Hi,
After editing a text file holding the b vecs to be supplied as input to dt_recon this tool did not interpret the text file correctly. It turned out that dt_recon did not recognise the end-of line character in this file: this was decimal code 13 (called "CR"). It seems that dt_recon only accepts decimal code 10 (called "LF"). Is it possible to change dt_recon?
I'm on a Mac, OSX 10.6.8.
Cheers, Ed
On 11/9/11 07:59 , Ed Gronenschild wrote:
After editing a text file holding the b vecs to be supplied as input to dt_recon this tool did not interpret the text file correctly. It turned out that dt_recon did not recognise the end-of line character in this file: this was decimal code 13 (called "CR"). It seems that dt_recon only accepts decimal code 10 (called "LF"). Is it possible to change dt_recon?
What did you use to edit the b-vec file? Different operating systems use different end-of-line (EOL) conventions on text files:
Windows: <cr><lf> "Old"-style (and largely depreciated) Mac: <cr> Unix (including Mac and Linux): <lf>
My guess is that you might have used a (possibly old) Mac-based editor to edit your file. Often such editors have the option to save as "UNIX" format. Choose that.
It's not necessary to change 'dt_recon'. Simply convert your old-style Mac <cr> text file to a new style <lf> file with:
sed s/x0d/x0a/ old-b-vec-file> new-b-vec-file
This replaces the '0x0d' (10 in hex) characters in the file with '0x0a' (13 in hex).
For more details, see: http://www.peterbenjamin.com/seminars/crossplatform/texteol.html
Hi Rudolph,
I used TextEdit. On a Mac with OS version earlier than OS10.6 this problem didn't occur. With TextEdit it is not possible to save as UNIX format. Thanks for the trick to use sed.
Ed
On 9 Nov 2011, at 15:27, Rudolph Pienaar wrote:
On 11/9/11 07:59 , Ed Gronenschild wrote:
After editing a text file holding the b vecs to be supplied as input to dt_recon this tool did not interpret the text file correctly. It turned out that dt_recon did not recognise the end-of line character in this file: this was decimal code 13 (called "CR"). It seems that dt_recon only accepts decimal code 10 (called "LF"). Is it possible to change dt_recon?
What did you use to edit the b-vec file? Different operating systems use different end-of-line (EOL) conventions on text files:
Windows: <cr><lf> "Old"-style (and largely depreciated) Mac: <cr> Unix (including Mac and Linux): <lf>
My guess is that you might have used a (possibly old) Mac-based editor to edit your file. Often such editors have the option to save as "UNIX" format. Choose that.
It's not necessary to change 'dt_recon'. Simply convert your old-style Mac <cr> text file to a new style <lf> file with:
sed s/x0d/x0a/ old-b-vec-file > new-b-vec-file This replaces the '0x0d' (10 in hex) characters in the file with '0x0a' (13 in hex).
For more details, see: http://www.peterbenjamin.com/seminars/crossplatform/texteol.html
-- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA
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On 11/9/11 09:36 , Ed Gronenschild wrote:
Hi Rudolph,
I used TextEdit. On a Mac with OS version earlier than OS10.6 this problem didn't occur. With TextEdit it is not possible to save as UNIX format. Thanks for the trick to use sed.
Ed
I'm not a great fan of the built in 'TextEdit'. That having been said, did you check under its preferences and make sure that it is setup as 'plain text' and not 'rich text'? I just tested on my TextEdit (Lion, 10.7.2) and it saved in <lf> and not <cr> convention.
You might try 'aquamacs' on the Mac... assuming you're an emacs-ish type person. It works reasonably well. Another editor is "TextWrangler" (available in the Mac OSX App Store for free). If you look in its preferences, under "Text Files" there is an explicit option to save as "Classic Mac, UNIX, or Windows". The default is "UNIX".
Oh, and make sure that the 's/x0d/x0a/' are enclosed in single quotes. I see that my copy-paste in the earlier email somehow lost the quotes. If you have a file called "file1.txt" and want to do the <cr>/<lf> sub and save to "file2.txt", the exact command is
sed 's/0xd/xoa/' file1.txt > file2.txt
HTH
On 11/9/11 09:49 , Rudolph Pienaar wrote:
sed 's/0xd/xoa/' file1.txt > file2.txt
sed 's/0xd/x0a/' file1.txt > file2.txt
Oops... critical typo.
freesurfer@nmr.mgh.harvard.edu
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Ed Gronenschild -
Rudolph Pienaar