >> > > Thank you for your prompt answer - the command > >> worked. This is the > >> > > atlas mentioned: > >> http://atlas.brainnetome.org/brainnetome.html > >> http://atlas.brainnetome.org/brainnetome.html > >> > > What is approximately the smallest > possible segment > >> when using PVC? > >> > > Also, does the exclusion of extracerebral > structures > >> harm? I > >> > used that > >> > > flag because it complained: > >> > > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot > >> BN_Atlas.annot --ctab > >> > > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > >> > > ERROR: > /media/subjects/XYZ/mri/apas+head.mgz exists. > >> This is ok > >> > > but you must indicate whether to use what > is there > >> (--no-xcerseg) > >> > > or create a new one and overwrite what is > there > >> (--xcerseg) > >> > > or specify your own headseg (--head) > >> > > > >> > > and did not want to override my apas+head.mgz > >> > > > >> > > Thanks, > >> > > Boris > >> > > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, > Douglas N.,Ph.D. > >> > > <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> > >> > mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>>> > >> > wrote: > >> > > > >> > > I don't know what the Brainnetome is, > but it > >> looks like you have > >> > > it in > >> > > annotation form. I think that command should > >> work. Why are > >> > you using > >> > > --no-xcerseg? This will cause it to not > include > >> extracerebral > >> > > structures. Also note that you cannot use > >> arbitrarily small > >> > segments > >> > > when doing PVC. > >> > > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann > wrote: > >> > > > > >> > > > External Email - Use Caution > >> > > > > >> > > > Dear all, > >> > > > > >> > > > my intention is to use the > Brainnetome Atlas > >> > > parcellation/segmentation > >> > > > in PETSurfer to obtain PVC corrected > SUVRs for > >> the atlas > >> > ROIs. I > >> > > used: > >> > > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz > --ctx-annot > >> > BN_Atlas.annot --ctab > >> > > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > >> > --no-xcerseg > >> > > > > >> > > > Is this the right approach to obtain > a high > >> resolution > >> > > segmentation to > >> > > > run PVC methods? > >> > > > > >> > > > Thanks, > >> > > > Boris > >> > > > > >> > > > > _______________________________________________ > >> > > > Freesurfer mailing list > >> > > > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> > mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > > mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> > mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > >> > > > >> > > > _______________________________________________ > >> > > Freesurfer mailing list > >> > > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> > mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> > mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > >> > > > >> > > > _______________________________________________ > >> > > Freesurfer mailing list > >> > > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> > mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
Ok. i figured it out. The problem was just that you can not specify the file type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem.
Now I run in a new issue:
gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'
Wed Jan 8 17:04:12 CET 2020
setenv SUBJECTS_DIR /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects cd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects /usr/local/freesurfer/bin/gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo
$Id: mri_gtmseg.c,v 1.10 2016/08/02 21:07:24 greve Exp $ cwd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects cmdline mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild subject 1122_test USF 2 OutputUSF 2 apasfile BN_apas+head.mgz wmannotfile NULL ctxannotfile BN_Atlas.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 0 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 mri_gtmseg supposed to be reproducible but seed not set Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/1122_test/mri/BN_apas+head.mgz Loading surfaces t = 2.1510 Loading annotations t = 4.8510 Not segmenting WM reading colortable from annotation file... colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt) reading colortable from annotation file... colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt) Relabeling any unlateralized hypointenities as lateralized hypointenities MRIrelabelHypoHemi(): looping over volume nthreads = 1 Relabeling CC as WM Relabeling any hypointensities as WM MRIunsegmentWM(): looping over volume nthreads = 1 Upsampling segmentation USF = 2 t = 7.3520 MRIhiresSeg(): filling unknowns with 257 Beginning cortical segmentation using BN_Atlas.annot t = 41.3800 MRIannot2CorticalSeg(): looping over volume nthreads = 1 MRIannot2CorticalSeg(): found 2347 unknown, filled with 257 Not subsegmenting WM Found 279 segs in the final list MRIgtmSeg() done, t = 224.1820 Computing colortable ERROR: cannot find match for subcortical segid 227 ERROR: mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo gtmseg exited with errors
Before I run gtmseg I used xcerebralseg --s 1122_test --m aparc+BN_Atlas_subcotex.mgz --atlas '/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_subcortex.gca' --o BN_apas+head.mgz
Any ideas on that?
Best, Boris
Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu>:
Are you sure you have permission to view that file?
On 1/6/20 5:01 PM, Boris Rauchmann wrote:
External Email - Use CautionI’m sure just double checked it. I don’t know what’s wrong here.
Von meinem iPhone gesendet
Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu>:
This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder?
On 1/3/20 3:07 PM, Boris Rauchmann wrote:
External Email - Use CautionThank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here?
