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.
<dgr...@mgh.harvard.edu<mailto:dgr...@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 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.
>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>:
>> This is not making any sense to me. Are you sure you are in
>> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that
>> BN_Atlas_subcotex.mgz is in the same folder?
>>
>>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Thank you for testing it. As before I get the same error message.
>>> Do you know what I´m doing wrong here?
>>>
>>> Best,
>>> Boris
>>>
>>> MacBook-Pro:mri boris$ 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.
>>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
>>>> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@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
>>>>>> <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
>>>>>>> >> > >
>>>>>>> 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>>>
>>>>>>> >> >
>>>>>>> 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>>
>>>>>>> >> >
>>>>>>> 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>>
>>>>>>> >> 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>>
>>>>>>> >> 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>>
>>>>>>> > 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>
>>>>>> <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>
>>>> <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<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
