When you say that you looked at the labels/segmentations and that nothing looked horribly wrong, would that mean that the labels are accurate and that they are not really outliers?
On 12/5/19 7:26 PM, Joshi, Nandita wrote: > External Email - Use Caution > > Hi Dr. Greve, > > Thanks so much for your response. The primary reason for my wanting to do > this is due to a large number of outliers in terms of area and volume. Our > subject population is cognitively impaired older adults > 60 yrs. The custom > surface based template might help in investigating the area outliers, but it > wouldn't help in investigating the volume outliers. Since the DK atlas is > constructed from a population 18-86 years including 10 people with > Alzheimer's Disease, I am not even sure if making a new volume atlas would > help. > > Attached are graphs showing the distribution of the region wise area, volume, > and thickness of all subjects in lh (filled circles) and rh (open circles). I > looked into the aparc and aseg labels in specific regions for the subjects > that are outliers, but nothing seems to have gone horribly wrong in terms of > parcellation. Any pointers on how I can investigate and if a custom volume > template might help? > > Thanks, > Nandita > > > > On 12/5/19, 1:36 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > dgr...@mgh.harvard.edu> wrote: > > We currently do not have a mac build of mri_aparc2aseg, and we recommend > downloading the freesurfer dev release to resolve this issue. > > > > On 12/5/19 1:00 PM, Joshi, Nandita wrote: > > External Email - Use Caution > > > > Thank you so much for that! The README file instructs to download > make_average_subject and platform specific mri_aparc2aseg. However, the mac > version of mri_aparc2aseg is missing in the patch. Could it be possible to > download it from elsewhere? > > > > - Nandita > > > > > > > > On 12/5/19, 12:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on > behalf of Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on > behalf of dgr...@mgh.harvard.edu> wrote: > > > > USE CAUTION: External Message. > > > > See the REAME file here > > > https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfer_6.0.0-2Dpatch_&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI&m=HRcVNlmwdK9YHH6teQ4oW9oc6SDFzz79TS63mOlbWIY&s=6p4504imNdnEktx-WXKqAlxMvMCQ1EYnJW_deB2CAWI&e= > > > > > > On 12/5/19 11:47 AM, Joshi, Nandita wrote: > > > > > > External Email - Use Caution > > > > > > Hello, > > > > > > I am trying to make a study specific template based on the > > > instructions at: > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_SurfaceRegAndTemplates&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI&m=HRcVNlmwdK9YHH6teQ4oW9oc6SDFzz79TS63mOlbWIY&s=LmIaVqBLyDekwkZsc46m3nOdn25B7E96m_UuRzDu3Ew&e= > > > > > > However, on running the first step: > > > > > > make_average_subject --out newtemplate --subjects subj1 subj2 > subj3 ... > > > > > > I get an error while running the recon-all is trying to run the > aparc > > > to aseg step: > > > > > > #@# AParc-to-ASeg aparc Thu Dec5 11:29:33 EST 2019 > > > > > > /Users/nandita/FreeSurfer_recon/newtemplate > > > > > > \n mri_aparc2aseg --s newtemplate --volmask --aseg > aseg.presurf.hypos > > > --relabel mri/norm.mgz mri/transforms/talairach.m3z > > > /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca > > > mri/aseg.auto_noCCseg.label_intensities.txt \n > > > > > > relabeling unlikely voxels interior to white matter surface: > > > > > > norm: mri/norm.mgz > > > > > > XFORM: mri/transforms/talairach.m3z > > > > > > GCA: > /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca > > > > > > label intensities: mri/aseg.auto_noCCseg.label_intensities.txt > > > > > > SUBJECTS_DIR /Users/nandita/FreeSurfer_recon > > > > > > subject newtemplate > > > > > > outvol > /Users/nandita/FreeSurfer_recon/newtemplate/mri/aparc+aseg.mgz > > > > > > useribbon 0 > > > > > > baseoffset 0 > > > > > > RipUnknown 0 > > > > > > Reading lh white surface > > > > > > /Users/nandita/FreeSurfer_recon/newtemplate/surf/lh.white > > > > > > Reading lh pial surface > > > > > > /Users/nandita/FreeSurfer_recon/newtemplate/surf/lh.pial > > > > > > Loading lh annotations from > > > /Users/nandita/FreeSurfer_recon/newtemplate/label/lh.aparc.annot > > > > > > reading colortable from annotation file... > > > > > > colortable with 36 entries read (originally > > > > /Users/nandita/FreeSurfer_recon/newtemplate/label/tmpdir.annot2std.41916/seg.1.100110189.ctab) > > > > > > Reading rh white surface > > > > > > /Users/nandita/reeSurfer_recon/newtemplate/surf/rh.white > > > > > > Reading rh pial surface > > > > > > /Users/nandita/FreeSurfer_recon/newtemplate/surf/rh.pial > > > > > > Loading rh annotations from > > > > /Users/nandita/ADRC/FreeSurfer_recon/newtemplate/label/rh.aparc.annot > > > > > > reading colortable from annotation file... > > > > > > colortable with 36 entries read (originally > > > > /Users/nandita/FreeSurfer_recon/newtemplate/label/tmpdir.annot2std.47059/seg.1.100110189.ctab) > > > > > > Have color table for lh white annotation > > > > > > Have color table for rh white annotation > > > > > > Loading ribbon segmentation from > > > /Users/nandita/FreeSurfer_recon/newtemplate/mri/ribbon.mgz > > > > > > Building hash of lh white > > > > > > Building hash of lh pial > > > > > > Building hash of rh white > > > > > > Building hash of rh pial > > > > > > Loading aseg from > > > > /Users/nandita/FreeSurfer_recon/newtemplate/mri/aseg.presurf.hypos.mgz > > > > > > ASeg Vox2RAS: ----------- > > > > > > -1.00000 0.00000 0.00000 128.00000; > > > > > > 0.00000 0.00000 1.00000-128.00000; > > > > > > 0.00000-1.00000 0.00000 128.00000; > > > > > > 0.00000 0.00000 0.00000 1.00000; > > > > > > mghRead(mri/norm.mgz, -1): could not open file > > > > > > ------------------------- > > > > > > Labeling Slice > > > > > > relabeling unlikely voxels in interior of white matter > > > > > > Segmentation fault > > > > > > Darwin Nanditas-MacBook-Pro.local 17.7.0 Darwin Kernel Version > 17.7.0: > > > Sun Jun2 20:31:42 PDT 2019; > root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64 > > > > > > recon-all -s newtemplate exited with ERRORS at Thu Dec5 > 11:29:52 EST 2019 > > > > > > On inspecting the mri folder, it seems the norm.mgz file has > not been > > > created at all. Looking at the flowchart of steps for the > recon-all > > > command, norm.mgz is supposed to be created in the CA Normalize > step, > > > which requires the talairach.lta in the > newtemplate/mri/transforms > > > folder, which seems to be missing as well. The only transform > created > > > in the transform folder is talairach.xfm. The talairach.lta is > created > > > in the EM GCA registration step. Do I re-run the EM GCA > registration, > > > CA normalize, and then contonue from aparc to aseg? I am not > sure if > > > since I am creating my own template, the EM GCA step requires > any > > > modifications? Any help will be appreciated. > > > > > > Thanks, > > > > > > Nandita > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI&m=HRcVNlmwdK9YHH6teQ4oW9oc6SDFzz79TS63mOlbWIY&s=zJ1S7JojJH4eJNf5L992h-7M4p0030LaYiT6ljZ4lBQ&e= > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI&m=HRcVNlmwdK9YHH6teQ4oW9oc6SDFzz79TS63mOlbWIY&s=zJ1S7JojJH4eJNf5L992h-7M4p0030LaYiT6ljZ4lBQ&e= > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI&m=wvTVN6V23k839lg_BNjhpvOJPbzoBSkJo0AXLRh3e7c&s=Oy4G_oUCj9eqihaPfelNsoQgwOcvmI3qYaBuN4CEmWE&e= > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI&m=wvTVN6V23k839lg_BNjhpvOJPbzoBSkJo0AXLRh3e7c&s=Oy4G_oUCj9eqihaPfelNsoQgwOcvmI3qYaBuN4CEmWE&e= > > > _______________________________________________ > 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
