bdp problem with nii.gz on windows

Forums Forums BrainSuite Diffusion Pipeline (BDP) bdp problem with nii.gz on windows

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    • #101
      steso
      Participant

      Hi guys
      I try to run the distortion correction on some datasets but running into troubles. For once it takes almost 1min until something happens everytime I run bdp.exe (even if I just want to display the help) is this normal? Has it to do with the MCR? Is there a way around?
      Next up, if I feed in a t1 image (bfc corrected, previously generated in BrainSuite), I get a gunzip error:

      Error using gunzip>gunzipwrite (line 184) 
      File "test_t1.bfc.nii.gz" is not in GZIP format. 
      

      I tried to unzip the file myself but then the naming is wrong and I get another error.
      Is there also a way to run just the bfc on a dataset using the commandline instead of clicking in brainsuite?
      By the way, I’m using Windows 7, bdp version 15b (build #0051), BrainSuite 15b (build #2364).

      Thanks in advance

      • This topic was modified 4 years, 12 months ago by steso.
    • #103
      David Shattuck
      Keymaster

      Hi Steso –

      The slow startup is due to MCR. It takes some time to load all of the Matlab libraries, unfortunately. I am not aware of a way to get around it, but we will look into it.

      What did you use to try to unzip it?

      It is possible that the file is corrupt. Does the BrainSuite gui open it correctly?

      thanks,
      David Shattuck

    • #104
      steso
      Participant

      I can open the T1 in BrainSuite without any problems, also in mricron or unzip it with 7-zip, no problem. The error occurs when running the distortion correction in bdp:

      bdp.exe t1.bfc.nii.gz –nii dwi.nii –bmat table.mat –dwi-mask mask.nii

      Reading input flags…

      Checking input files…
      Error using gunzip>gunzipwrite (line 184)
      File “t1.bfc.nii.gz” is not in GZIP format.

      Error in gunzip>gunzipEntries (line 122)

      Error in gunzip (line 64)

      Error in load_untouch_nii_gz (line 53)

      Error in check_nifti_file (line 40)

      Error in bdp_setup (line 745)

      Error in BrainSuite_Diffusion_pipeline (line 14)

      MATLAB:gunzip:notGzipFormat

      Best

      Stefan

      • #107
        cbhushan
        Moderator

        Hi Stefan,

        Are you able to process other subjects successfully with bdp?

        Would it be possible for you to send all the files which you used in this particular run (t1.bfc.nii.gz, dwi.nii, table.mat, mask.nii) to us? If yes, please email the details on our support email address.

    • #108
      steso
      Participant

      Hi

      I started from scratch, regenerated the bfc file in BrainSuite and now it’s working! Probably, the file was still somehow corrupted even though I was able to open it in other tools.
      I’ll keep you posted if I run into other problems.
      Thanks again

      Best

      Stefan

      • #109
        David Shattuck
        Keymaster

        Hi Stefan –

        I’m glad to hear it is working now. My best guess is that the file was uncompressed at some point, but retained the .gz extension. The file readers that I use in the GUI and command line tools will open files whether they are compressed or not, regardless of the extension, but the readers used in BDP will explicitly decompress .gz files before processing them. If you are curious and still have the original file, you could check whether or not the files is the same size as your uncompressed volume.

        thanks,
        David Shattuck

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