Dear Doug,
I am using quite recent dev version built 8/2/2017.
mris_label2annot of this version is following:
$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve
Regards,
Antonin
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
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