[Brains-users] FW: Problem I'm having with Brains2

[Hans Johnson]

------ Forwarded Message
From: Eugene Zeien <eugene-zeien at uiowa.edu>
Date: Wed, 25 May 2005 15:54:10 -0500
To: "Samuel, Ellen K J" <ellen-samuel at uiowa.edu>
Cc: <hans-johnson at uiowa.edu>, <dapeng-li at uiowa.edu>, Eric D Axelson
<eric-axelson at uiowa.edu>, Leigh J Beglinger <leigh-beglinger at uiowa.edu>
Subject: Re: Problem I'm having with Brains2

Hey, Ellen.  How ya been.

The auto-magic function 'save resampled-image' only works well
with our old familiar data.  You will have to resort to using
the 'save image' function and filling in the filename, as well
as selecting the directory where the file is to be saved.
Once you get everything coerced into 'standard' names in the
10_ACPC directory, the auto-magic tools should work smoothly
for the remainder of your standard workup.  I took the liberty
of loading the 3DSPGR, applied the T1.xfrm, and saved as
10_ACPC/dicom-format_10_T1.hdr

We could simply rename the dicom-format_10_Unknown.hdr as
dicom-format_10_T2.hdr (white CSF is T2, right?)

like so,

cd /raid1/IPIG/predict_MR/site-999/demo2/dicom-format/10_ACPC
mv dicom-format_10_Unknown.hdr dicom-format_10_T2.hdr

Let me know if there's anything else I can do.
Samuel, Ellen K J wrote:
> Hi everyone,
> I haven't heard anything about this, so I was wondering if there has
> been any progress made or if there is anything I can do to help out. The
> German site is quite antsy about hearing whether or not we can work up
> the scan.
> 
> Thanks!
> 
> Ellen
> 
> 
>>_____________________________________________
>>From:  Samuel, Ellen K J
>>Sent: Wednesday, May 18, 2005 4:08 PM
>>To: 'hans-johnson at uiowa.edu'; 'dapeng-li at uiowa.edu'; 'Eugene Zeien'
>>Cc: Eric D Axelson; Leigh J Beglinger
>>Subject: Problem I'm having with Brains2
>>
>>Hi Hans, Dapeng and Gene,
>>I'm having a problem with brains2, and I'm not sure if it is
>>bug-worthy or if I am just doing something wrong. This problem has
>>happened twice to me. Here's what happens:
>>
>>I start standard workup. This time I am working with
>>/IPLlinux/raid1/IPIG/predict_MR/site-999/demo2/dicom-format. I got up
>>to the part in standard workup where I am resampling. I resample the
>>T1 and save it and the transform. I resample the T2 and save it and
>>the transforms (xfrm and init). I reopen brains2 and run air on MR5.
>>The standard file and reslice files do not appear. When I go to find
>>them myself the file I get from 10_ACPC is
>>"dicom-format_10_Unknown.hdr" not the "..._10_T1.hdr" that I'm used
>>to. I put the "dicom-format_10_Unknown.hdr" in there anyway and get
>>the T2 from the PDT2 directory. Then I run air. When its done it comes
>>up with the T1 and "unknown" image that is also the T1.
>>
>>Included at the end of this email is an email from me to Dapeng (and
>>his response) from a couple of weeks ago about the same problem I had
>>with a different scan. I just very quickly looked at the scan from a
>>few weeks ago that Dapeng looked at and as far as I can tell the
>>problem is still happening.
>>
>>I wanted to let you guys know about this because I have a feeling that
>>it is going to be a constant problem with all the sites sending all
>>sorts of different files. Please let me know if this is something that
>>I should submit a bug report for. I would be happy to do that.
>>
>>Thanks,
>>Ellen
>>
>>Hi, Ellen,
>>
>>I have change the dir name 00000000 to a MRQID.  As for the problem
>>with Brains2, I have no idea. It might need to check the source code
>>to see what happens there.
>>
>>Dapeng
>>
>>Quoting "Samuel, Ellen K J" <ellen-samuel at uiowa.edu>:
>>
>>
>>>Hi Dapeng,
>>>Eric and I have been having a few problems with 2001 (which I think
>>>might also happen with some of our other files). I think Brains2 is
>>>having problems with the way the files are named. Brains2 can tell
>>>that the raw files in 3DSPGR are T1s, but after the image has been
>>>resampled and saved for some reason Brains2 changes the file type to
>>
>>>"unknown" and saves it as 00000000_10_unknown.hdr instead of
>>>...T1.hdr. Eric and I tried changing the file name to
>>>00000000_10_T1.hdr and Brains2 won't let us open it (the error
>>
>>message 
>>
>>>said something about "0, 256"- sorry, I didn't write it down. If it
>>>would be helpful I can go back and get it for you). I have cc'd Gene
>>
>>>in the hopes that this happens all the time and that his renaming
>>
>>program already fixes all this.
>>
>>>Also, I think Brains2 might be having a problem with the images name
>>
>>>"image0, image1... etc." or else I might just be getting confused by
>>
>>it.
>>
>>>I'm used to "MRQID_#_Image#_.dcm".
>>>One last thing- Eric mentioned it might be good if you could change
>>>the MRQID on this scan to something else other than 00000000. Is
>>
>>that 
>>
>>>possible?
>>>
>>>
>>>Please let me know if this is at all confusing of if you need more
>>>information. We can talk about it some more tomorrow after internal
>>>meeting if that would help.
>>
>>
> 


------ End of Forwarded Message