mri_convert does, but how will you know left from right?

On Tue, 12 Aug 2008, [GB2312] ÀîÈÕ wrote:

I can't get access to the original dicoms, does the mri_convert command have some options to change the .img data to the right .mgz format data? And why the .img has this problem. thanks, and my english is poor,sorry.

2008/8/12, Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

the problem is using .img (analyze) format. Can you get access to the original dicoms?

On Tue, 12 Aug 2008, [GB2312] ÀîÈÕ wrote:

Hi Bruce Fischl,

...

I started with the .img and .hdr data, First I used command 'mri_convert' and convert the data to .mgz format. and then I used tkmedit to display. Can you tell me how to correct it?

thanks

Tim

2008/8/11, Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Tim,

can you tell us what form the data that you started with was in? Something is wrong with the direction cosines as tkmedit is displaying the brain upside-down (and it thinks that sagittal is horizontal).

cheers, Bruce

On Mon, 11 Aug 2008, [GB2312] ÀîÈÕ wrote:

Hello:

...

I am a new to FreeSurfer, and i run the following command : recon-all -autorecon1 -s temp , and it exit with some errors:

Mon Aug 11 15:49:56 CST 2008 talairach_avi done

cp transforms/talairach.auto.xfm transforms/talairach.xfm

#-------------------------------------------- #@# Talairach Failure Detection Mon Aug 11 15:49:57 CST 2008 /home/liri/liri/freesurfer/subjects/temp/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux liri-desktop 2.6.24-19-generic #1 SMP Fri Jul 11 23:41:49 UTC 2008 i686 GNU/Linux

recon-all exited with ERRORS at Mon Aug 11 15:49:57 CST 2008

I have seen that it might be caused by the direction cosines in the input file were all wrong (coronal, saggital, horizontal wrong). so I checked the nu.mgz, and it displays

different from the bert subject, if this is the reason , how can i correct it.

thanks tim