Hi Chris, in the color table file, do you have an "unkown" entryas the first entry? There should be one or else use --no-unknown. doug
On 02/16/2013 11:07 PM, 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 -- 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: 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.
