| Author |
 Topic  |
|
|
rkozink
Junior Member
31 Posts |
 Posted - Apr 12 2006 : 3:53:09 PM
|
I have three subjects that I have preprocessed (two visits, three runs per visit) using SPM and I am now trying to run a block analysis with mrtest. Two of the three subjects have processed fine and have produced t-maps that look fine. Both of these subjects were scanned in September of last year. My third subject, who was scanned last month, has preprocessed okay (as best as I can tell), but is producing t-maps as shown below. All subjects were preprocessed and analyzed in the same manner.
I appreciate any ideas.
Rachel |
|
|
petty
BIAC Staff
USA
453 Posts |
Posted - Apr 13 2006 : 08:59:18 AM
|
can't see the image ...
you have to save it somewhere everyone has access and link it from there. |
 |
|
|
tharsh
BIAC Faculty
USA
76 Posts |
Posted - Apr 13 2006 : 09:49:56 AM
|
Also- was this the 3T or 4T, EPI or spiral (although seeing the image may make this info unnecessary)? And any problems apparent in the QA?
|
***********************
Todd Harshbarger
Instructor
BIAC, Duke University
todd.harshbarger@duke.edu
*********************** |
|
|
|
rkozink
Junior Member
31 Posts |
Posted - Apr 13 2006 : 10:19:39 AM
|
Sorry about the previous image attempt. All scans were on the 4T, spiral. Here goes again...
Thanks
Rachel |
|
|
|
rkozink
Junior Member
31 Posts |
Posted - Apr 17 2006 : 10:04:00 AM
|
For this data, I had to create .hdr files using bxh2analyze so that I could process the data in SPM. In attempts to discover what may have gone wrong, I decided to go back and recreate the .hdr files and try preprocessing the data again. The first time I used bxh2analyze, I created new .hdr and .img files. This time I decided to just produce the .hdr files since I already .img files from the original scan. I received the following error when using bxh2analyze:
Warning: this machine's byte order does not match the byte order of the data described in the XML file. If you are writing .hdr files to match already existing data, be aware that the byte order may be incorrect.
I don't know what this means and if this could be the source of my problem. I appreciate any help.
Rachel |
|
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Apr 17 2006 : 11:19:28 AM
|
The Analyze 7.5 format requires that the metadata in the .hdr files be in the same byte order as the .img files. bxh2analyze, like most tools that write Analyze 7.5 data, writes data in the byte order of the machine you are running on. bxh2analyze is warning you that it has noticed that the byte-order of the data for which you are creating .hdr files is different than the current machine's byte order, so the byte orders of the new .hdr files and the old. img files are not likely to match. However, if you create new .hdr and .img files, they are guaranteed to match.
I would recommend either creating both .hdr and .img files, or, if your data is little-endian (you should see lsbfirst in the .bxh file) you can also run bxh2analyze on a BIAC Windows machine (in \\gall\programs\BXH\bin\bxh2analyze) which is a little-endian platform. |
|
|
|
rkozink
Junior Member
31 Posts |
Posted - Apr 18 2006 : 08:11:45 AM
|
Syam,
I created both the .hdr and .img files, which eliminated the warning message that I was seeing, but my mrtest tmaps still look as they did before.
Rachel |
|
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Apr 18 2006 : 09:07:33 AM
|
| Sorry, I didn't mean to imply that this would solve your root problem. Just wanted to make sure you weren't compounding the issue. Unfortunately, I'm not familiar with mrtest at all, but I can say that the byte-order issue is probably unrelated. If everything was working correctly, what should the output of mrtest look like? |
|
|
|
rkozink
Junior Member
31 Posts |
Posted - Apr 21 2006 : 10:34:14 AM
|
| Thanks everyone for their help. I was able to resolve the problem by using an older version of bxh2analyze to generate the .hdr and .img files. |
|
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Apr 21 2006 : 10:47:49 AM
|
quote:
Originally posted by rkozink
Thanks everyone for their help. I was able to resolve the problem by using an older version of bxh2analyze to generate the .hdr and .img files.
I'm very curious to know what might have changed between
versions to cause your problem. Can you run:
bxh2analyze --version
with both versions so that I know what versions to look at?
Thanks!
|
|
|
|
rkozink
Junior Member
31 Posts |
Posted - Apr 21 2006 : 2:25:58 PM
|
| Initially, I was using version 1.8.5pre. I got the older version from the following folder on gall: BXH\bin.old_20050105 |
|
|
| |
Topic |
|
mrtest
