Re: [caret-users] About Monkey to Human Deformation
Hi Reza, See inline reply below. Donna On 03/14/2007 03:40 PM, Reza Rajimehr wrote: Hi Donna, The Data File button is disabled in my Caret, so I think I have to use the caret commands. Just a question: what are "source" and "target" paths in the first caret command. I assume that the source path is a monkey (macaque F99) directory, which has the input metric file, and the target path is a human PALS directory. Is this correct? Correct, but in this case, I'm wondering whether you can set both source and target directories to CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN and simply use the deform_map in that directory. This directory contains some, but not all of the source and target files cited in the deform_map file. I have already added the .deform_map file to the directory, which has the input metric file. This is not normally necessary. Typically, the file you want to deform is in the source directory, while the deform_map you use is in the target (atlas) directory. The output file (usually the same as the input file with "deformed_" prepended) usually is written to the atlas target directory. But in your case, setting both source and target directories to the absolute path of your CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN directory may work. Then you could navigate to your data file as needed, and let Caret write your deformed data file to your CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN directory. Thanks for your help, Reza Hi Reza, Hmmm. I can almost replicate this behavior. When I load CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map, both the individual and atlas directory buttons are disabled, but Data File and Deformed File... are both enabled (see attached capture). I thought perhaps this might be because the deform_map was read-only, but I get the same behavior with a copy that is writeable. Normally, one can change the individual and atlas directories, as one must do when using a deform_map from one of our datasets (unless you're David Van Essen, in which case the paths work fine). Using the Data File button, I could navigate to an input metric and successfully deform the data file. But if your buttons are disabled, then you might try using the following two caret commands to get the job done: DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE caret_command -def-map-path \ SURFACE APPLY DEFORMATION MAP caret_command -surface-deformation-apply \ \ \ [source-topo-file] [source-deformed-topo-file] \ [atlas-topo-file] Deform a data file. Note: "source-topo-file", "source-deformed-topo-file" and "atlas-topo-file" are only required when deforming coordinate files. "file-type" is one of: AREAL_ESTIMATION BORDER_FLAT BORDER_PROJECTION BORDER_SPHERICAL CELL CELL_PROJECTION COORDINATE COORDINATE_FLAT FOCI FOCI_PROJECTION LAT_LON METRIC PAINT PROB_ATLAS RGB_PAINT SURFACE_SHAPE TOPOGRAPHY Donna On 03/14/2007 03:11 AM, Reza Rajimehr wrote: Dear David, In the "Apply Deformation Map" dialog box, I specified the following items: 1) Deformation Map File: the 23-LDMK deform_map file 2) File Type: Metric 3) Flat Max Edge Length: 10.00 4) Metric Deformation: Nearest Node (not sure which one is better?) 5) Smooth One Iteration (Except Flat) The other buttons were not clickable (the dialog box does not allow me to use them). When I click the "Apply" button, I immediately receive the following error message: Deform Error Is deformation map file valid? You must select a data file for deformation. You must select the output name for the deformed file. I tried to apply deformation map from two different .spec files: 1) Macaque F99 atlas directory, which has deformed metric files (from individual macaque to F99). I added/appended the .deform_map file to this .spec file before applying deformation. 2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06 directory). I added/appended my metric files to this .spec file before applying deformation. In both cases, I got the same error. Thanks for your helpful comments/suggestions, Reza Reza, On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote: Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map Once you have a deform_map file, you can use it to register data sets from monkey to human WITHOUT re-running a registration. This is done using the Surface: Deformation: Apply Deformation Map option. If you want to register paint files, metric files, a
Re: [caret-users] About Monkey to Human Deformation
On Mar 14, 2007, at 3:40 PM, Reza Rajimehr wrote: The Data File button is disabled in my Caret, so I think I have to use the caret commands. Reza, The Data File button will be enabled once a deformation map file has been loaded. To load a deformation map file, press the "Deformation Map File" button and select the deformation map file that was produced by the deformation process. John
