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
