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.
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.
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Chris McNorgan -
Douglas N Greve