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xu
Junior Member
25 Posts |
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syam.gadde
BIAC Staff
USA
421 Posts |
 Posted - Mar 21 2008 : 1:55:13 PM
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This is a gzip-compressed "tar" file, so unzip won't work. You can uncompress and extract this data using:
tar -xvzf buckner_data-tutorial_subjs.tar.gz |
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xu
Junior Member
25 Posts |
Posted - Mar 21 2008 : 2:52:40 PM
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Thanks Syam.
quote:
Originally posted by syam.gadde
This is a gzip-compressed "tar" file, so unzip won't work. You can uncompress and extract this data using:
tar -xvzf buckner_data-tutorial_subjs.tar.gz
I tried following:
[xu@golgi: .../FreeSurfer_Data] $ tar -xvzf buckner_data-tutorial_subjs.tar.gz
tar: Not a recognized flag: z
Usage: tar -{c|r|t|u|x} [-BdFhilmopsvw]
[-Number] [-fFile]
[-bBlocks] [-S [Feet] [Feet @Density] [Blocksb]]
[-LInputList] [-NBlocks] [-C Directory] File ...
[xu@golgi: ... /FreeSurfer_Data]$ tar -xvf buckner_data-tutorial_subjs.tar.gz
tar: 0511-169 A directory checksum error on media; 0 not equal to 70436.
What is wrong above?
Thanks,
Amy
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 21 2008 : 2:55:01 PM
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Apparently tar on golgi does not support uncompression. Try:
gzip -dc buckner_data-tutorial_subjs.tar.gz | tar -xvf - |
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xu
Junior Member
25 Posts |
Posted - Mar 21 2008 : 4:08:30 PM
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Thanks Syam, I got.
But end of uncompression file I got message as:
gzip: buckner_data-tutorial_subjs.tar.gz: unexpected end of file
tar: 0511-169 A directory checksum error on media; 1 not equal to 64078.
Should I ignore this message?
Amy
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 21 2008 : 4:15:22 PM
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It's unclear why you got the error message. However, you can verify that the output is the right size like this:
gzip -l buckner_data-tutorial_subjs.tar.gz
That will tell you what the compressed and uncompressed size of the total data is in bytes. Then you can find out how much space is used in the output directory (I don't know what it is called, so I'm calling it buckner_data-tutorial_subjs) in kilobytes:
du -k -s buckner_data-tutorial_subjs
The first number should be around 1000 times the second (They won't be exact) |
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xu
Junior Member
25 Posts |
Posted - Mar 21 2008 : 4:34:41 PM
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Thanks Syam,
I tried:
[xu@golgi: ... /FreeSurfer_Data] $ gzip -l buckner_data-tutorial_subjs.tar.gz
compressed uncompr. ratio uncompressed_name
628658632 187534915 -235.2% buckner_data-tutorial_subjs.tar
[xu@golgi: ... /FreeSurfer_Data] $ du -k -s Buckner_data
912324 Buckner_data
Above shows uncompressed files are much smaller than compressed one, right?
Amy |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 24 2008 : 10:56:36 AM
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I think it means that the standard gzip/tar on golgi can't handle the size of this tar file.
I installed an updated version of tar, maybe this will work better:
/usr/local/packages/tar-1.14/bin/tar -xvzf buckner_data-tutorial_subjs.tar.gz |
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xu
Junior Member
25 Posts |
Posted - Mar 24 2008 : 11:38:08 AM
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Syam,
Thanks a lot. I got same results and closer error message as before:
gzip: stdin: unexpected end of file
/usr/local/packages/tar-1.14/bin/tar: Unexpected EOF in archive
/usr/local/packages/tar-1.14/bin/tar: Unexpected EOF in archive
/usr/local/packages/tar-1.14/bin/tar: Error is not recoverable: exiting now
Amy
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 24 2008 : 11:56:11 AM
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It looks like your tar.gz file is not complete? I looked at the freesurfer download ftp site, and the file looks like it should be 7GB?
7141194279 buckner_data-tutorial_subjs.tar.gz
But it looks like your file is only 600MB or so? (628658632) |
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xu
Junior Member
25 Posts |
Posted - Mar 24 2008 : 2:06:51 PM
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Syam,
Do you know why I got following problem:
[xu@golgi: /] $ ftp surfer.nmr.mgh.harvard.edu
ftp: connect: A remote host did not respond within the timeout period.
Thanks,
Amy |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 24 2008 : 2:10:14 PM
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| You cannot access servers outside of BIAC from golgi, apparently. |
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Topic |
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Problem on unzip FreeSurfer Tutorial Data
