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