Hi Chris this is probably a question for Doug, which means it will have to wait as he's away. Can you repost in a week or so if you haven't gotten a response?
thanks Bruce On Sat, 16 Feb 2013, Chris McNorgan wrote: > Hi all, > > I posted this back in January, and got a direct email reply from someone on > the mailing list, who gave me a helpful tip, but it doesn't seem to be > working out quite right. > > The problem: I have 3 .annot files per hemisphere, each based on the > ?h.aparc.annot files (36 regions), but in each file, a different subset of > these 36 regions has been further subdivided using the connectomemapper > toolkit. I would like to merge all the subdivided regions, the definitions of > which are spread across 3 files, into a single .annot file for each > hemisphere. > > The one response I received said: > After running cmtk on a subject you'll notice that in /FREESURFER/labels > there are folders for each parcellation called "regenerated_?h_500" for > example that contain all of the subdivided labels from that resolution > Lausanne parcellation. I used mris_label2annot > (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_label2annot) to combine all of > the desired labels into a single annot. The trick is that you need to type > each label name one at a time with an --l flag (easy to make a script to do > this quickly) and you need to supply a clut file, which has to be in the > format freesurfer is expecting (which is also easy to generate, and the > colors can be arbitrary). > > I've been trying this for a few days now without success. I also tried > deconstructing the original .annot files using mri_annotation2label and then > reassembling the label files using mris_label2annot (in the event that the > label files I had been previously using were somehow mangled). Either > approach seems to land me in the same place. > > The regions are generally in the right general anatomical area, but most are > out of place within those regions. For example I've got renderings comparing > the original definition of precentral_1 (highlighted region in purple in > ORIGINAL.tiff), which has become precentral_20 (in REDONE.tiff). Similarly, > parsoparcularis_10 has become parsoparcularis_1. But parahippocampal_1 was > found in the paracentral region. All of these shifts look as though the label > came from an adjacent region (alphabetically, as my ctab and scripts list the > regions alphabetically). > > Also notable is that the left has 500 entries in the ctab file, but running > my script gives the following output: > ...<snip> > 499 8697855 transversetemporal_3 > 500 8763647 transversetemporal_4 > 501 -1 NOT_FOUND > Mapping unhit to unknown > Found 1526 unhit vertices > > Similarly, the script for the right side also tries to map 503/502 entries. > These errors and the fact that the reassignments look like they are > off-by-one errors leads me to suspect that it might have something to do with > my ctab files, as the region boundaries seem to be maintained. If anyone has > any suggestions, I'm going to include links to the renderings, my scripts > that execute mris_label2annot for each hemisphere, and my ctab files. I'm > hoping I've left enough clues for someone to see where I'm going wrong. > > Thanks, > Chris > > > I've linked 7 files to this email: > ORIGINAL.tiff <http://ubuntuone.com/1ABD5WZOw65wPj3NK2M69D>(1.0 MB)Ubuntu One > <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/1ABD5WZOw65wPj3NK2M69D > REDONE.tiff <http://ubuntuone.com/2PGqBjqUXCJl5RffOUkE3L>(1.0 MB)Ubuntu One > <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/2PGqBjqUXCJl5RffOUkE3L > lausanne_left.sh <http://ubuntuone.com/2PBnWtBTjXLCpVqxz7dgEP>(16.0 KB)Ubuntu > One > <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/2PBnWtBTjXLCpVqxz7dgEP > lausanne_right.sh <http://ubuntuone.com/3uag3ZBIhRNisK2sB8MrhM>(16.1 > KB)Ubuntu One > <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/3uag3ZBIhRNisK2sB8MrhM > lh.lausanne_annot.ctab.csv <http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU>(17.0 > KB)Ubuntu One > <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU > rh.lausanne_annot.ctab.csv <http://ubuntuone.com/49H8V1gj7Ucq9FlIr8Onwg>(18.2 > KB)Ubuntu One > <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/49H8V1gj7Ucq9FlIr8Onwg > lh.lausanne_annot.ctab.csv <http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU>(17.0 > KB)Ubuntu One > <https://one.ubuntu.com/referrals/referee/2149434/?next=/>http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU > Mozilla Thunderbird <http://www.getthunderbird.com> makes it easy to share > large files over email. > > _______________________________________________ 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. 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