Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
1. You may need a new version of mri_label2label (I can get it to you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks doug, can I have a newer version? My version (mri_label2lable --version) is stable4 and it doesn't have a --paint option.
Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
- You may need a new version of mri_label2label (I can get it to
you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I've put an x64 version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2label
If that does not match your OS, then let me know
doug
Ben Kennedy wrote:
Thanks doug, can I have a newer version? My version (mri_label2lable --version) is stable4 and it doesn't have a --paint option.
Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
- You may need a new version of mri_label2label (I can get it to
you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I have the new version. I still think I need an intermediate step to make it work though. I need to specify something for --regmethod (either volume or surface). I have a volume+coordinates and I'm going to a surface, so I'm not sure which to specify. I tried both and the 'volume' needed a talairach.xfm and the 'surface' needed a sphere.reg.
I see why I need the intermediate step, but I'm not sure where to find it.
Thanks, Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
- You may need a new version of mri_label2label (I can get it to
you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
you should not have to spec a regmethod (defaults to surface with --paint). Is it giving you an error? BTW, it's a lot easier for me to debug if you send the command line and the terminal output.
Ben Kennedy wrote:
I have the new version. I still think I need an intermediate step to make it work though. I need to specify something for --regmethod (either volume or surface). I have a volume+coordinates and I'm going to a surface, so I'm not sure which to specify. I tried both and the 'volume' needed a talairach.xfm and the 'surface' needed a sphere.reg.
I see why I need the intermediate step, but I'm not sure where to find it.
Thanks, Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
- You may need a new version of mri_label2label (I can get it to
you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Sorry, I forgot to add the --paint line.
Here's what I've got.
I have a label file (penetration.label): #!ascii label /Users/labuser/Desktop/penetration.label , from subject NHP_jan_unbias vox2ras=TkReg 34 -1 45.000 0.000 -12.000 85.000000 -1 45.000 0.000 -13.000 87.000000 -1 44.000 0.000 -13.000 81.000000 -1 45.000 0.000 -14.000 87.000000 -1 44.000 0.000 -14.000 88.000000 -1 44.000 0.000 -15.000 107.000000 -1 43.000 0.000 -15.000 109.000000 -1 44.000 0.000 -16.000 110.000000 -1 43.000 0.000 -16.000 106.000000 -1 43.000 0.000 -17.000 95.000000 -1 42.000 0.000 -17.000 93.000000 -1 43.000 0.000 -18.000 87.000000 -1 42.000 0.000 -18.000 91.000000 -1 43.000 0.000 -19.000 91.000000 -1 42.000 0.000 -19.000 91.000000 -1 42.000 0.000 -20.000 87.000000 -1 41.000 0.000 -20.000 86.000000 -1 42.000 0.000 -21.000 82.000000 -1 41.000 0.000 -21.000 81.000000 -1 41.000 0.000 -22.000 75.000000 -1 40.000 0.000 -22.000 76.000000 -1 41.000 0.000 -23.000 86.000000 -1 40.000 0.000 -23.000 91.000000 -1 41.000 0.000 -24.000 87.000000 -1 40.000 0.000 -24.000 86.000000 -1 40.000 0.000 -25.000 87.000000 -1 39.000 0.000 -25.000 84.000000 -1 40.000 0.000 -26.000 90.000000 -1 39.000 0.000 -26.000 86.000000 -1 39.000 0.000 -27.000 100.000000 -1 38.000 0.000 -27.000 97.000000 -1 39.000 0.000 -28.000 114.000000 -1 38.000 0.000 -28.000 115.000000 -1 38.000 0.000 -29.000 96.000000
I use this command: $ ./mri_label2label --srclabel ~/Desktop/penetration.label --s NHP_jan_unbias --trglabel ~/Desktop/penetration_surface.label --paint 3 --hemi rh
The result looks like this (penetration_surface.label: $ cat ~/Desktop/penetration_surface.label #!ascii label , from subject NHP_jan_unbias vox2ras=TkReg 18 30045 44.901 1.553 -13.750 85.0000000000 29307 45.201 0.830 -14.191 87.0000000000 29326 43.525 0.210 -14.311 81.0000000000 29324 45.387 0.030 -14.468 87.0000000000 29325 44.453 0.143 -14.425 107.0000000000 29390 43.352 0.272 -16.790 110.0000000000 29366 42.568 0.357 -16.475 106.0000000000 28586 41.994 -0.624 -16.531 93.0000000000 28615 42.961 -0.665 -16.915 87.0000000000 29391 42.679 -0.280 -16.663 91.0000000000 28614 43.812 -0.553 -17.158 91.0000000000 29451 39.310 0.425 -26.735 87.0000000000 28689 39.798 -0.459 -26.829 86.0000000000 28690 38.803 -0.460 -26.753 76.0000000000 28691 37.785 -0.416 -26.870 86.0000000000 28717 38.941 -0.482 -29.100 91.0000000000 28718 37.947 -0.450 -29.120 87.0000000000 0 0.000 0.000 0.000 0.0000000000
everything seems great so far.
