mri_convert problem

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Scott.H.Johnson＠Dartmouth.EDU

14 Jun 2004 14 Jun '04

3:54 p.m.

Hello,

We are tryying to convert some raw images from our GE LX scanner into cor format using "mri_convert" with plans to do inflation etc.

We have tried a number of ways (see below) to no avail. The program tells us it is "reading images from 001/I.001," but never comes back..... If anyone has any suggestions, I would be very grateful. I am certain that we are overlooking something really obvious.....

mri_convert 001/I.001 ./anat1

mri_convert -ot cor 001/I.001 ./anat1

note that we have the structure subjectID/mri/orig

within the dir "orig" we have 001 002 003 and each contains a 124 slice spgr consecutively numbered starting with I.001

"orig" also contains empty anat1 anat2 anat3 dirs

Many thanks,

Scott

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Bruce Fischl

15 Jun 15 Jun

9 a.m.

have you tried specifying the input type? What error do you get?

Bruce

On 14 Jun 2004, Scott H. Johnson wrote:

...

Hello,

We are tryying to convert some raw images from our GE LX scanner into cor format using "mri_convert" with plans to do inflation etc.

We have tried a number of ways (see below) to no avail. The program tells us it is "reading images from 001/I.001," but never comes back..... If anyone has any suggestions, I would be very grateful. I am certain that we are overlooking something really obvious.....

mri_convert 001/I.001 ./anat1

mri_convert -ot cor 001/I.001 ./anat1

note that we have the structure subjectID/mri/orig

within the dir "orig" we have 001 002 003 and each contains a 124 slice spgr consecutively numbered starting with I.001

"orig" also contains empty anat1 anat2 anat3 dirs

Many thanks,

Scott

Darren Weber

22 Jun 22 Jun

7:04 p.m.

Hi Scott,

this might be a work around, in case you need something quickly. I put some of Soheil's matlab code into the mri_toolbox at http://eeg.sf.net/ and it should read your GE data OK. See the ge_series_read, ge_series2avw and the avw2cor functions, their documentation is available via the matlab help command and here online,

http://eeg.sourceforge.net/mridoc/index.html

I've not tried to do this with mri_convert, so I can't comment on that.

Best, Darren

Scott H. Johnson wrote:

...

Hello, We are tryying to convert some raw images from our GE LX scanner into cor format using "mri_convert" with plans to do inflation etc.

We have tried a number of ways (see below) to no avail. The program tells us it is "reading images from 001/I.001," but never comes back..... If anyone has any suggestions, I would be very grateful. I am certain that we are overlooking something really obvious.....

mri_convert 001/I.001 ./anat1 mri_convert -ot cor 001/I.001 ./anat1

note that we have the structure subjectID/mri/orig

within the dir "orig" we have 001 002 003 and each contains a 124 slice spgr consecutively numbered starting with I.001

"orig" also contains empty anat1 anat2 anat3 dirs

Many thanks, Scott

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Bruce Fischl
Darren Weber
Scott.H.Johnson＠Dartmouth.EDU