Re: [caret-users] About Monkey to Human Deformation
Hi Donna, The Data File button is disabled in my Caret, so I think I have to use the caret commands. Just a question: what are "source" and "target" paths in the first caret command. I assume that the source path is a monkey (macaque F99) directory, which has the input metric file, and the target path is a human PALS directory. Is this correct? I have already added the .deform_map file to the directory, which has the input metric file. Thanks for your help, Reza > Hi Reza, > > Hmmm. I can almost replicate this behavior. When I load > CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map, > both the individual and atlas directory buttons are disabled, but Data > File and Deformed File... are both enabled (see attached capture). I > thought perhaps this might be because the deform_map was read-only, but > I get the same behavior with a copy that is writeable. Normally, one > can change the individual and atlas directories, as one must do when > using a deform_map from one of our datasets (unless you're David Van > Essen, in which case the paths work fine). > > Using the Data File button, I could navigate to an input metric and > successfully deform the data file. But if your buttons are disabled, > then you might try using the following two caret commands to get the job > done: > >DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE > caret_command -def-map-path \ > > >SURFACE APPLY DEFORMATION MAP > caret_command -surface-deformation-apply \ >\ > \ > [source-topo-file] [source-deformed-topo-file] \ > [atlas-topo-file] > > Deform a data file. > > Note: "source-topo-file", "source-deformed-topo-file" and > "atlas-topo-file" are only required when deforming > coordinate files. > > "file-type" is one of: > AREAL_ESTIMATION > BORDER_FLAT > BORDER_PROJECTION > BORDER_SPHERICAL > CELL > CELL_PROJECTION > COORDINATE > COORDINATE_FLAT > FOCI > FOCI_PROJECTION > LAT_LON > METRIC > PAINT > PROB_ATLAS > RGB_PAINT > SURFACE_SHAPE > TOPOGRAPHY > > Donna > > On 03/14/2007 03:11 AM, Reza Rajimehr wrote: >> Dear David, >> >> In the "Apply Deformation Map" dialog box, I specified the following >> items: >> >> 1) Deformation Map File: the 23-LDMK deform_map file >> 2) File Type: Metric >> 3) Flat Max Edge Length: 10.00 >> 4) Metric Deformation: Nearest Node (not sure which one is better?) >> 5) Smooth One Iteration (Except Flat) >> >> The other buttons were not clickable (the dialog box does not allow me >> to >> use them). >> >> When I click the "Apply" button, I immediately receive the following >> error >> message: >> >> Deform Error >> Is deformation map file valid? You must select a data file for >> deformation. You must select the output name for the deformed file. >> >> I tried to apply deformation map from two different .spec files: >> >> 1) Macaque F99 atlas directory, which has deformed metric files (from >> individual macaque to F99). I added/appended the .deform_map file to >> this >> .spec file before applying deformation. >> >> 2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06 >> directory). I added/appended my metric files to this .spec file before >> applying deformation. >> >> In both cases, I got the same error. >> >> >> Thanks for your helpful comments/suggestions, >> >> Reza >> >> >> >>> Reza, >>> >>> On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote: >>> >>> Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map >>> Once you have a deform_map file, you can use it to register data >>> sets from monkey to human WITHOUT re-running a registration. This >>> is done using the Surface: Deformation: Apply Deformation Map >>> option. If you want to register paint files, metric files, and most >>> other files, you don't need anything other than the deform_map file >>> to get the job done, and the dialog window is fairly self- >>> explanatory. If you want to register a border projection file or a >>> coordinate file, then you need additional coordinate and topology >>> files that are available as part of the Caret Sept_06 tutorial dataset: >>> http://sumsdb.wustl.edu/sums/archivelist.do? >>> archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec >>> >>> The only reason to actually re-run an interspecies registration is IF >>> you don't like the particular set of landmarks used and you want to >>> try your own. If so, you should start with borderproj files also in: >>> http://sumsdb.wustl.edu/sums/archivelist.do? >>> archive_id=
Re: [caret-users] About Monkey to Human Deformation