I load up my surface in tksurfer: $ tksurfer NHP_jan_unbias rh inflated surfer: current subjects dir: /Volumes/Spare1/Hans_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/labuser/Downloads surfer: Reading header info from /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/T1/COR-.info ltMNIreadEx: could not open file /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/transforms/talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=95278, faces=190552 Loading /Applications/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % . . . now I try to load the label file using File->Load Label Value File... and I get an error: % sclv_load_label_value_file: error reading line 1: 18
Am I missing how to load the label file into tksurfer?
Thanks for the help so far, I'm starting to feel like I'm questioning the correct things now! Ben
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
you should not have to spec a regmethod (defaults to surface with --paint). Is it giving you an error? BTW, it's a lot easier for me to debug if you send the command line and the terminal output.
Ben Kennedy wrote:
I have the new version. I still think I need an intermediate step to make it work though. I need to specify something for --regmethod (either volume or surface). I have a volume+coordinates and I'm going to a surface, so I'm not sure which to specify. I tried both and the 'volume' needed a talairach.xfm and the 'surface' needed a sphere.reg.
I see why I need the intermediate step, but I'm not sure where to find it.
Thanks, Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
- You may need a new version of mri_label2label (I can get it to
you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
it's not a Label Value File, it's just a Label (further down the menu list).
Benjamin B Kennedy wrote:
Sorry, I forgot to add the --paint line.
Here's what I've got.
I have a label file (penetration.label): #!ascii label /Users/labuser/Desktop/penetration.label , from subject NHP_jan_unbias vox2ras=TkReg 34 -1 45.000 0.000 -12.000 85.000000 -1 45.000 0.000 -13.000 87.000000 -1 44.000 0.000 -13.000 81.000000 -1 45.000 0.000 -14.000 87.000000 -1 44.000 0.000 -14.000 88.000000 -1 44.000 0.000 -15.000 107.000000 -1 43.000 0.000 -15.000 109.000000 -1 44.000 0.000 -16.000 110.000000 -1 43.000 0.000 -16.000 106.000000 -1 43.000 0.000 -17.000 95.000000 -1 42.000 0.000 -17.000 93.000000 -1 43.000 0.000 -18.000 87.000000 -1 42.000 0.000 -18.000 91.000000 -1 43.000 0.000 -19.000 91.000000 -1 42.000 0.000 -19.000 91.000000 -1 42.000 0.000 -20.000 87.000000 -1 41.000 0.000 -20.000 86.000000 -1 42.000 0.000 -21.000 82.000000 -1 41.000 0.000 -21.000 81.000000 -1 41.000 0.000 -22.000 75.000000 -1 40.000 0.000 -22.000 76.000000 -1 41.000 0.000 -23.000 86.000000 -1 40.000 0.000 -23.000 91.000000 -1 41.000 0.000 -24.000 87.000000 -1 40.000 0.000 -24.000 86.000000 -1 40.000 0.000 -25.000 87.000000 -1 39.000 0.000 -25.000 84.000000 -1 40.000 0.000 -26.000 90.000000 -1 39.000 0.000 -26.000 86.000000 -1 39.000 0.000 -27.000 100.000000 -1 38.000 0.000 -27.000 97.000000 -1 39.000 0.000 -28.000 114.000000 -1 38.000 0.000 -28.000 115.000000 -1 38.000 0.000 -29.000 96.000000
I use this command: $ ./mri_label2label --srclabel ~/Desktop/penetration.label --s NHP_jan_unbias --trglabel ~/Desktop/penetration_surface.label --paint 3 --hemi rh
The result looks like this (penetration_surface.label: $ cat ~/Desktop/penetration_surface.label #!ascii label , from subject NHP_jan_unbias vox2ras=TkReg 18 30045 44.901 1.553 -13.750 85.0000000000 29307 45.201 0.830 -14.191 87.0000000000 29326 43.525 0.210 -14.311 81.0000000000 29324 45.387 0.030 -14.468 87.0000000000 29325 44.453 0.143 -14.425 107.0000000000 29390 43.352 0.272 -16.790 110.0000000000 29366 42.568 0.357 -16.475 106.0000000000 28586 41.994 -0.624 -16.531 93.0000000000 28615 42.961 -0.665 -16.915 87.0000000000 29391 42.679 -0.280 -16.663 91.0000000000 28614 43.812 -0.553 -17.158 91.0000000000 29451 39.310 0.425 -26.735 87.0000000000 28689 39.798 -0.459 -26.829 86.0000000000 28690 38.803 -0.460 -26.753 76.0000000000 28691 37.785 -0.416 -26.870 86.0000000000 28717 38.941 -0.482 -29.100 91.0000000000 28718 37.947 -0.450 -29.120 87.0000000000 0 0.000 0.000 0.000 0.0000000000
everything seems great so far.
