| T O P I C R E V I E W |
| wang |
Posted - Jul 16 2007 : 07:18:47 AM
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 |
| 15 L A T E S T R E P L I E S (Newest First) |
| vinod |
Posted - Jul 30 2007 : 11:26:51 PM
No worries :). Everytime we change analysis types from the standard, I guess its better to generate the template again using the GUI for the type of analysis we want to run rather than modify the previous template. It is definitely not obvious how these flags are set for these analysis. Like there in no way its obvious why the poststats_yn = 1 will not do registration but poststats_yn = 0 will do registration.
I still envy how you tried out pre-stats (motion correction and slice timing correction) in less than 10 mins. Mine takes at least an hour if not more on golgi. I knew golgi was slow but didnt think the performance difference was this drastic! |
| Dichter |
Posted - Jul 30 2007 : 11:20:11 PM
Vinod saved the day: my template fsf file had fmri(poststats_yn) set to 1. Apparently that setting was causing problems via batch scripts but not via the GUI. Setting it to zero resolved the issue. Thanks, Vinod! |
| vinod |
Posted - Jul 30 2007 : 8:19:16 PM
If you modify the .fsf manually from outside GUI, this is highly possible. There are a lot of flags in the .fsf file which the GUI automatically updates, but you overlook when you manually change. For instance, you can go into the .fsf file and say "set fmri(analysis) 6" to run stats + post-stats only. But unless you also go and change the "set fmri(filtering_yn) 1" to 0, it will still perform pre-processing. But if you run through the GUI, the flag gets automatically updated. I learnt this the hard way :).
So, I would recommend checking all the registration based flags in your .fsf file. For example, there is a flag called reg_yn, make sure that is not a zero. SAme with other flags like reginitial_highres_yn and regstandard_yn. Another way to look for differences between what happens with the .fsf file you created and the design.fsf file which is created when running from the GUI using the "diff" command. |
| syam.gadde |
Posted - Jul 30 2007 : 7:59:04 PM
Not sure why identical .fsf files are doing different things...
For the failed run, the report.log file will tend to have errors listed in it. Generally you want to find the first error that crops up there. Any clues there? |
| Dichter |
Posted - Jul 30 2007 : 7:30:23 PM
So, I killed all jobs, deleted everything, and started the batch script over. Once again, the first lower-level analysis folder had no 'reg' folder (the line "rm -rf prefiltered_func_data*" is the last thing in the log file), but running the analysis via the GUI with the identical fsf file created the reg folder. Has anyone else encountered this?? |
| Dichter |
Posted - Jul 30 2007 : 6:46:34 PM
Thanks so much. The log file simply ends just before the "/bin/mkdir reg" command should appear. Re-running a run "manually" with the same fsf file appears to correct the problem.
Apparently, large batch jobs don't always go smoothly. Have others encountered this? |
| vinod |
Posted - Jul 30 2007 : 5:00:12 PM
Then it looks likely that there are some other errors in your lower level analysis. Can you look at the report.log file in the same folder and look for errors? Also is there a stats folder created? If even the stats folder is not created, then it indicates that there is some other error thats preventing the analysis from proceeding, like faulty three-column format file. |
| Dichter |
Posted - Jul 30 2007 : 4:51:55 PM
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. |
| vinod |
Posted - Jul 30 2007 : 2:19:33 PM
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. |
| syam.gadde |
Posted - Jul 30 2007 : 09:32:37 AM
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. |
| petty |
Posted - Jul 30 2007 : 09:18:27 AM
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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| Dichter |
Posted - Jul 29 2007 : 4:48:29 PM
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. |
| wang |
Posted - Jul 18 2007 : 10:24:46 AM
Oh, it was my mistake. Thanks.
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| syam.gadde |
Posted - Jul 18 2007 : 10:22:59 AM
The '#' at the beginning of the line means it is a comment. You will need to remove the '#' to have FEAT read it. |
| wang |
Posted - Jul 18 2007 : 10:20:27 AM
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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