Best, Boris
MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg MacBook-Pro:mri boris$
Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>: OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again? On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
External Email - Use CautionMy-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial ERROR: cannot find aseg I get the same result using aseg.mgz Thanks, Boris > Am 12.12.2019 um 17:37 schrieb Bruce Fischl > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>: > Hi Boris > can you send us the full command line and screen output of the > commands that are failing? > cheers > Bruce > On Thu, 12 Dec 2019, Boris Rauchmann wrote: >> External Email - Use Caution >> Thanks. unfortunately I get an error message when I use the --aseg >> flag for BN_Atlas_subcotex.mgz but >> even, if I'm using the original aseg.mgz I get: ERROR: cannot find >> aseg >> .../fs_all_subjects/xyz/mri/aseg.mgz >> The file BN_Atlas_subcotex.mgz was created using: >> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz >> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z >> $SUBJECTS_DIR/BN_Atlas_subcortex.gca >> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz >> Best, >> Boris >> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: >> What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but >> with your >> subcortical ROIs added? If so, you can try merging it with >> the aparc, eg, >> mri_aparc2aseg --s subject --volmask --aseg >> BN_Atlas_subcotex.mgz --o >> aparc+BN_Atlas_subcotex.mgz >> Then use aparc+BN_Atlas_subcotex.mgz as input to >> xcerebralseg, and then >> run gtmseg as you have done below. >> Let me know if that works >> doug >> On 12/2/19 1:18 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > In this example tried it with only the subcortical >> segmentations from >> > my atlas. Please find the logfile attached. It gives me >> back: "tissue >> > type is not set" but I set it to 2 in the LUT.txt >> > >> > In principle look the following commands right to you? >> > >> > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m >> > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca >> > >> > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab >> > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz >> > >> > Ideally I would have a gtmseg with both, the subcortical >> and the >> > cortical structures, but only the subcortical would also be >> fine as >> > long as I can get mri_gtmpvc running on it. >> > >> > Thanks, >> > Boris >> > >> > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> wrote: >> > >> > Can you send the log file for each of the gtmseg runs? >> > >> > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> >> >> External Email - Use Caution >> >> >> >> Thank you! I have a gca for subcortical and two gcs >> (lh/rh) for >> >> cortical structures. >> >> I created an annot (rh/lh) and a mgz using
mris_ca_label
>> >> and mri_ca_label for parcellation/segmentation stats. >> >> >> >> For the PET analysis I have the following problem: >> >> >> >> If I use this command: gtmseg --s test --o test.mgz
--ctab
>> >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> >> --ctx-annot BN_Atlas.annot --ctab >> '/xyz/BN_Atlas_246_LUT.txt' >> >> >> >> It gives me the right regions for subcortical >> structures but it >> >> looks like it uses the standard FS parcellation with >> my labels >> >> for the cortical parcellations (only 93 cortical >> regions instead >> >> of 210). >> >> >> >> If I use gtmseg --s 0059test --o
onlyhead.gtmseg_test.mgz
>> >> --ctx-annot BN_Atlas.annot --ctab >> '/xyz/BN_Atlas_246_LUT.txt' >> >> --no-xcerseg I get all my 210 cortical parcellations >> but the >> >> standard FS subcortical segmentations. >> >> >> >> How can I use both in one gtmseg so that I can >> proceed with it >> >> doing my PET analysis in PETSurfer? It is not totally >> clear for >> >> me what to merge using xcerebralseg. >> >> >> >> Thanks a lot! >> >> >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas
N.,Ph.D.
>> >> <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >> wrote: >> >> >> >> It gets the subcortical from apas+head.mgz which >> gets created >> >> along the >> >> way by xcerebralseg. You can create your own with >> >> xcerebralseg by >> >> specifying your volume as the mergevol. I think >> this will >> >> work, but I'm >> >> not sure. I'm assuming you've used the GCA to >> create your own >> >> subcortical seg for the given subject >> >> >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> >> > >> >> > External Email - Use Caution >> >> > >> >> > I just realized that the above mentioned command >> (gtmseg >> >> --s XYZ --o >> >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> >> > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> >> --no-xcerseg) >> >> > gives me only the cortical segmentation. Is >> there any way >> >> to also >> >> > include the subcortical segmentation based on my >> individual >> >> atlas? I >> >> > also have an Atlas_subcortex.gca file available. >> >> > >> >> > Best, >> >> > Boris >> >> > >> >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas >> N.,Ph.D. >> >> > <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> >> mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu>> wrote: >> >> > >> >> > There is no cut off for the minimum size. As >> it gets >> >> smaller, the PVC >> >> > noise amplification will become bigger (it >> also depends >> >> on the >> >> > shape as >> >> > well). >> >> > >> >> > I think the --no-xcerseg is the right way to >> go now >> >> > >> >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> >> > > >> >> > > External Email - Use Caution >> >> > > >> >> > > Thank you for your prompt answer - the
command
>> >> worked. This is the >> >> > > atlas mentioned: >> >> http://atlas.brainnetome.org/brainnetome.html >> >> http://atlas.brainnetome.org/brainnetome.html >> >> > > What is approximately the smallest >> possible segment >> >> when using PVC? >> >> > > Also, does the exclusion of extracerebral >> structures >> >> harm? I >> >> > used that >> >> > > flag because it complained: >> >> > > >> >> > > gtmseg --s XYZ --o BN.gtmseg.mgz
--ctx-annot
>> >> BN_Atlas.annot --ctab >> >> > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> >> > > ERROR: >> /media/subjects/XYZ/mri/apas+head.mgz exists. >> >> This is ok >> >> > > but you must indicate whether to use what >> is there >> >> (--no-xcerseg) >> >> > > or create a new one and overwrite what is >> there >> >> (--xcerseg) >> >> > > or specify your own headseg (--head) >> >> > > >> >> > > and did not want to override my
apas+head.mgz
>> >> > > >> >> > > Thanks, >> >> > > Boris >> >> > > >> >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, >> Douglas N.,Ph.D. >> >> > > <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> >> mailto:DGREVE@mgh.harvard.edu >> >> mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu> >> >> > mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu >> >> mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu>>> >> >> > wrote: >> >> > > >> >> > > I don't know what the Brainnetome is, >> but it >> >> looks like you have >> >> > > it in >> >> > > annotation form. I think that command
should
>> >> work. Why are >> >> > you using >> >> > > --no-xcerseg? This will cause it to not >> include >> >> extracerebral >> >> > > structures. Also note that you cannot use >> >> arbitrarily small >> >> > segments >> >> > > when doing PVC. >> >> > > >> >> > > On 8/13/19 10:26 AM, Boris Rauchmann >> wrote: >> >> > > > >> >> > > > External Email - Use Caution >> >> > > > >> >> > > > Dear all, >> >> > > > >> >> > > > my intention is to use the >> Brainnetome Atlas >> >> > > parcellation/segmentation >> >> > > > in PETSurfer to obtain PVC corrected >> SUVRs for >> >> the atlas >> >> > ROIs. I >> >> > > used: >> >> > > > >> >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz >> --ctx-annot >> >> > BN_Atlas.annot --ctab >> >> > > > >> >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> >> > --no-xcerseg >> >> > > > >> >> > > > Is this the right approach to obtain >> a high >> >> resolution >> >> > > segmentation to >> >> > > > run PVC methods? >> >> > > > >> >> > > > Thanks, >> >> > > > Boris >> >> > > > >> >> > > > >> _______________________________________________ >> >> > > > Freesurfer mailing list >> >> > > > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > > <mailto:
Freesurfer@nmr.mgh.harvard.edu
>> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > > > >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > > >> >> > > >> >> > > >> _______________________________________________ >> >> > > Freesurfer mailing list >> >> > > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > > >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > > >> >> > > >> >> > > >> _______________________________________________ >> >> > > Freesurfer mailing list >> >> > > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > > >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
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On 1/8/2020 10:17 AM, Boris Rauchmann wrote:
External Email - Use Caution
Ok. i figured it out. The problem was just that you can not specify the file type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem. Ah, ok. This is actually fixed in our development version.
