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wang
BIAC Alum
USA
57 Posts |
 Posted - Jul 16 2007 : 07:18:47 AM
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I would like to use one T1 high-resolution anatomical image and one T2 low-resolution anatomical image (same resolution as the functionals) for co-registration. I used the T1 image as initial and T2 as main structural image in FSL analysis. There was no error report, however, the co-registration was far way off. I guess the problem is that the template brain was T1 image, my main structral image was T2, right? Any other possibilities? Is there a T2 template brain for co-registration in FSL? Thanks.
Lihong |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 16 2007 : 09:30:27 AM
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I think you should try it the other way around. If you specify both an initial and main structural images, the registration process goes like this:
functional -> initial
initial-> main
main ->standard
You want each pair to be as similar as possible. The default standard brain is a T1 image, and I don't know if there are other reasonable alternatives.
If the T1 and T2 and functional images are all in the same orientation, then I think you can just specify an initial matrix for the main->standard registration by using MkFlirtInitMtx.pl on the T1 and putting the output of that into the init_standard line of the .fsf. |
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wang
BIAC Alum
USA
57 Posts |
Posted - Jul 16 2007 : 11:56:09 AM
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Thanks Syam. All the three types of images are in the same orientation. Since there is no T2 standard brain, to make each pair to be as similar as possible, then I guess I'd better use
functional -> initial(T2 low resolution file),
initial (T2) -> main (T1 high resolution),
main (T1) ->standard
Do you think there is any problem of doing this way? Thanks.
Lihong |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 16 2007 : 12:38:51 PM
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| Yes, that looks like the way I would try it. Let us know if it works! |
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vinod
Average Member
USA
68 Posts |
Posted - Jul 17 2007 : 3:05:20 PM
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| Yes, thats the way I have been doing it and it seems to work reasonably well. Also you don't need to use the full 12 DOF for the first two steps in your FSL registration I think. I would think using just 6 DOF should suffice as they are all from the same subjects and any changes should be either translation or rotation. However, you might need the full 12 DOF for the transformation to standard space. |
Vinod Venkatraman
IPCN Graduate Student
Huettel Lab
"UNIX is basically a simple operating system, but you have to be a genius to understand the simplicity." - Dennis Ritchie |
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wang
BIAC Alum
USA
57 Posts |
Posted - Jul 18 2007 : 07:18:45 AM
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Yes, it works very well. Thanks Syam and Vinod!
Lihong |
lihong |
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wang
BIAC Alum
USA
57 Posts |
Posted - Jul 18 2007 : 10:07:07 AM
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The coregistration seems fine, but when I checked the log file, I got a Warning - registration to initial_highres turned on but
no initial_highres image specified in setup file or in
FEAT directory! Will not register to initial_highres.
It seems it did not use the T2 orientation inital info, but only used the T1 main structural image for registration. Neverthless, the results look okay with the T1 highr_res only, which makes the T2 image less necessary.
Lihong
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lihong |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 18 2007 : 10:16:33 AM
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| Check your .fsf to see if you told it what T2 image to use (initial_highres_files). If that field is not set, then it won't use it. Anyway, if you can get by with just the T1, then that's good too. |
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wang
BIAC Alum
USA
57 Posts |
Posted - Jul 18 2007 : 10:20:27 AM
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I specified in the setting here:
# Session's structural image for analysis 1
# set initial_highres_files(1) "T2ANAT"
# Subject's structural image for analysis 1
set highres_files(1) "T1ANAT"
Do I also need to specify at the end of fsf file?
# Initial structural space registration initialisation transform
set fmri(init_initial_highres) ""
# Structural space registration initialisation transform
set fmri(init_highres) ""
# Standard space registration initialisation transform
set fmri(init_standard) "INITFILE"
Thanks.
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lihong |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 18 2007 : 10:22:59 AM
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| The '#' at the beginning of the line means it is a comment. You will need to remove the '#' to have FEAT read it. |
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wang
BIAC Alum
USA
57 Posts |
Posted - Jul 18 2007 : 10:24:46 AM
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Oh, it was my mistake. Thanks.
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lihong |
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Dichter
BIAC Faculty
190 Posts |
Posted - Jul 29 2007 : 4:48:29 PM
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| I'm running second-level analyses on lower-level feat directories and I'm getting an error message that registration has not been run on the lower level feats, so the second-level analysis cannot proceed. Which settings should I be checking to trouble-shoot this? Thanks. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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petty
BIAC Staff
USA
453 Posts |
Posted - Jul 30 2007 : 09:18:27 AM
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in the lower level analyses make sure registration was done, either on just the template or both template and additional subject brain.
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 30 2007 : 09:32:37 AM
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| To expound on Chris' post, in a first-level analysis .feat directory, you can tell if registration was done and successful if there is a subdirectory called "reg" and if there is a file inside it called example_func2standard.mat. Loading the design.fsf file into the FEAT GUI will tell you whether registration was actually set up in the first place. |
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vinod
Average Member
USA
68 Posts |
Posted - Jul 30 2007 : 2:19:33 PM
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| Also, it is also possible that the registration was set up correctly but the first-level analysis did not complete due to other errors in some sessions. Yeah, so basically I would just go back and look at the log files from the first-level analysis to see if everything worked fine. |
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Dichter
BIAC Faculty
190 Posts |
Posted - Jul 30 2007 : 4:51:55 PM
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| Thanks, all. So when I load the design.fsf file into the GUI, it indiactes to register to my main structural image and to the standard space brain; however, the "reg" folder is not being created??? I guess I should just delete the output folders and try runing the analyis again to see if other errors interupted this. Thanks. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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two antomical images for registration
