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 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
>>>
>>>      _______________________________________________
>>>      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