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On 1/6/20 5:01 PM, Boris Rauchmann wrote:
External Email - Use CautionI’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. DGREVE@mgh.harvard.edu:
This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder?
On 1/3/20 3:07 PM, Boris Rauchmann wrote:
External Email - Use CautionThank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here?
Best, Boris
MacBook-Pro:mri boris$ 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 CautionMy-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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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. > <DGREVE@mgh.harvard.edu mailto:DGREVE@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. > > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@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. > >> <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@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. > >> > <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@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. > >> > > <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> > >> > mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@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
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