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> 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> 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>> 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
>> > > 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>>>
>> > 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
>> > > >
>> > > > _______________________________________________
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>> > <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
>> > >
>> > >
>> > > _______________________________________________
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>> > <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
>> > >
>> > >
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>> >
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Log file for gtmseg
Mon Dec 2 18:49:27 CET 2019
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 --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
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 0120test --usf 2 --o gtmseg+subcort_BN.mgz --apas apas+head+subcort_BN.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo --ctab subcort_BN_LUT.txt
$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 0120test --usf 2 --o gtmseg+subcort_BN.mgz --apas apas+head+subcort_BN.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo --ctab subcort_BN_LUT.txt
sysname Linux
hostname linuxrechner2
machine x86_64
user demenzbild
subject 0120test
USF 2
OutputUSF 2
apasfile apas+head+subcort_BN.mgz
wmannotfile NULL
ctxannotfile aparc.annot
ctxlhbase 1000
ctxrhbase 2000
SubSegWM 0
KeepHypo 0
KeepCC 0
dmax 5.000000
nlist 0
lhmin 1000
lhmax 1900
rhmin 2000
rhmax 2900
Merging CTAB master with merge ctab
Starting MRIgtmSeg()
Starting MRIgtmSeg() USF=2
Loading /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/apas+head+subcort_BN.mgz
Loading surfaces t = 3.0110
Loading annotations t = 8.2580
Not segmenting WM
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 = 11.5600
MRIhiresSeg(): filling unknowns with 0
Beginning cortical segmentation using aparc.annot t = 102.6010
MRIannot2CorticalSeg(): looping over volume
nthreads = 1
MRIannot2CorticalSeg(): found 0 unknown, filled with 0
Not subsegmenting WM
Found 37 segs in the final list
MRIgtmSeg() done, t = 124.5940
Computing colortable
WARNING: segid 211 mAmygL tissue type is not set
WARNING: segid 212 mAmygR tissue type is not set
WARNING: segid 213 lAmygL tissue type is not set
WARNING: segid 214 lAmygR tissue type is not set
WARNING: segid 215 rHippL tissue type is not set
WARNING: segid 216 rHippR tissue type is not set
WARNING: segid 217 cHippL tissue type is not set
WARNING: segid 218 cHippR tissue type is not set
WARNING: segid 219 vCaL tissue type is not set
WARNING: segid 220 vCaR tissue type is not set
WARNING: segid 221 GPL tissue type is not set
WARNING: segid 222 GPR tissue type is not set
WARNING: segid 223 NACL tissue type is not set
WARNING: segid 224 NACR tissue type is not set
WARNING: segid 225 vmPuL tissue type is not set
WARNING: segid 226 vmPuR tissue type is not set
WARNING: segid 227 dCaL tissue type is not set
WARNING: segid 228 dCaR tissue type is not set
WARNING: segid 229 dlPuL tissue type is not set
WARNING: segid 230 dlPuR tissue type is not set
WARNING: segid 231 mPFthaL tissue type is not set
WARNING: segid 232 mPFthaR tissue type is not set
WARNING: segid 233 mPMthaL tissue type is not set
WARNING: segid 234 mPMthaR tissue type is not set
WARNING: segid 235 SthaL tissue type is not set
WARNING: segid 236 SthaR tissue type is not set
WARNING: segid 237 rTthaL tissue type is not set
WARNING: segid 238 rTthaR tissue type is not set
WARNING: segid 239 PPthaL tissue type is not set
WARNING: segid 240 PPthaR tissue type is not set
WARNING: segid 241 OthaL tissue type is not set
WARNING: segid 242 OthaR tissue type is not set
WARNING: segid 243 cTthaL tissue type is not set
WARNING: segid 244 cTthaR tissue type is not set
WARNING: segid 245 lPFthaL tissue type is not set
WARNING: segid 246 lPFthaR tissue type is not set
Writing output file to /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.mgz
Writing colortable to /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.ctab
Writing lta file to /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.lta
mri_gtmseg finished in 2.23177 minutes
mri_gtmseg done
$Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $
cwd
cmdline mri_segstats --seg /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.mgz --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.ctab --sum /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/stats/gtmseg+subcort_BN.stats --excludeid 0 --etiv --subject 0120test
sysname Linux
hostname linuxrechner2
machine x86_64
user demenzbild
whitesurfname white
UseRobust 0
atlas_icv (eTIV) = 1439176 mm^3 (det: 1.353625 )
Loading /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.mgz
Voxel Volume is 0.125 mm^3
Generating list of segmentation ids
Found 38 segmentations
Computing statistics for each segmentation
Reporting on 37 segmentations
Using PrintSegStat
mri_segstats done
Started at Mon Dec 2 18:49:27 CET 2019
Ended at Mon Dec 2 18:54:09 CET 2019
Gtmseg-Run-Time-Sec 282
Gtmseg-Run-Time-Hours 0.08
To check run:
tkmeditfv 0120test nu.mgz -seg gtmseg+subcort_BN.mgz gtmseg+subcort_BN.ctab -opacity 1
gtmseg Done
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