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. <
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>:
> >> 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>>:
> >>>> 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>>:
> >>>>>> 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>> 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>> 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>>
> >>>>>>> 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>>> 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>>>>
> >>>>>>> >> > 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 <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
>
>
> _______________________________________________
> 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