I load up my surface in tksurfer: $ tksurfer NHP_jan_unbias rh inflated surfer: current subjects dir: /Volumes/Spare1/Hans_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/labuser/Downloads surfer: Reading header info from /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/T1/COR-.info ltMNIreadEx: could not open file /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/transforms/talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=95278, faces=190552 Loading /Applications/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % . . . now I try to load the label file using File->Load Label Value File... and I get an error: % sclv_load_label_value_file: error reading line 1: 18
Am I missing how to load the label file into tksurfer?
Thanks for the help so far, I'm starting to feel like I'm questioning the correct things now! Ben
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
you should not have to spec a regmethod (defaults to surface with --paint). Is it giving you an error? BTW, it's a lot easier for me to debug if you send the command line and the terminal output.
Ben Kennedy wrote:
I have the new version. I still think I need an intermediate step to make it work though. I need to specify something for --regmethod (either volume or surface). I have a volume+coordinates and I'm going to a surface, so I'm not sure which to specify. I tried both and the 'volume' needed a talairach.xfm and the 'surface' needed a sphere.reg.
I see why I need the intermediate step, but I'm not sure where to find it.
Thanks, Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
- You may need a new version of mri_label2label (I can get it to
you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks Doug, everything is working out now.
Ben
On May 29, 2008, at 5:25 PM, Doug Greve wrote:
it's not a Label Value File, it's just a Label (further down the menu list).
Benjamin B Kennedy wrote:
Sorry, I forgot to add the --paint line.
Here's what I've got.
I have a label file (penetration.label): #!ascii label /Users/labuser/Desktop/penetration.label , from subject NHP_jan_unbias vox2ras=TkReg 34 -1 45.000 0.000 -12.000 85.000000 -1 45.000 0.000 -13.000 87.000000 -1 44.000 0.000 -13.000 81.000000 -1 45.000 0.000 -14.000 87.000000 -1 44.000 0.000 -14.000 88.000000 -1 44.000 0.000 -15.000 107.000000 -1 43.000 0.000 -15.000 109.000000 -1 44.000 0.000 -16.000 110.000000 -1 43.000 0.000 -16.000 106.000000 -1 43.000 0.000 -17.000 95.000000 -1 42.000 0.000 -17.000 93.000000 -1 43.000 0.000 -18.000 87.000000 -1 42.000 0.000 -18.000 91.000000 -1 43.000 0.000 -19.000 91.000000 -1 42.000 0.000 -19.000 91.000000 -1 42.000 0.000 -20.000 87.000000 -1 41.000 0.000 -20.000 86.000000 -1 42.000 0.000 -21.000 82.000000 -1 41.000 0.000 -21.000 81.000000 -1 41.000 0.000 -22.000 75.000000 -1 40.000 0.000 -22.000 76.000000 -1 41.000 0.000 -23.000 86.000000 -1 40.000 0.000 -23.000 91.000000 -1 41.000 0.000 -24.000 87.000000 -1 40.000 0.000 -24.000 86.000000 -1 40.000 0.000 -25.000 87.000000 -1 39.000 0.000 -25.000 84.000000 -1 40.000 0.000 -26.000 90.000000 -1 39.000 0.000 -26.000 86.000000 -1 39.000 0.000 -27.000 100.000000 -1 38.000 0.000 -27.000 97.000000 -1 39.000 0.000 -28.000 114.000000 -1 38.000 0.000 -28.000 115.000000 -1 38.000 0.000 -29.000 96.000000
I use this command: $ ./mri_label2label --srclabel ~/Desktop/penetration.label --s NHP_jan_unbias --trglabel ~/Desktop/penetration_surface.label --paint 3 --hemi rh
