[David Shattuck]

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

[steso]

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

[Anonymous]

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.

[steso]

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

[David Shattuck]

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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