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jimmy.dias
BIAC Alum
USA
210 Posts |
 Posted - Apr 08 2005 : 12:21:24 PM
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Hi all,
Those of you who ran scripts coreg_normalize or normalize on Golgi between January 24, 2005 and April 07, 2005 (8:34 a.m), the output BXH file specifies incorrectly that the orientation of the data is in 'LAS' order instead of the correct 'RAS' order.
Any processing steps that have been run on the output of coreg_normalize and normalize will also have incorrect orientation information in the output BXH files. These headers too will need to be fixed.
Orientation snapshot throughout SPM99 pipeline:
Assuming an initial orientation of LPI.
LPI -> tralign -> LPI
LPI -> motioncorrection -> LPI
LPI -> LAS -> normalization -> RAS
RAS -> smooth -> RAS
Data orientation is preserved i.e. output has same orientation as input, when using tralign, smooth, and motioncorrect. With normalize and coreg_normalize however, orientation is not preserved as the input is first reoriented to 'LAS' to match the SPM99 template, and then flipped L-R during SPM99 normalization to finally output a 'RAS' ordered dataset.
I'm working on a script that will search the storage servers and fix these incorrect bxh files. In the interim, if you'd like to run any processing/analysis requiring correct orientation information on normalized datasets preprocessed during the above time period do the following:
Check orientation by doing the following in MATLAB:
getorientation(readmr('run004_01.bxh'))
If orientation is in 'LAS' order, use bxhsetorient at the Golgi prompt to fix this header.
e.g. bxhsetorient --inplace RAS ncrun004_01.bxh
Jimmy
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dagenbach
Starting Member
4 Posts |
Posted - Apr 10 2005 : 10:49:25 PM
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| I just re-preprocessed subjects I ran this spring using bputil on Golgi. I was looking at the snra's using showsrs2 and they no longer automatically specify the orientation. They used to automatically specify the orientation as "Custom RAS Flag" and RAS Flag as "ras". |
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jimmy.dias
BIAC Alum
USA
210 Posts |
Posted - Apr 11 2005 : 09:07:06 AM
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Hi Elise,
So I've looked at snra's in your processing directory (/data/users/dagenbac/bputil) for exams 20050330_44553, 20050324_44528,
and 20050323_44519 and they all have orientation information in the BXH file. Which subject are you referring to?
Jimmy |
Edited by - jimmy.dias on Apr 11 2005 09:07:43 AM |
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dagenbach
Starting Member
4 Posts |
Posted - Apr 11 2005 : 09:42:54 AM
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Hi Jimmy,
If you're here, would you mind coming downstairs to look at this? Things still look funny.
Thank you-
Elise |
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Topic |
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Golgi spm99 preprocessing orientation