The result looks like this (penetration_surface.label: $ cat ~/Desktop/penetration_surface.label #!ascii label , from subject NHP_jan_unbias vox2ras=TkReg 18 30045 44.901 1.553 -13.750 85.0000000000 29307 45.201 0.830 -14.191 87.0000000000 29326 43.525 0.210 -14.311 81.0000000000 29324 45.387 0.030 -14.468 87.0000000000 29325 44.453 0.143 -14.425 107.0000000000 29390 43.352 0.272 -16.790 110.0000000000 29366 42.568 0.357 -16.475 106.0000000000 28586 41.994 -0.624 -16.531 93.0000000000 28615 42.961 -0.665 -16.915 87.0000000000 29391 42.679 -0.280 -16.663 91.0000000000 28614 43.812 -0.553 -17.158 91.0000000000 29451 39.310 0.425 -26.735 87.0000000000 28689 39.798 -0.459 -26.829 86.0000000000 28690 38.803 -0.460 -26.753 76.0000000000 28691 37.785 -0.416 -26.870 86.0000000000 28717 38.941 -0.482 -29.100 91.0000000000 28718 37.947 -0.450 -29.120 87.0000000000 0 0.000 0.000 0.000 0.0000000000
everything seems great so far.
I load up my surface in tksurfer: $ tksurfer NHP_jan_unbias rh inflated surfer: current subjects dir: /Volumes/Spare1/Hans_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/labuser/Downloads surfer: Reading header info from /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/T1/COR-.info ltMNIreadEx: could not open file /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/transforms/ talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=95278, faces=190552 Loading /Applications/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % . . . now I try to load the label file using File->Load Label Value File... and I get an error: % sclv_load_label_value_file: error reading line 1: 18
Am I missing how to load the label file into tksurfer?
Thanks for the help so far, I'm starting to feel like I'm questioning the correct things now! Ben
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
you should not have to spec a regmethod (defaults to surface with --paint). Is it giving you an error? BTW, it's a lot easier for me to debug if you send the command line and the terminal output.
Ben Kennedy wrote:
I have the new version. I still think I need an intermediate step to make it work though. I need to specify something for -- regmethod (either volume or surface). I have a volume +coordinates and I'm going to a surface, so I'm not sure which to specify. I tried both and the 'volume' needed a talairach.xfm and the 'surface' needed a sphere.reg.
I see why I need the intermediate step, but I'm not sure where to find it.
Thanks, Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
- You may need a new version of mri_label2label (I can get it
to you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
Dear Freesurfer,
I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub- voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this?
Thanks, Ben K _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Doug,
With the new version of mri_label2label, what is the meaning assigned to the value in --paint? Is 'd' the distance in voxels from the normal of the white matter surface to the point that's being projected?
Is there was way to specify this by using something lie --projfrac?
Thanks, Ben
On May 30, 2008, at 10:24 AM, Ben Kennedy wrote:
Thanks Doug, everything is working out now.
Ben
On May 29, 2008, at 5:25 PM, Doug Greve wrote:
it's not a Label Value File, it's just a Label (further down the menu list).
Benjamin B Kennedy wrote:
Sorry, I forgot to add the --paint line.
Here's what I've got.