Now I run in a new issue: I think at last one problem is that your subcortical seg BN_Atlas_subcortex.mgz really only has subcortical segmentations, but it needs to have the whole head segmeted, including segments for cortex (something like the aseg.mgz). Without that, mri_aparc_aseg completes ok but the actual segmentation does not have any cortex which is then needed by gtmseg. The road forward is a little tricky. You can try something like this: mergeseg --src aseg.mgz --merge BN_Atlas_subcortex.mgz --o newseg.mgz This takes the segments from BN and superimposes them on aseg.mgz. You have to make sure that the segmentation numbers don't conflict and you will have to have a colortable that includes all of the BN and the original aseg. Finally, you will need to resolve any inconsistencies, eg, hippo is defined in aseg.mgz and in BN, but they will not overlap perfectly, so there will still be some voxels labeled as the original aseg hippo. You will have to reassign these voxels to a label in BN (same with other structures). You could do this on the output of merge seg, or you could go back and regenerate your gca using resolved merged segmentations as input
gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt' Wed Jan 8 17:04:12 CET 2020
setenv SUBJECTS_DIR /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects cd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects /usr/local/freesurfer/bin/gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo
$Id: mri_gtmseg.c,v 1.10 2016/08/02 21:07:24 greve Exp $ cwd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects cmdline mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild subject 1122_test USF 2 OutputUSF 2 apasfile BN_apas+head.mgz wmannotfile NULL ctxannotfile BN_Atlas.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 0 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 mri_gtmseg supposed to be reproducible but seed not set Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/1122_test/mri/BN_apas+head.mgz Loading surfaces t = 2.1510 Loading annotations t = 4.8510 Not segmenting WM reading colortable from annotation file... colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt) reading colortable from annotation file... colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt) Relabeling any unlateralized hypointenities as lateralized hypointenities MRIrelabelHypoHemi(): looping over volume nthreads = 1 Relabeling CC as WM Relabeling any hypointensities as WM MRIunsegmentWM(): looping over volume nthreads = 1 Upsampling segmentation USF = 2 t = 7.3520 MRIhiresSeg(): filling unknowns with 257 Beginning cortical segmentation using BN_Atlas.annot t = 41.3800 MRIannot2CorticalSeg(): looping over volume nthreads = 1 MRIannot2CorticalSeg(): found 2347 unknown, filled with 257 Not subsegmenting WM Found 279 segs in the final list MRIgtmSeg() done, t = 224.1820 Computing colortable ERROR: cannot find match for subcortical segid 227 ERROR: mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo gtmseg exited with errors
Before I run gtmseg I used xcerebralseg --s 1122_test --m aparc+BN_Atlas_subcotex.mgz --atlas '/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_subcortex.gca' --o BN_apas+head.mgz
Any ideas on that?
Best, Boris
Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>: Are you sure you have permission to view that file?
On 1/6/20 5:01 PM, Boris Rauchmann wrote:
External Email - Use CautionI’m sure just double checked it. I don’t know what’s wrong here.
Von meinem iPhone gesendet
Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>:
This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder?
On 1/3/20 3:07 PM, Boris Rauchmann wrote:
External Email - Use CautionThank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here?