Reza, Did you press the "Data File..." button to choose an input metric file for deformation? The Apply Deformation Map Dialog requires the user to select one specific data file for deformation, it does not deform all of the files automatically which is done as part of the spherical registration. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Mar 14, 2007, at 3:11 AM, Reza Rajimehr wrote: Dear David, In the "Apply Deformation Map" dialog box, I specified the following items: 1) Deformation Map File: the 23-LDMK deform_map file 2) File Type: Metric 3) Flat Max Edge Length: 10.00 4) Metric Deformation: Nearest Node (not sure which one is better?) 5) Smooth One Iteration (Except Flat) The other buttons were not clickable (the dialog box does not allow me to use them). When I click the "Apply" button, I immediately receive the following error message: Deform Error Is deformation map file valid? You must select a data file for deformation. You must select the output name for the deformed file. I tried to apply deformation map from two different .spec files: 1) Macaque F99 atlas directory, which has deformed metric files (from individual macaque to F99). I added/appended the .deform_map file to this .spec file before applying deformation. 2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06 directory). I added/appended my metric files to this .spec file before applying deformation. In both cases, I got the same error. Thanks for your helpful comments/suggestions, Reza Reza, On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote: Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map Once you have a deform_map file, you can use it to register data sets from monkey to human WITHOUT re-running a registration. This is done using the Surface: Deformation: Apply Deformation Map option. If you want to register paint files, metric files, and most other files, you don't need anything other than the deform_map file to get the job done, and the dialog window is fairly self- explanatory. If you want to register a border projection file or a coordinate file, then you need additional coordinate and topology files that are available as part of the Caret Sept_06 tutorial dataset: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec The only reason to actually re-run an interspecies registration is IF you don't like the particular set of landmarks used and you want to try your own. If so, you should start with borderproj files also in: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec and make your additions and subtractions from there. See Part 4 of the latest Caret tutorial for more details on monkey- human comparisons. http://sumsdb.wustl.edu/sums/directory.do? id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 I specified this as my .deform_map file in the Spherical Parameters tab in the Spherical Surface Deformation dialog box. My question is what I should specify as .borderproj file. I have a borderproj file in my F99 directory (that I used for the registration of individual macaque to F99). I also have a borderproj file in my PALS directory (that I used for the registration of individual human to PALS). Should I use these borderproj files in the Individual and Atlas tabs in the Spherical Surface Deformation dialog box? Or there are other files that I should use? I also assume that the macaque F99 .spec file should be used in the Individual tab, and the human PALS .spec file should be used in the Atlas tab. See above. These steps should not be necessary for your purposes. I hope this helps. David Thanks for your help, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
Re: [caret-users] About Monkey to Human Deformation
Hi Reza, Hmmm. I can almost replicate this behavior. When I load CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map, both the individual and atlas directory buttons are disabled, but Data File and Deformed File... are both enabled (see attached capture). I thought perhaps this might be because the deform_map was read-only, but I get the same behavior with a copy that is writeable. Normally, one can change the individual and atlas directories, as one must do when using a deform_map from one of our datasets (unless you're David Van Essen, in which case the paths work fine). Using the Data File button, I could navigate to an input metric and successfully deform the data file. But if your buttons are disabled, then you might try using the following two caret commands to get the job done: DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE caret_command -def-map-path \ SURFACE APPLY DEFORMATION MAP caret_command -surface-deformation-apply \ \ \ [source-topo-file] [source-deformed-topo-file] \ [atlas-topo-file] Deform a data file. Note: "source-topo-file", "source-deformed-topo-file" and "atlas-topo-file" are only required when deforming coordinate files. "file-type" is one of: AREAL_ESTIMATION BORDER_FLAT BORDER_PROJECTION BORDER_SPHERICAL CELL CELL_PROJECTION COORDINATE COORDINATE_FLAT FOCI FOCI_PROJECTION LAT_LON METRIC PAINT PROB_ATLAS RGB_PAINT SURFACE_SHAPE TOPOGRAPHY Donna On 03/14/2007 03:11 AM, Reza Rajimehr wrote: Dear David, In the "Apply Deformation Map" dialog box, I specified the following items: 1) Deformation Map File: the 23-LDMK deform_map file 2) File Type: Metric 3) Flat Max Edge Length: 10.00 4) Metric Deformation: Nearest Node (not sure which one is better?) 