I have a label file (penetration.label): #!ascii label /Users/labuser/Desktop/penetration.label , from subject NHP_jan_unbias vox2ras=TkReg 34 -1 45.000 0.000 -12.000 85.000000 -1 45.000 0.000 -13.000 87.000000 -1 44.000 0.000 -13.000 81.000000 -1 45.000 0.000 -14.000 87.000000 -1 44.000 0.000 -14.000 88.000000 -1 44.000 0.000 -15.000 107.000000 -1 43.000 0.000 -15.000 109.000000 -1 44.000 0.000 -16.000 110.000000 -1 43.000 0.000 -16.000 106.000000 -1 43.000 0.000 -17.000 95.000000 -1 42.000 0.000 -17.000 93.000000 -1 43.000 0.000 -18.000 87.000000 -1 42.000 0.000 -18.000 91.000000 -1 43.000 0.000 -19.000 91.000000 -1 42.000 0.000 -19.000 91.000000 -1 42.000 0.000 -20.000 87.000000 -1 41.000 0.000 -20.000 86.000000 -1 42.000 0.000 -21.000 82.000000 -1 41.000 0.000 -21.000 81.000000 -1 41.000 0.000 -22.000 75.000000 -1 40.000 0.000 -22.000 76.000000 -1 41.000 0.000 -23.000 86.000000 -1 40.000 0.000 -23.000 91.000000 -1 41.000 0.000 -24.000 87.000000 -1 40.000 0.000 -24.000 86.000000 -1 40.000 0.000 -25.000 87.000000 -1 39.000 0.000 -25.000 84.000000 -1 40.000 0.000 -26.000 90.000000 -1 39.000 0.000 -26.000 86.000000 -1 39.000 0.000 -27.000 100.000000 -1 38.000 0.000 -27.000 97.000000 -1 39.000 0.000 -28.000 114.000000 -1 38.000 0.000 -28.000 115.000000 -1 38.000 0.000 -29.000 96.000000
I use this command: $ ./mri_label2label --srclabel ~/Desktop/penetration.label --s NHP_jan_unbias --trglabel ~/Desktop/penetration_surface.label --paint 3 --hemi rh
The result looks like this (penetration_surface.label: $ cat ~/Desktop/penetration_surface.label #!ascii label , from subject NHP_jan_unbias vox2ras=TkReg 18 30045 44.901 1.553 -13.750 85.0000000000 29307 45.201 0.830 -14.191 87.0000000000 29326 43.525 0.210 -14.311 81.0000000000 29324 45.387 0.030 -14.468 87.0000000000 29325 44.453 0.143 -14.425 107.0000000000 29390 43.352 0.272 -16.790 110.0000000000 29366 42.568 0.357 -16.475 106.0000000000 28586 41.994 -0.624 -16.531 93.0000000000 28615 42.961 -0.665 -16.915 87.0000000000 29391 42.679 -0.280 -16.663 91.0000000000 28614 43.812 -0.553 -17.158 91.0000000000 29451 39.310 0.425 -26.735 87.0000000000 28689 39.798 -0.459 -26.829 86.0000000000 28690 38.803 -0.460 -26.753 76.0000000000 28691 37.785 -0.416 -26.870 86.0000000000 28717 38.941 -0.482 -29.100 91.0000000000 28718 37.947 -0.450 -29.120 87.0000000000 0 0.000 0.000 0.000 0.0000000000
everything seems great so far.
I load up my surface in tksurfer: $ tksurfer NHP_jan_unbias rh inflated surfer: current subjects dir: /Volumes/Spare1/Hans_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/labuser/Downloads surfer: Reading header info from /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/T1/COR-.info ltMNIreadEx: could not open file /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/transforms/ talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=95278, faces=190552 Loading /Applications/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /Applications/freesurfer/lib/tcl/ tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % . . . now I try to load the label file using File->Load Label Value File... and I get an error: % sclv_load_label_value_file: error reading line 1: 18
Am I missing how to load the label file into tksurfer?
Thanks for the help so far, I'm starting to feel like I'm questioning the correct things now! Ben
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
you should not have to spec a regmethod (defaults to surface with --paint). Is it giving you an error? BTW, it's a lot easier for me to debug if you send the command line and the terminal output.
Ben Kennedy wrote:
I have the new version. I still think I need an intermediate step to make it work though. I need to specify something for -- regmethod (either volume or surface). I have a volume +coordinates and I'm going to a surface, so I'm not sure which to specify. I tried both and the 'volume' needed a talairach.xfm and the 'surface' needed a sphere.reg.
I see why I need the intermediate step, but I'm not sure where to find it.
Thanks, Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates:
- You may need a new version of mri_label2label (I can get it
to you if so) 2. You have to use the proper coordinates
doug
Ben Kennedy wrote:
> Dear Freesurfer, > > I've been playing around with Freesurfer and monkey MR > volumes, and I'm trying to find some sort of foothold to use > Freesurfer more effectively. I have the surfaces and > inflated volumes of the brain, and I also have a bunch of > sub-voxel coordinates (in the T1 volume) of recorded sites > that I want to project onto these surfaces and inflations. > Is there any straightforward (but I'll take convoluted also) > way to do this? > > Thanks, > Ben K > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
d is the distance (in mm) from the surface within which a label point must be in order to be assigned to a vertex. It is just a simple distance (no normal involved). Can you elaborate on what you would want a --projfrac to do in this case?
Ben Kennedy wrote:
Doug,
With the new version of mri_label2label, what is the meaning assigned to the value in --paint? Is 'd' the distance in voxels from the normal of the white matter surface to the point that's being projected?