Best, Boris
MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg MacBook-Pro:mri boris$
Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>>: OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again? On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
External Email - Use CautionMy-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial ERROR: cannot find aseg I get the same result using aseg.mgz Thanks, Boris
Am 12.12.2019 um 17:37 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu>>: Hi Boris can you send us the full command line and screen output of the commands that are failing? cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote: > External Email - Use Caution > Thanks. unfortunately I get an error message when I use the --aseg > flag for BN_Atlas_subcotex.mgz but > even, if I'm using the original aseg.mgz I get: ERROR: cannot find > aseg > .../fs_all_subjects/xyz/mri/aseg.mgz > The file BN_Atlas_subcotex.mgz was created using: > mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz > $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z > $SUBJECTS_DIR/BN_Atlas_subcortex.gca > $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz > Best, > Boris > On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote: > What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but > with your > subcortical ROIs added? If so, you can try merging it with > the aparc, eg, > mri_aparc2aseg --s subject --volmask --aseg > BN_Atlas_subcotex.mgz --o > aparc+BN_Atlas_subcotex.mgz > Then use aparc+BN_Atlas_subcotex.mgz as input to > xcerebralseg, and then > run gtmseg as you have done below. > Let me know if that works > doug > On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > In this example tried it with only the subcortical > segmentations from > > my atlas. Please find the logfile attached. It gives me > back: "tissue > > type is not set" but I set it to 2 in the LUT.txt > > > > In principle look the following commands right to you? > > > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > > > Ideally I would have a gtmseg with both, the subcortical > and the > > cortical structures, but only the subcortical would also be > fine as > > long as I can get mri_gtmpvc running on it. > > > > Thanks, > > Boris > > > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote: > > > > Can you send the log file for each of the gtmseg runs? > > > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: > >> > >> External Email - Use Caution > >> > >> Thank you! I have a gca for subcortical and two gcs > (lh/rh) for > >> cortical structures. > >> I created an annot (rh/lh) and a mgz using mris_ca_label > >> and mri_ca_label for parcellation/segmentation stats. > >> > >> For the PET analysis I have the following problem: > >> > >> If I use this command: gtmseg --s test --o test.mgz --ctab > >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz > >> --ctx-annot BN_Atlas.annot --ctab > '/xyz/BN_Atlas_246_LUT.txt' > >> > >> It gives me the right regions for subcortical > structures but it > >> looks like it uses the standard FS parcellation with > my labels > >> for the cortical parcellations (only 93 cortical > regions instead > >> of 210). > >> > >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz > >> --ctx-annot BN_Atlas.annot --ctab > '/xyz/BN_Atlas_246_LUT.txt' > >> --no-xcerseg I get all my 210 cortical parcellations > but the > >> standard FS subcortical segmentations. > >> > >> How can I use both in one gtmseg so that I can > proceed with it > >> doing my PET analysis in PETSurfer? It is not totally > clear for > >> me what to merge using xcerebralseg. > >> > >> Thanks a lot! > >> > >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. > >> <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu > <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> > wrote: > >> > >> It gets the subcortical from apas+head.mgz which > gets created > >> along the > >> way by xcerebralseg. You can create your own with > >> xcerebralseg by > >> specifying your volume as the mergevol. I think > this will > >> work, but I'm > >> not sure. I'm assuming you've used the GCA to > create your own > >> subcortical seg for the given subject > >> > >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: > >> > > >> > External Email - Use Caution > >> > > >> > I just realized that the above mentioned command > (gtmseg > >> --s XYZ --o > >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab > >> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > >> --no-xcerseg) > >> > gives me only the cortical segmentation. Is > there any way > >> to also > >> > include the subcortical segmentation based on my > individual > >> atlas? I > >> > also have an Atlas_subcortex.gca file available. > >> > > >> > Best, > >> > Boris > >> > > >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas > N.,Ph.D. > >> > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu > <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> > >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu > >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>>> wrote: > >> > > >> > There is no cut off for the minimum size. As > it gets > >> smaller, the PVC > >> > noise amplification will become bigger (it > also depends > >> on the > >> > shape as > >> > well). > >> > > >> > I think the --no-xcerseg is the right way to > go now > >> > > >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: > >> > > > >> > > External Email - Use Caution > >> > > > >> > > Thank you for your prompt answer - the command > >> worked. This is the > >> > > atlas mentioned: > >> http://atlas.brainnetome.org/brainnetome.html > >> http://atlas.brainnetome.org/brainnetome.html > >> > > What is approximately the smallest > possible segment > >> when using PVC? > >> > > Also, does the exclusion of extracerebral > structures > >> harm? I > >> > used that > >> > > flag because it complained: > >> > > > >> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot > >> BN_Atlas.annot --ctab > >> > > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > >> > > ERROR: > /media/subjects/XYZ/mri/apas+head.mgz exists. > >> This is ok > >> > > but you must indicate whether to use what > is there > >> (--no-xcerseg) > >> > > or create a new one and overwrite what is > there > >> (--xcerseg) > >> > > or specify your own headseg (--head) > >> > > > >> > > and did not want to override my apas+head.mgz > >> > > > >> > > Thanks, > >> > > Boris > >> > > > >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, > Douglas N.,Ph.D. > >> > > <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu > <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> > >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> > >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu > <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> > >> > <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu > >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> > >> <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu > <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>>>> > >> > wrote: > >> > > > >> > > I don't know what the Brainnetome is, > but it > >> looks like you have > >> > > it in > >> > > annotation form. I think that command should > >> work. Why are > >> > you using > >> > > --no-xcerseg? This will cause it to not > include > >> extracerebral > >> > > structures. Also note that you cannot use > >> arbitrarily small > >> > segments > >> > > when doing PVC. > >> > > > >> > > On 8/13/19 10:26 AM, Boris Rauchmann > wrote: > >> > > > > >> > > > External Email - Use Caution > >> > > > > >> > > > Dear all, > >> > > > > >> > > > my intention is to use the > Brainnetome Atlas > >>�� > > parcellation/segmentation > >> > > > in PETSurfer to obtain PVC corrected > SUVRs for > >> the atlas > >> > ROIs. I > >> > > used: > >> > > > > >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz > --ctx-annot > >> > BN_Atlas.annot --ctab > >> > > > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' > >> > --no-xcerseg > >> > > > > >> > > > Is this the right approach to obtain > a high > >> resolution > >> > > segmentation to > >> > > > run PVC methods? > >> > > > > >> > > > Thanks, > >> > > > Boris > >> > > > > >> > > > > _______________________________________________ > >> > > > Freesurfer mailing list > >> > > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> > > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > >> > > > >> > > > _______________________________________________ > >> > > Freesurfer mailing list > >> > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > >> > > > >> > > > _______________________________________________ > >> > > Freesurfer mailing list > >> > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> > 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Thanks, that solution seems to work finally. I just ignored the remaining voxels labeled according to the standard aseg scheme and proceeded with the the PET analysis and the combined LUT. I will ignore the remaining fragment labels from the original aseg and only use the output from the BN labels (starting with 211), these are the only results im really interested in. Is that ok?
