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> 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>>: > >> > >> 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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