Is there was way to specify this by using something lie --projfrac?
Thanks, Ben
On May 30, 2008, at 10:24 AM, Ben Kennedy wrote:
Thanks Doug, everything is working out now.
Ben
On May 29, 2008, at 5:25 PM, Doug Greve wrote:
it's not a Label Value File, it's just a Label (further down the menu list).
Benjamin B Kennedy wrote:
Sorry, I forgot to add the --paint line.
Here's what I've got.
I have a label file (penetration.label): #!ascii label /Users/labuser/Desktop/penetration.label , from subject NHP_jan_unbias vox2ras=TkReg 34 -1 45.000 0.000 -12.000 85.000000 -1 45.000 0.000 -13.000 87.000000 -1 44.000 0.000 -13.000 81.000000 -1 45.000 0.000 -14.000 87.000000 -1 44.000 0.000 -14.000 88.000000 -1 44.000 0.000 -15.000 107.000000 -1 43.000 0.000 -15.000 109.000000 -1 44.000 0.000 -16.000 110.000000 -1 43.000 0.000 -16.000 106.000000 -1 43.000 0.000 -17.000 95.000000 -1 42.000 0.000 -17.000 93.000000 -1 43.000 0.000 -18.000 87.000000 -1 42.000 0.000 -18.000 91.000000 -1 43.000 0.000 -19.000 91.000000 -1 42.000 0.000 -19.000 91.000000 -1 42.000 0.000 -20.000 87.000000 -1 41.000 0.000 -20.000 86.000000 -1 42.000 0.000 -21.000 82.000000 -1 41.000 0.000 -21.000 81.000000 -1 41.000 0.000 -22.000 75.000000 -1 40.000 0.000 -22.000 76.000000 -1 41.000 0.000 -23.000 86.000000 -1 40.000 0.000 -23.000 91.000000 -1 41.000 0.000 -24.000 87.000000 -1 40.000 0.000 -24.000 86.000000 -1 40.000 0.000 -25.000 87.000000 -1 39.000 0.000 -25.000 84.000000 -1 40.000 0.000 -26.000 90.000000 -1 39.000 0.000 -26.000 86.000000 -1 39.000 0.000 -27.000 100.000000 -1 38.000 0.000 -27.000 97.000000 -1 39.000 0.000 -28.000 114.000000 -1 38.000 0.000 -28.000 115.000000 -1 38.000 0.000 -29.000 96.000000
I use this command: $ ./mri_label2label --srclabel ~/Desktop/penetration.label --s NHP_jan_unbias --trglabel ~/Desktop/penetration_surface.label --paint 3 --hemi rh
The result looks like this (penetration_surface.label: $ cat ~/Desktop/penetration_surface.label #!ascii label , from subject NHP_jan_unbias vox2ras=TkReg 18 30045 44.901 1.553 -13.750 85.0000000000 29307 45.201 0.830 -14.191 87.0000000000 29326 43.525 0.210 -14.311 81.0000000000 29324 45.387 0.030 -14.468 87.0000000000 29325 44.453 0.143 -14.425 107.0000000000 29390 43.352 0.272 -16.790 110.0000000000 29366 42.568 0.357 -16.475 106.0000000000 28586 41.994 -0.624 -16.531 93.0000000000 28615 42.961 -0.665 -16.915 87.0000000000 29391 42.679 -0.280 -16.663 91.0000000000 28614 43.812 -0.553 -17.158 91.0000000000 29451 39.310 0.425 -26.735 87.0000000000 28689 39.798 -0.459 -26.829 86.0000000000 28690 38.803 -0.460 -26.753 76.0000000000 28691 37.785 -0.416 -26.870 86.0000000000 28717 38.941 -0.482 -29.100 91.0000000000 28718 37.947 -0.450 -29.120 87.0000000000 0 0.000 0.000 0.000 0.0000000000
everything seems great so far.
I load up my surface in tksurfer: $ tksurfer NHP_jan_unbias rh inflated surfer: current subjects dir: /Volumes/Spare1/Hans_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/labuser/Downloads surfer: Reading header info from /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/T1/COR-.info ltMNIreadEx: could not open file /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/transforms/ talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=95278, faces=190552 Loading /Applications/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /Applications/freesurfer/lib/tcl/ tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % . . . now I try to load the label file using File->Load Label Value File... and I get an error: % sclv_load_label_value_file: error reading line 1: 18
Am I missing how to load the label file into tksurfer?