Here an example stats file I got:
1 2 Left-Cerebral-White-Matter wm 41550 13909.534 0.989 0.0935 2 7 Left-Cerebellum-White-Matter wm 2276 1037.525 0.854 0.0811 3 8 Left-Cerebellum-Cortex cortex 10936 6010.637 1.015 0.1339 4 10 Left-Thalamus-Proper subcort_gm 3 0.024 -0.815 0.2251 5 11 Left-Caudate subcort_gm 3 0.035 21.480 0.1746 6 12 Left-Putamen subcort_gm 25 0.459 3.161 0.0615 7 13 Left-Pallidum subcort_gm 49 1.497 1.474 0.0667 8 16 Brain-Stem subcort_gm 4599 2714.856 0.929 0.1000 9 17 Left-Hippocampus subcort_gm 2 0.023 -3.152 0.1702 10 18 Left-Amygdala subcort_gm 1 0.005 -7.082 0.1060 11 24 CSF csf 7468 2623.527 0.251 0.2568 12 26 Left-Accumbens-area subcort_gm 0 0.004 0.879 nan 13 28 Left-VentralDC subcort_gm 714 205.288 1.358 0.1427 14 31 Left-choroid-plexus csf 220 18.333 5.945 0.6080 15 41 Right-Cerebral-White-Matter wm 40645 13911.597 0.987 0.0841 16 46 Right-Cerebellum-White-Matter wm 2146 990.941 0.862 0.0826 17 47 Right-Cerebellum-Cortex cortex 11029 6187.241 0.985 0.1317 18 49 Right-Thalamus-Proper subcort_gm 11 0.140 0.032 0.2024 19 50 Right-Caudate subcort_gm 1 0.009 -2.162 0.0258 20 51 Right-Putamen subcort_gm 44 2.020 3.727 0.1893 21 52 Right-Pallidum subcort_gm 24 0.316 5.739 0.1814 22 53 Right-Hippocampus subcort_gm 3 0.026 16.575 0.2951 23 54 Right-Amygdala subcort_gm 7 0.081 4.637 0.0897 24 58 Right-Accumbens-area subcort_gm 0 0.000 -4.474 nan 25 60 Right-VentralDC subcort_gm 728 198.051 1.430 0.2142 26 63 Right-choroid-plexus csf 136 10.088 6.633 0.5924 27 211 mAmyg_L subcort_gm 264 48.960 1.126 0.1262 28 212 mAmyg_R subcort_gm 268 46.429 1.292 0.1920 29 213 lAmyg_L subcort_gm 131 6.503 1.889 0.1003 30 214 lAmyg_R subcort_gm 181 13.490 1.382 0.1237 31 215 rHipp_L subcort_gm 1020 260.090 1.166 0.1828 32 216 rHipp_R subcort_gm 833 241.777 1.149 0.2291 33 217 cHipp_L subcort_gm 911 288.346 1.578 0.3201 34 218 cHipp_R subcort_gm 1050 330.445 1.273 0.2312 35 219 vCa_L subcort_gm 626 170.254 1.205 0.0829 36 220 vCa_R subcort_gm 477 84.269 1.491 0.0933 37 221 GP_L subcort_gm 597 133.161 1.369 0.0977 38 222 GP_R subcort_gm 514 93.978 1.491 0.0811 39 223 NAC_L subcort_gm 412 67.647 1.348 0.1591 40 224 NAC_R subcort_gm 503 87.917 1.240 0.1258 41 225 vmPu_L subcort_gm 465 128.509 1.740 0.0783 42 226 vmPu_R subcort_gm 367 83.411 1.588 0.0699 43 227 dCa_L subcort_gm 997 255.259 0.821 0.1448 44 228 dCa_R subcort_gm 1271 405.156 1.017 0.1380 45 229 dlPu_L subcort_gm 678 122.256 1.356 0.0960 46 230 dlPu_R subcort_gm 585 150.878 1.319 0.0942 47 231 mPFtha_L subcort_gm 278 34.255 0.562 0.0971 48 232 mPFtha_R subcort_gm 293 33.479 0.513 0.1725 49 233 mPMtha_L subcort_gm 166 8.628 0.960 0.0501 50 234 mPMtha_R subcort_gm 316 41.442 0.915 0.0645 51 235 Stha_L subcort_gm 222 25.913 1.007 0.0551 52 236 Stha_R subcort_gm 241 53.103 1.229 0.0608 53 237 rTtha_L subcort_gm 344 12.690 2.379 0.2204 54 238 rTtha_R subcort_gm 240 35.057 0.800 0.1077 55 239 PPtha_L subcort_gm 331 23.986 1.627 0.0688 56 240 PPtha_R subcort_gm 319 21.868 0.954 0.1150 57 241 Otha_L subcort_gm 244 28.491 0.014 0.1617 58 242 Otha_R subcort_gm 158 7.610 0.548 0.1713 59 243 cTtha_L subcort_gm 212 10.919 1.547 0.1571 60 244 cTtha_R subcort_gm 250 25.427 3.840 0.2807 61 245 lPFtha_L subcort_gm 532 94.580 1.016 0.0732 62 246 lPFtha_R subcort_gm 466 54.950 1.086 0.0751 63 1001 ctx-lh-bankssts cortex 595 124.965 1.709 0.0686 64 1002 ctx-lh-caudalanteriorcingulate cortex 370 66.174 1.304 0.0951 65 1003 ctx-lh-caudalmiddlefrontal cortex 1039 223.909 1.706 0.0871 66 1005 ctx-lh-cuneus cortex 598 78.428 1.719 0.1002 67 1006 ctx-lh-entorhinal cortex 332 50.969 1.633 0.1099 68 1007 ctx-lh-fusiform cortex 1787 368.987 1.610 0.1025 69 1008 ctx-lh-inferiorparietal cortex 2521 591.841 1.773 0.1011 70 1009 ctx-lh-inferiortemporal cortex 2209 565.372 1.514 0.1144 71 1010 ctx-lh-isthmuscingulate cortex 558 100.622 1.419 0.1414 72 1011 ctx-lh-lateraloccipital cortex 2243 461.999 1.620 0.1021 73 1012 ctx-lh-lateralorbitofrontal cortex 1540 367.233 1.539 0.1629 74 1013 ctx-lh-lingual cortex 1158 218.085 1.641 0.1091 75 1014 ctx-lh-medialorbitofrontal cortex 1065 254.158 1.480 0.1427 76 1015 ctx-lh-middletemporal cortex 2187 515.131 1.615 