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.
<dgr...@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.
> <dgr...@mgh.harvard.edu <mailto:dgr...@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.
>> <dgr...@mgh.harvard.edu <mailto:dgr...@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.
>> > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>
>> <mailto:dgr...@mgh.harvard.edu
>> <mailto:dgr...@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.
>> > > <dgr...@mgh.harvard.edu
>> <mailto:dgr...@mgh.harvard.edu>
>> <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>
>> > <mailto:dgr...@mgh.harvard.edu
>> <mailto:dgr...@mgh.harvard.edu>
>> <mailto:dgr...@mgh.harvard.edu
<mailto:dgr...@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