Thanks for the help so far, I'm starting to feel like I'm questioning the correct things now! Ben
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
you should not have to spec a regmethod (defaults to surface with --paint). Is it giving you an error? BTW, it's a lot easier for me to debug if you send the command line and the terminal output.
Ben Kennedy wrote:
I have the new version. I still think I need an intermediate step to make it work though. I need to specify something for -- regmethod (either volume or surface). I have a volume +coordinates and I'm going to a surface, so I'm not sure which to specify. I tried both and the 'volume' needed a talairach.xfm and the 'surface' needed a sphere.reg.
I see why I need the intermediate step, but I'm not sure where to find it.
Thanks, Ben
On May 28, 2008, at 11:39 AM, Doug Greve wrote:
> you can create a label with the coordinates, the use > mri_label2label with the --paint option to sample them to the > closest surface vertex. Two caveates: > > 1. You may need a new version of mri_label2label (I can get it > to you if so) > 2. You have to use the proper coordinates > > doug > > Ben Kennedy wrote: > >> Dear Freesurfer, >> >> I've been playing around with Freesurfer and monkey MR >> volumes, and I'm trying to find some sort of foothold to use >> Freesurfer more effectively. I have the surfaces and >> inflated volumes of the brain, and I also have a bunch of >> sub-voxel coordinates (in the T1 volume) of recorded sites >> that I want to project onto these surfaces and inflations. >> Is there any straightforward (but I'll take convoluted also) >> way to do this? >> >> Thanks, >> Ben K >> _______________________________________________ >> 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 > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You're right, without a normal, it isn't clear what --projfrac would do. With a pretty simple algorithm, I can modify my question: is there a way to use mri_label2label (or another tool) so that a label point is assigned to a vertex if it is a fraction of the thickness and/ or within a normal distance from the surface? Mapping to the closest vertex is OK, it doesn't have to be the closest normal vertex. Does it require that the sphere.reg be in place?
Basically, I have a bunch of 3D points in the volume, and I want to visualize ones that are in the gray matter (and even better if it's a fraction of the gray matter) on a surface. I think I can preprocess the data enough to dump all of the points outside of the cortical ribbon, and then set 'dmax' to something artificially high, but it looks like freesurfer already handles this.
thanks, Ben
On Jun 9, 2008, at 11:18 AM, Doug Greve wrote:
d is the distance (in mm) from the surface within which a label point must be in order to be assigned to a vertex. It is just a simple distance (no normal involved). Can you elaborate on what you would want a --projfrac to do in this case?
Ben Kennedy wrote:
Doug,
With the new version of mri_label2label, what is the meaning assigned to the value in --paint? Is 'd' the distance in voxels from the normal of the white matter surface to the point that's being projected?
Is there was way to specify this by using something lie --projfrac?
Thanks, Ben
On May 30, 2008, at 10:24 AM, Ben Kennedy wrote:
Thanks Doug, everything is working out now.
Ben
On May 29, 2008, at 5:25 PM, Doug Greve wrote:
it's not a Label Value File, it's just a Label (further down the menu list).
Benjamin B Kennedy wrote:
Sorry, I forgot to add the --paint line.
Here's what I've got.
