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