5) Smooth One Iteration (Except Flat) The other buttons were not clickable (the dialog box does not allow me to use them). When I click the "Apply" button, I immediately receive the following error message: Deform Error Is deformation map file valid? You must select a data file for deformation. You must select the output name for the deformed file. I tried to apply deformation map from two different .spec files: 1) Macaque F99 atlas directory, which has deformed metric files (from individual macaque to F99). I added/appended the .deform_map file to this .spec file before applying deformation. 2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06 directory). I added/appended my metric files to this .spec file before applying deformation. In both cases, I got the same error. Thanks for your helpful comments/suggestions, Reza Reza, On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote: Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map Once you have a deform_map file, you can use it to register data sets from monkey to human WITHOUT re-running a registration. This is done using the Surface: Deformation: Apply Deformation Map option. If you want to register paint files, metric files, and most other files, you don't need anything other than the deform_map file to get the job done, and the dialog window is fairly self- explanatory. If you want to register a border projection file or a coordinate file, then you need additional coordinate and topology files that are available as part of the Caret Sept_06 tutorial dataset: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec The only reason to actually re-run an interspecies registration is IF you don't like the particular set of landmarks used and you want to try your own. If so, you should start with borderproj files also in: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec and make your additions and subtractions from there. See Part 4 of the latest Caret tutorial for more details on monkey- human comparisons. http://sumsdb.wustl.edu/sums/directory.do? id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 I specified this as my .deform_map file in the Spherical Parameters tab in the Spherical Surface Deformation dialog box. My question is what I should specify as .borderproj file. I have a borderproj file in my F99 directory (that I used for the registration of individual macaque to F99). I also have a borderproj file in my PALS directory (that I used for the registration of individual human to PALS). Should I use these borderproj files in the Individual and Atlas tabs in the Spherical Surface Deformation dia
Re: [caret-users] About Monkey to Human Deformation
Dear David, In the "Apply Deformation Map" dialog box, I specified the following items: 1) Deformation Map File: the 23-LDMK deform_map file 2) File Type: Metric 3) Flat Max Edge Length: 10.00 4) Metric Deformation: Nearest Node (not sure which one is better?) 5) Smooth One Iteration (Except Flat) The other buttons were not clickable (the dialog box does not allow me to use them). When I click the "Apply" button, I immediately receive the following error message: Deform Error Is deformation map file valid? You must select a data file for deformation. You must select the output name for the deformed file. I tried to apply deformation map from two different .spec files: 1) Macaque F99 atlas directory, which has deformed metric files (from individual macaque to F99). I added/appended the .deform_map file to this .spec file before applying deformation. 2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06 directory). I added/appended my metric files to this .spec file before applying deformation. In both cases, I got the same error. Thanks for your helpful comments/suggestions, Reza > Reza, > > On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote: > >> Dear caret-users, >> >> David Van Essen suggested me to use the following .deform_map file for >> deformation of macaque F99 to Human PALS: >> >> RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- >> LDMK-VE.73730.spec.deform_map > > Once you have a deform_map file, you can use it to register data > sets from monkey to human WITHOUT re-running a registration. This > is done using the Surface: Deformation: Apply Deformation Map > option. If you want to register paint files, metric files, and most > other files, you don't need anything other than the deform_map file > to get the job done, and the dialog window is fairly self- > explanatory. If you want to register a border projection file or a > coordinate file, then you need additional coordinate and topology > files that are available as part of the Caret Sept_06 tutorial dataset: > http://sumsdb.wustl.edu/sums/archivelist.do? > archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec > > The only reason to actually re-run an interspecies registration is IF > you don't like the particular set of landmarks used and you want to > try your own. If so, you should start with borderproj files also in: > http://sumsdb.wustl.edu/sums/archivelist.do? > archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec > and make your additions and subtractions from there. > > See Part 4 of the latest Caret tutorial for more details on monkey- > human comparisons. > http://sumsdb.wustl.edu/sums/directory.do? > id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 > >> >> I specified this as my .deform_map file in the Spherical Parameters >> tab in >> the Spherical Surface Deformation dialog box. My question is what I >> should >> specify as .borderproj file. I have a borderproj file in my F99 >> directory >> (that I used for the registration of individual macaque to F99). I >> also >> have a borderproj file in my PALS directory (that I used for the >> registration of individual human to PALS). Should I use these >> borderproj >> files in the Individual and Atlas tabs in the Spherical Surface >> Deformation dialog box? Or there are other files that I should use? >> >> I also assume that the macaque F99 .spec file should be used in the >> Individual tab, and the human PALS .spec file should be used in the >> Atlas >> tab. > > See above. These steps should not be necessary for your purposes. > > I hope this helps. > > David > >> >> Thanks for your help, >> Reza >> >> >> Reza Rajimehr, MD >> >> NMR Athinoula A. Martinos Center >> Department of Radiology >> Massachusetts General Hospital (MGH) >> Building 149, 13th St. >> Charlestown, MA 02129 >> >> Email: [EMAIL PROTECTED] >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
Re: [caret-users] About Monkey to Human Deformation
Reza, On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote: Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map Once you have a deform_map file, you can use it to register data sets from monkey to human WITHOUT re-running a registration. This is done using the Surface: Deformation: Apply Deformation Map option. If you want to register paint files, metric files, and most other files, you don't need anything other than the deform_map file to get the job done, and the dialog window is fairly self- explanatory. If you want to register a border projection file or a coordinate file, then you need additional coordinate and topology files that are available as part of the Caret Sept_06 tutorial dataset: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec The only reason to actually re-run an interspecies registration is IF you don't like the particular set of landmarks used and you want to try your own. If so, you should start with borderproj files also in: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec and make your additions and subtractions from there. See Part 4 of the latest Caret tutorial for more details on monkey- human comparisons. http://sumsdb.wustl.edu/sums/directory.do? id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 I specified this as my .deform_map file in the Spherical Parameters tab in the Spherical Surface Deformation dialog box. My question is what I should specify as .borderproj file. I have a borderproj file in my F99 directory (that I used for the registration of individual macaque to F99). I also have a borderproj file in my PALS directory (that I used for the registration of individual human to PALS). Should I use these borderproj files in the Individual and Atlas tabs in the Spherical Surface Deformation dialog box? Or there are other files that I should use? I also assume that the macaque F99 .spec file should be used in the Individual tab, and the human PALS .spec file should be used in the Atlas tab. See above. These steps should not be necessary for your purposes. I hope this helps. David Thanks for your help, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
[caret-users] About Monkey to Human Deformation
Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map I specified this as my .deform_map file in the Spherical Parameters tab in the Spherical Surface Deformation dialog box. My question is what I should specify as .borderproj file. I have a borderproj file in my F99 directory (that I used for the registration of individual macaque to F99). I also have a borderproj file in my PALS directory (that I used for the registration of individual human to PALS). Should I use these borderproj files in the Individual and Atlas tabs in the Spherical Surface Deformation dialog box? Or there are other files that I should use? I also assume that the macaque F99 .spec file should be used in the Individual tab, and the human PALS .spec file should be used in the Atlas tab. Thanks for your help, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