I have a label file (penetration.label): #!ascii label /Users/labuser/Desktop/penetration.label , from subject NHP_jan_unbias vox2ras=TkReg 34 -1 45.000 0.000 -12.000 85.000000 -1 45.000 0.000 -13.000 87.000000 -1 44.000 0.000 -13.000 81.000000 -1 45.000 0.000 -14.000 87.000000 -1 44.000 0.000 -14.000 88.000000 -1 44.000 0.000 -15.000 107.000000 -1 43.000 0.000 -15.000 109.000000 -1 44.000 0.000 -16.000 110.000000 -1 43.000 0.000 -16.000 106.000000 -1 43.000 0.000 -17.000 95.000000 -1 42.000 0.000 -17.000 93.000000 -1 43.000 0.000 -18.000 87.000000 -1 42.000 0.000 -18.000 91.000000 -1 43.000 0.000 -19.000 91.000000 -1 42.000 0.000 -19.000 91.000000 -1 42.000 0.000 -20.000 87.000000 -1 41.000 0.000 -20.000 86.000000 -1 42.000 0.000 -21.000 82.000000 -1 41.000 0.000 -21.000 81.000000 -1 41.000 0.000 -22.000 75.000000 -1 40.000 0.000 -22.000 76.000000 -1 41.000 0.000 -23.000 86.000000 -1 40.000 0.000 -23.000 91.000000 -1 41.000 0.000 -24.000 87.000000 -1 40.000 0.000 -24.000 86.000000 -1 40.000 0.000 -25.000 87.000000 -1 39.000 0.000 -25.000 84.000000 -1 40.000 0.000 -26.000 90.000000 -1 39.000 0.000 -26.000 86.000000 -1 39.000 0.000 -27.000 100.000000 -1 38.000 0.000 -27.000 97.000000 -1 39.000 0.000 -28.000 114.000000 -1 38.000 0.000 -28.000 115.000000 -1 38.000 0.000 -29.000 96.000000
I use this command: $ ./mri_label2label --srclabel ~/Desktop/penetration.label --s NHP_jan_unbias --trglabel ~/Desktop/penetration_surface.label --paint 3 --hemi rh
The result looks like this (penetration_surface.label: $ cat ~/Desktop/penetration_surface.label #!ascii label , from subject NHP_jan_unbias vox2ras=TkReg 18 30045 44.901 1.553 -13.750 85.0000000000 29307 45.201 0.830 -14.191 87.0000000000 29326 43.525 0.210 -14.311 81.0000000000 29324 45.387 0.030 -14.468 87.0000000000 29325 44.453 0.143 -14.425 107.0000000000 29390 43.352 0.272 -16.790 110.0000000000 29366 42.568 0.357 -16.475 106.0000000000 28586 41.994 -0.624 -16.531 93.0000000000 28615 42.961 -0.665 -16.915 87.0000000000 29391 42.679 -0.280 -16.663 91.0000000000 28614 43.812 -0.553 -17.158 91.0000000000 29451 39.310 0.425 -26.735 87.0000000000 28689 39.798 -0.459 -26.829 86.0000000000 28690 38.803 -0.460 -26.753 76.0000000000 28691 37.785 -0.416 -26.870 86.0000000000 28717 38.941 -0.482 -29.100 91.0000000000 28718 37.947 -0.450 -29.120 87.0000000000 0 0.000 0.000 0.000 0.0000000000
everything seems great so far.
I load up my surface in tksurfer: $ tksurfer NHP_jan_unbias rh inflated surfer: current subjects dir: /Volumes/Spare1/Hans_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/labuser/Downloads surfer: Reading header info from /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/T1/COR-.info ltMNIreadEx: could not open file /Volumes/Spare1/Hans_data//NHP_jan_unbias/mri/transforms/ talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=95278, faces=190552 Loading /Applications/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /Applications/freesurfer/lib/tcl/ tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % . . . now I try to load the label file using File->Load Label Value File... and I get an error: % sclv_load_label_value_file: error reading line 1: 18
Am I missing how to load the label file into tksurfer?
Thanks for the help so far, I'm starting to feel like I'm questioning the correct things now! Ben
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
you should not have to spec a regmethod (defaults to surface with --paint). Is it giving you an error? BTW, it's a lot easier for me to debug if you send the command line and the terminal output.
Ben Kennedy wrote:
> I have the new version. I still think I need an intermediate > step to make it work though. I need to specify something for > -- regmethod (either volume or surface). I have a volume > +coordinates and I'm going to a surface, so I'm not sure > which to specify. I tried both and the 'volume' needed a > talairach.xfm and the 'surface' needed a sphere.reg. > > I see why I need the intermediate step, but I'm not sure > where to find it. > > Thanks, > Ben > > > On May 28, 2008, at 11:39 AM, Doug Greve wrote: > >> you can create a label with the coordinates, the use >> mri_label2label with the --paint option to sample them to >> the closest surface vertex. Two caveates: >> >> 1. You may need a new version of mri_label2label (I can get >> it to you if so) >> 2. You have to use the proper coordinates >> >> doug >> >> Ben Kennedy wrote: >> >>> Dear Freesurfer, >>> >>> I've been playing around with Freesurfer and monkey MR >>> volumes, and I'm trying to find some sort of foothold to >>> use Freesurfer more effectively. I have the surfaces >>> and inflated volumes of the brain, and I also have a >>> bunch of sub-voxel coordinates (in the T1 volume) of >>> recorded sites that I want to project onto these surfaces >>> and inflations. Is there any straightforward (but I'll >>> take convoluted also) way to do this? >>> >>> Thanks, >>> Ben K >>> _______________________________________________ >>> 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 >> greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
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Ben Kennedy -
Benjamin B Kennedy
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Doug Greve