0.1146 77 1016 ctx-lh-parahippocampal cortex 382 47.547 1.106 0.1159 78 1017 ctx-lh-paracentral cortex 644 106.788 1.464 0.1035 79 1018 ctx-lh-parsopercularis cortex 832 168.841 1.478 0.0728 80 1019 ctx-lh-parsorbitalis cortex 554 117.573 1.381 0.1071 81 1020 ctx-lh-parstriangularis cortex 678 130.710 1.667 0.0828 82 1021 ctx-lh-pericalcarine cortex 390 47.638 1.575 0.0770 83 1022 ctx-lh-postcentral cortex 2099 367.425 1.527 0.0933 84 1023 ctx-lh-posteriorcingulate cortex 529 95.601 1.554 0.1022 85 1024 ctx-lh-precentral cortex 2722 535.813 1.465 0.0852 86 1025 ctx-lh-precuneus cortex 1849 381.092 1.666 0.1002 87 1026 ctx-lh-rostralanteriorcingulate cortex 336 64.563 1.368 0.0903 88 1027 ctx-lh-rostralmiddlefrontal cortex 2737 619.430 1.574 0.0873 89 1028 ctx-lh-superiorfrontal cortex 4575 1101.963 1.552 0.0923 90 1029 ctx-lh-superiorparietal cortex 2505 430.339 1.645 0.0859 91 1030 ctx-lh-superiortemporal cortex 2517 575.940 1.559 0.1020 92 1031 ctx-lh-supramarginal cortex 1925 466.262 1.609 0.0921 93 1032 ctx-lh-frontalpole cortex 293 51.884 1.653 0.1294 94 1033 ctx-lh-temporalpole cortex 547 131.885 1.500 0.1562 95 1034 ctx-lh-transversetemporal cortex 319 49.071 1.572 0.0740 96 1035 ctx-lh-insula cortex 1621 362.309 1.323 0.0805 97 2001 ctx-rh-bankssts cortex 452 80.636 1.581 0.0649 98 2002 ctx-rh-caudalanteriorcingulate cortex 430 84.382 1.328 0.1183 99 2003 ctx-rh-caudalmiddlefrontal cortex 975 201.479 1.678 0.0699 100 2005 ctx-rh-cuneus cortex 582 80.806 1.758 0.0961 101 2006 ctx-rh-entorhinal cortex 289 43.979 1.594 0.1093 102 2007 ctx-rh-fusiform cortex 1607 361.265 1.495 0.0887 103 2008 ctx-rh-inferiorparietal cortex 3102 744.405 1.622 0.0779 104 2009 ctx-rh-inferiortemporal cortex 2324 612.805 1.469 0.1153 105 2010 ctx-rh-isthmuscingulate cortex 449 72.682 1.539 0.1213 106 2011 ctx-rh-lateraloccipital cortex 2145 493.213 1.535 0.1295 107 2012 ctx-rh-lateralorbitofrontal cortex 1519 366.246 1.576 0.1602 108 2013 ctx-rh-lingual cortex 1215 246.293 1.424 0.0999 109 2014 ctx-rh-medialorbitofrontal cortex 1305 339.745 1.431 0.1371 110 2015 ctx-rh-middletemporal cortex 2409 582.090 1.586 0.1214 111 2016 ctx-rh-parahippocampal cortex 379 47.722 1.137 0.1003 112 2017 ctx-rh-paracentral cortex 872 150.762 1.495 0.0849 113 2018 ctx-rh-parsopercularis cortex 692 140.443 1.484 0.0957 114 2019 ctx-rh-parsorbitalis cortex 624 133.260 1.487 0.1093 115 2020 ctx-rh-parstriangularis cortex 848 172.425 1.586 0.1047 116 2021 ctx-rh-pericalcarine cortex 399 47.618 1.599 0.0767 117 2022 ctx-rh-postcentral cortex 1965 341.079 1.497 0.0902 118 2023 ctx-rh-posteriorcingulate cortex 608 110.509 1.490 0.1064 119 2024 ctx-rh-precentral cortex 2851 600.118 1.408 0.0789 120 2025 ctx-rh-precuneus cortex 1991 429.967 1.655 0.0960 121 2026 ctx-rh-rostralanteriorcingulate cortex 407 82.757 1.508 0.1203 122 2027 ctx-rh-rostralmiddlefrontal cortex 3064 725.576 1.621 0.0891 123 2028 ctx-rh-superiorfrontal cortex 4110 1001.983 1.549 0.0944 124 2029 ctx-rh-superiorparietal cortex 2413 427.643 1.638 0.0866 125 2030 ctx-rh-superiortemporal cortex 2326 561.451 1.538 0.1110 126 2031 ctx-rh-supramarginal cortex 2051 456.793 1.586 0.0923 127 2032 ctx-rh-frontalpole cortex 321 60.867 1.478 0.1243 128 2033 ctx-rh-temporalpole cortex 582 141.009 1.623 0.1824 129 2034 ctx-rh-transversetemporal cortex 210 25.529 1.678 0.0695 130 2035 ctx-rh-insula cortex 1499 383.186 1.295 0.0828
Am 10.01.2020 um 18:45 schrieb Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu:
gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'
I'm guessing that the fragments might cause problems later either in gtmseg as a hard failure or in gtmpvc as an ill-conditioned matrix. But you can try it out:)
On 1/11/2020 6:04 PM, Boris Rauchmann wrote:
External Email - Use Caution
Thanks, that solution seems to work finally. I just ignored the remaining voxels labeled according to the standard aseg scheme and proceeded with the the PET analysis and the combined LUT. I will ignore the remaining fragment labels from the original aseg and only use the output from the BN labels (starting with 211), these are the only results im really interested in. Is that ok?
