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mb
BIAC Alum

27 Posts
Posted - Nov 03 2004 :  1:45:33 PM  Show Profile  Reply with Quote
When there are missing slices and the tech is able to recover the data, is it possible to not have copy01 appended to the good images or is there some script that will quickly rename them?

Thanks,
Mary Beth

jimmy.dias
BIAC Alum

USA
210 Posts
Posted - Nov 03 2004 :  3:34:25 PM  Show Profile  Visit jimmy.dias's Homepage  Reply with Quote
Hi Mary Beth,

All images associated with pfiles that have missing slices will be put into a directory name prepended with "missing_slices_". If the tech is able to recover data that originally had missing slices, you'll see the complete image set in the runXXX_YY directory. The missing slices image set will still be accessible in the missing_slices_runXXX_YY directory but is named so that it will not be used by bputil. That change will be deployed today. Other fixes had been made to cope with the missing slices problem but have now been scrapped. If, at any time after today, you encounter a run directory that has missing slices and is not in a "missing_slices" directory, email me the exam number, the experiment ID (e.g. Study.01), and the run number and I'll look into it.

Those of you since Oct 22nd of this year may have had the full dataset recovered afterwards by the tech. In these cases you should see all the resulting images in the runXXX_YY directory. All these images should be of the same filesize and at the most one or two should have copy01 appended to the filenames. Look at the filesizes to determine which one has the full image. If you can't determine which one has the full image, email me with the exam number and date and I'll see what I can do. Remember that this is only for those datasets that were immediately recovered by the tech, NOT just for any studies with missing slices.

Hope that helps,
Jimmy
Edited by - jimmy.dias on Nov 03 2004 3:55:53 PM
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charles.michelich
BIAC Alum

USA
183 Posts
Posted - Nov 03 2004 :  5:33:18 PM  Show Profile  Reply with Quote
You cannot tell if you have missing slices from the size of the image files because the recon still writes out the full image file size even if the raw data is missing.

You need to read the data and visually inspect it for missing slices. You can usually identify missing slices by looking at the time course of a voxel inside the brain in each slice. There is not a BXH file for the copy01 files so the easiest way to read them is using the 'Volume' format in readmr. For example:
img = readmr('V*.img_copy01',{'Volume',[xSz ySz zSz]});
showsrs2(img);
where xSz, ySz, zSz are the dimensions of the image.

Enjoy,
Chuck
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