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.
<dgr...@mgh.harvard.edu<mailto:dgr...@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
>> <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>
>> <mailto:fis...@nmr.mgh.harvard.edu<mailto:fis...@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.
>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
>>> <mailto:dgr...@mgh.harvard.edu<mailto: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>
>>> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
>>> <mailto: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>
>>> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
>>> <mailto: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>>
>>> <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:
>>> >> >
>>> >> > 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>
>>> <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<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>
>>> >>
>>> <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
>>> >> > >
>>> >> > >
>>> >> > > _______________________________________________
>>> >> > > 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>
>>> >>
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>> >> > >
>>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >> > >
>>> >> > >
>>> >> > > _______________________________________________
>>> >> > > Freesurfer mailing list
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>>> 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>
>>> >>
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>>> >> > >
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>>> >> >
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>>> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> >>
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