what version are you using? I thought I fixed the missing-last-label problem in v6
On 03/01/2017 06:42 PM, Antonin Skoch wrote: > Dear Doug, > > thank you, adding --no-unknown indeed fixed the global shuffling of > the label names. However, last line of .ctab seems not to be read this > time and produced .annot does not contain perirhinal label. > > My modified .ctab file looks like this: > > 0 Unknown 0 0 0 0 > 1 G&S_frontomargin 23 220 60 0 > 2 G&S_occipital_inf 23 60 180 0 > 3 G&S_paracentral 63 100 60 0 > 4 G&S_subcentral 63 20 220 0 > 5 G&S_transv_frontopol 13 0 250 0 > 6 G&S_cingul-Ant 26 60 0 0 > 7 G&S_cingul-Mid-Ant 26 60 75 0 > 8 G&S_cingul-Mid-Post 26 60 150 0 > 9 G_cingul-Post-dorsal 25 60 250 0 > 10 G_cingul-Post-ventral 60 25 25 0 > 11 G_cuneus 180 20 20 0 > 12 G_front_inf-Opercular 220 20 100 0 > 13 G_front_inf-Orbital 140 60 60 0 > 14 G_front_inf-Triangul 180 220 140 0 > 15 G_front_middle 140 100 180 0 > 16 G_front_sup 180 20 140 0 > 17 G_Ins_lg&S_cent_ins 23 10 10 0 > 18 G_insular_short 225 140 140 0 > 19 G_occipital_middle 180 60 180 0 > 20 G_occipital_sup 20 220 60 0 > 21 G_oc-temp_lat-fusifor 60 20 140 0 > 22 G_oc-temp_med-Lingual 220 180 140 0 > 23 G_oc-temp_med-Parahip 65 100 20 0 > 24 G_orbital 220 60 20 0 > 25 G_pariet_inf-Angular 20 60 220 0 > 26 G_pariet_inf-Supramar 100 100 60 0 > 27 G_parietal_sup 220 180 220 0 > 28 G_postcentral 20 180 140 0 > 29 G_precentral 60 140 180 0 > 30 G_precuneus 25 20 140 0 > 31 G_rectus 20 60 100 0 > 32 G_subcallosal 60 220 20 0 > 33 G_temp_sup-G_T_transv 60 60 220 0 > 34 G_temp_sup-Lateral 220 60 220 0 > 35 G_temp_sup-Plan_polar 65 220 60 0 > 36 G_temp_sup-Plan_tempo 25 140 20 0 > 37 G_temporal_inf 220 220 100 0 > 38 G_temporal_middle 180 60 60 0 > 39 Lat_Fis-ant-Horizont 61 20 220 0 > 40 Lat_Fis-ant-Vertical 61 20 60 0 > 41 Lat_Fis-post 61 60 100 0 > 42 Medial_wall 25 25 25 0 > 43 Pole_occipital 140 20 60 0 > 44 Pole_temporal 220 180 20 0 > 45 S_calcarine 63 180 180 0 > 46 S_central 221 20 10 0 > 47 S_cingul-Marginalis 221 20 100 0 > 48 S_circular_insula_ant 221 60 140 0 > 49 S_circular_insula_inf 221 20 220 0 > 50 S_circular_insula_sup 61 220 220 0 > 51 S_collat_transv_ant 100 200 200 0 > 52 S_collat_transv_post 10 200 200 0 > 53 S_front_inf 221 220 20 0 > 54 S_front_middle 141 20 100 0 > 55 S_front_sup 61 220 100 0 > 56 S_interm_prim-Jensen 141 60 20 0 > 57 S_intrapariet&P_trans 143 20 220 0 > 58 S_oc_middle&Lunatus 101 60 220 0 > 59 S_oc_sup&transversal 21 20 140 0 > 60 S_occipital_ant 61 20 180 0 > 61 S_oc-temp_lat 221 140 20 0 > 62 S_oc-temp_med&Lingual 141 100 220 0 > 63 S_orbital_lateral 221 100 20 0 > 64 S_orbital_med-olfact 181 200 20 0 > 65 S_orbital-H_Shaped 101 20 20 0 > 66 S_parieto_occipital 101 100 180 0 > 67 S_pericallosal 181 220 20 0 > 68 S_postcentral 21 140 200 0 > 69 S_precentral-inf-part 21 20 240 0 > 70 S_precentral-sup-part 21 20 200 0 > 71 S_suborbital 21 20 60 0 > 72 S_subparietal 101 60 60 0 > 73 S_temporal_inf 21 180 180 0 > 74 S_temporal_sup 223 220 60 0 > 75 S_temporal_transverse 221 60 60 0 > 76 entorhinal_exvivo.thresh 222 62 67 0 > 77 perirhninal_exvivo.thresh 223 65 60 0 > > with newline in the end. > > However, I was able to successfully generate annotation with 2 labels > ( previous swap of names in .annot produced using --l options was my > fault since I did not read the help to the detail to learn that the > order of label files of --l arguments has to match the order of names > in .ctab). So I could possibly achieve my goal by run mri_aparc2aseg > on this simple 2-label annot and somehow merge the result with the > default aparc.a2009s to bring the rhinal labels into that. Do you see > any pitfall with that? > > In any case, however, before running aparc2aseg I have to cope with > another problem with rhinal labels - the rhinal.thresh labels are > overlapping and I would need to correctly assign vertices in the label > intersection (see my previous post > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51919.html > ). > > Regards, > > Antonin > > > Try adding --no-unknown to the label2annot command line > On 02/28/2017 04:45 PM, Antonin Skoch wrote: > > Dear experts, > > > > I would like to create modified aparc.a2009s+aseg file with relevant > > parts of parahippocampal cortical ribbon voxel labels replaced by > > labels derived from surface labels of entorhinal and parahippocampal > > cortex (created also by default in recon-all). This modified > > aparc.a2009s+aseg file I want to use for streamline assignment in > > structural connectome generation in MrTrix3. > > > > I think that mri_label2vol is not optimal way to do it since it would > > leave some voxels in the ribbon unassigned. > > > > I think that the better, but much complicated, way to do this is to > > modify aparc.a2009s.annot with the information from these labels and > > then run again mris_aparc2aseg. > > > > I tried to do this by using: > > > > mri_annotation2label > > > > and > > > > mris_label2annot --hemi lh --subject my_subject --ldir my_labels --a > > my_aparc.a2009s --ctab my_aparc.annot.a2009s.ctab --debug > > > > I took the aparc.annot.a2009s.ctab from the my_subject/label > > directory and added to the end 2 row with entorrhinal and perirhinal > > parcellations with unique RGB values to assure the relevant parts of > > parahippocampal gyrus label are replaced by these new labels I want to > > supply. > > > > But the resulting new .annot file is not correct - the labels are in > > correct position on cortical surfaces, but the label names of all > > labels are shuffled. > > > > I even tried the sequence of mri_annotation2label, mris_label2annot > > without adding new labels, just converting annotation to labels and > > back, and the annotation naming is also corrupted. > > > > I also tried to create new annotation just from 2 new labels, > > preparing .ctab file and running mris_label2annot by explicitly > > specifying my 2 labels like > > > > mris_label2annot --hemi lh --subject my_subject --l > > lh_labels/lh.perirhinal_exvivo.thresh.label --l > > lh_labels/lh.entorhinal_exvivo.thresh.label --a rhinal_aparc.a2009s > > --debug --ctab rhinal_aparc.annot.a2009s.ctab > > > > In this case the label names in annotation are swapped (entorhinal is > > perirhinal and vice versa), swapped are also file names of labels > > which I tried to back convert by using mri_annotation2label. > > > > I am using quite recent build of dev version of Freesurfer from > > 28/2/2017. > > > > Could you suggest where could be the problem? > > > > Or could you advice different, possibly more simple way, how to > > achieve my goal? > > > > Thank you in advance. > > > > Regards, > > > > Antonin Skoch > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