Here an example stats file I got:
1 2 Left-Cerebral-White-Matter wm 41550 13909.534 0.989 0.0935 2 7 Left-Cerebellum-White-Matter wm 2276 1037.525 0.854 0.0811 3 8 Left-Cerebellum-Cortex cortex 10936 6010.637 1.015 0.1339 4 10 Left-Thalamus-Proper subcort_gm 3 0.024 -0.815 0.2251 5 11 Left-Caudate subcort_gm 3 0.035 21.480 0.1746 6 12 Left-Putamen subcort_gm 25 0.459 3.161 0.0615 7 13 Left-Pallidum subcort_gm 49 1.497 1.474 0.0667 8 16 Brain-Stem subcort_gm 4599 2714.856 0.929 0.1000 9 17 Left-Hippocampus subcort_gm 2 0.023 -3.152 0.1702 10 18 Left-Amygdala subcort_gm 1 0.005 -7.082 0.1060 11 24 CSF csf 7468 2623.527 0.251 0.2568 12 26 Left-Accumbens-area subcort_gm 0 0.004 0.879 nan 13 28 Left-VentralDC subcort_gm 714 205.288 1.358 0.1427 14 31 Left-choroid-plexus csf 220 18.333 5.945 0.6080 15 41 Right-Cerebral-White-Matter wm 40645 13911.597 0.987 0.0841 16 46 Right-Cerebellum-White-Matter wm 2146 990.941 0.862 0.0826 17 47 Right-Cerebellum-Cortex cortex 11029 6187.241 0.985 0.1317 18 49 Right-Thalamus-Proper subcort_gm 11 0.140 0.032 0.2024 19 50 Right-Caudate subcort_gm 1 0.009 -2.162 0.0258 20 51 Right-Putamen subcort_gm 44 2.020 3.727 0.1893 21 52 Right-Pallidum subcort_gm 24 0.316 5.739 0.1814 22 53 Right-Hippocampus subcort_gm 3 0.026 16.575 0.2951 23 54 Right-Amygdala subcort_gm 7 0.081 4.637 0.0897 24 58 Right-Accumbens-area subcort_gm 0 0.000 -4.474 nan 25 60 Right-VentralDC subcort_gm 728 198.051 1.430 0.2142 26 63 Right-choroid-plexus csf 136 10.088 6.633 0.5924 27 211 mAmyg_L subcort_gm 264 48.960 1.126 0.1262 28 212 mAmyg_R subcort_gm 268 46.429 1.292 0.1920 29 213 lAmyg_L subcort_gm 131 6.503 1.889 0.1003 30 214 lAmyg_R subcort_gm 181 13.490 1.382 0.1237 31 215 rHipp_L subcort_gm 1020 260.090 1.166 0.1828 32 216 rHipp_R subcort_gm 833 241.777 1.149 0.2291 33 217 cHipp_L subcort_gm 911 288.346 1.578 0.3201 34 218 cHipp_R subcort_gm 1050 330.445 1.273 0.2312 35 219 vCa_L subcort_gm 626 170.254 1.205 0.0829 36 220 vCa_R subcort_gm 477 84.269 1.491 0.0933 37 221 GP_L subcort_gm 597 133.161 1.369 0.0977 38 222 GP_R subcort_gm 514 93.978 1.491 0.0811 39 223 NAC_L subcort_gm 412 67.647 1.348 0.1591 40 224 NAC_R subcort_gm 503 87.917 1.240 0.1258 41 225 vmPu_L subcort_gm 465 128.509 1.740 0.0783 42 226 vmPu_R subcort_gm 367 83.411 1.588 0.0699 43 227 dCa_L subcort_gm 997 255.259 0.821 0.1448 44 228 dCa_R subcort_gm 1271 405.156 1.017 0.1380 45 229 dlPu_L subcort_gm 678 122.256 1.356 0.0960 46 230 dlPu_R subcort_gm 585 150.878 1.319 0.0942 47 231 mPFtha_L subcort_gm 278 34.255 0.562 0.0971 48 232 mPFtha_R subcort_gm 293 33.479 0.513 0.1725 49 233 mPMtha_L subcort_gm 166 8.628 0.960 0.0501 50 234 mPMtha_R subcort_gm 316 41.442 0.915 0.0645 51 235 Stha_L subcort_gm 222 25.913 1.007 0.0551 52 236 Stha_R subcort_gm 241 53.103 1.229 0.0608 53 237 rTtha_L subcort_gm 344 12.690 2.379 0.2204 54 238 rTtha_R subcort_gm 240 35.057 0.800 0.1077 55 239 PPtha_L subcort_gm 331 23.986 1.627 0.0688 56 240 PPtha_R subcort_gm 319 21.868 0.954 0.1150 57 241 Otha_L subcort_gm 244 28.491 0.014 0.1617 58 242 Otha_R subcort_gm 158 7.610 0.548 0.1713 59 243 cTtha_L subcort_gm 212 10.919 1.547 0.1571 60 244 cTtha_R subcort_gm 250 25.427 3.840 0.2807 61 245 lPFtha_L subcort_gm 532 94.580 1.016 0.0732 62 246 lPFtha_R subcort_gm 466 54.950 1.086 0.0751 63 1001 ctx-lh-bankssts cortex 595 124.965 1.709 0.0686 64 1002 ctx-lh-caudalanteriorcingulate cortex 370 66.174 1.304 0.0951 65 1003 ctx-lh-caudalmiddlefrontal cortex 1039 223.909 1.706 0.0871 66 1005 ctx-lh-cuneus cortex 598 78.428 1.719 0.1002 67 1006 ctx-lh-entorhinal cortex 332 50.969 1.633 0.1099 68 1007 ctx-lh-fusiform cortex 1787 368.987 1.610 0.1025 69 1008 ctx-lh-inferiorparietal cortex 2521 591.841 1.773 0.1011 70 1009 ctx-lh-inferiortemporal cortex 2209 565.372 1.514 0.1144 71 1010 ctx-lh-isthmuscingulate cortex 558 100.622 1.419 0.1414 72 1011 ctx-lh-lateraloccipital cortex 2243 461.999 1.620 0.1021 73 1012 ctx-lh-lateralorbitofrontal cortex 1540 367.233 1.539 0.1629 74 1013 ctx-lh-lingual cortex 1158 218.085 1.641 0.1091 75 1014 ctx-lh-medialorbitofrontal cortex 1065 254.158 1.480 0.1427 76 1015 ctx-lh-middletemporal cortex 2187 515.131 1.615 0.1146 77 1016 ctx-lh-parahippocampal cortex 382 47.547 1.106 0.1159 78 1017 ctx-lh-paracentral cortex 644 106.788 1.464 0.1035 79 1018 ctx-lh-parsopercularis cortex 832 168.841 1.478 0.0728 80 1019 ctx-lh-parsorbitalis cortex 554 117.573 1.381 0.1071 81 1020 ctx-lh-parstriangularis cortex 678 130.710 1.667 0.0828 82 1021 ctx-lh-pericalcarine cortex 390 47.638 1.575 0.0770 83 1022 ctx-lh-postcentral cortex 2099 367.425 1.527 0.0933 84 1023 ctx-lh-posteriorcingulate cortex 529 95.601 1.554 0.1022 85 1024 ctx-lh-precentral cortex 2722 535.813 1.465 0.0852 86 1025 ctx-lh-precuneus cortex 1849 381.092 1.666 0.1002 87 1026 ctx-lh-rostralanteriorcingulate cortex 336 64.563 1.368 0.0903 88 1027 ctx-lh-rostralmiddlefrontal cortex 2737 619.430 1.574 0.0873 89 1028 ctx-lh-superiorfrontal cortex 4575 1101.963 1.552 0.0923 90 1029 ctx-lh-superiorparietal cortex 2505 430.339 1.645 0.0859 91 1030 ctx-lh-superiortemporal cortex 2517 575.940 1.559 0.1020 92 1031 ctx-lh-supramarginal cortex 1925 466.262 1.609 0.0921 93 1032 ctx-lh-frontalpole cortex 293 51.884 1.653 0.1294 94 1033 ctx-lh-temporalpole cortex 547 131.885 1.500 0.1562 95 1034 ctx-lh-transversetemporal cortex 319 49.071 1.572 0.0740 96 1035 ctx-lh-insula cortex 1621 362.309 1.323 0.0805 97 2001 ctx-rh-bankssts cortex 452 80.636 1.581 0.0649 98 2002 ctx-rh-caudalanteriorcingulate cortex 430 84.382 1.328 0.1183 99 2003 ctx-rh-caudalmiddlefrontal cortex 975 201.479 1.678 0.0699 100 2005 ctx-rh-cuneus cortex 582 80.806 1.758 0.0961 101 2006 ctx-rh-entorhinal cortex 289 43.979 1.594 0.1093 102 2007 ctx-rh-fusiform cortex 1607 361.265 1.495 0.0887 103 2008 ctx-rh-inferiorparietal cortex 3102 744.405 1.622 0.0779 104 2009 ctx-rh-inferiortemporal cortex 2324 612.805 1.469 0.1153 105 2010 ctx-rh-isthmuscingulate cortex 449 72.682 1.539 0.1213 106 2011 ctx-rh-lateraloccipital cortex 2145 493.213 1.535 0.1295 107 2012 ctx-rh-lateralorbitofrontal cortex 1519 366.246 1.576 0.1602 108 2013 ctx-rh-lingual cortex 1215 246.293 1.424 0.0999 109 2014 ctx-rh-medialorbitofrontal cortex 1305 339.745 1.431 0.1371 110 2015 ctx-rh-middletemporal cortex 2409 582.090 1.586 0.1214 111 2016 ctx-rh-parahippocampal cortex 379 47.722 1.137 0.1003 112 2017 ctx-rh-paracentral cortex 872 150.762 1.495 0.0849 113 2018 ctx-rh-parsopercularis cortex 692 140.443 1.484 0.0957 114 2019 ctx-rh-parsorbitalis cortex 624 133.260 1.487 0.1093 115 2020 ctx-rh-parstriangularis cortex 848 172.425 1.586 0.1047 116 2021 ctx-rh-pericalcarine cortex 399 47.618 1.599 0.0767 117 2022 ctx-rh-postcentral cortex 1965 341.079 1.497 0.0902 118 2023 ctx-rh-posteriorcingulate cortex 608 110.509 1.490 0.1064 119 2024 ctx-rh-precentral cortex 2851 600.118 1.408 0.0789 120 2025 ctx-rh-precuneus cortex 1991 429.967 1.655 0.0960 121 2026 ctx-rh-rostralanteriorcingulate cortex 407 82.757 1.508 0.1203 122 2027 ctx-rh-rostralmiddlefrontal cortex 3064 725.576 1.621 0.0891 123 2028 ctx-rh-superiorfrontal cortex 4110 1001.983 1.549 0.0944 124 2029 ctx-rh-superiorparietal cortex 2413 427.643 1.638 0.0866 125 2030 ctx-rh-superiortemporal cortex 2326 561.451 1.538 0.1110 126 2031 ctx-rh-supramarginal cortex 2051 456.793 1.586 0.0923 127 2032 ctx-rh-frontalpole cortex 321 60.867 1.478 0.1243 128 2033 ctx-rh-temporalpole cortex 582 141.009 1.623 0.1824 129 2034 ctx-rh-transversetemporal cortex 210 25.529 1.678 0.0695 130 2035 ctx-rh-insula cortex 1499 383.186 1.295 0.0828
Am 10.01.2020 um 18:45 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>:
gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'
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Greve, Douglas N.,Ph.D.