Hi Emily,
I've never tried to use unpacksdcmdir but you may try the Osirix tool,
it allows you to read in a dicom folder and save a new folder with
subfolders according to the sequences that were run. At the same time
you can also anonymize your data.
Does this help?
Best wishes,
Barbara
On 17/09/2016 22:17, Emily Louise Belleau wrote:
Hello Freesurfer Experts,
Our research team has recently collected data from Martinos Center.
The entire scanning protocol (including anatomical, functional runs,
DWI) is in one directory.
Therefore I have been using unpacksdcmdir to tell me what runs go with
each scanning sequence. I have had no trouble unpacking the functional
and anatomical runs. I have had difficulties unpacking the DWI data.
I have been recently warned that unpackdcmdir does not correctly
unpack DWI data. Is there a work around or another tool I could use?
It seems that most tools are for unpacking per run (dcmtonii), and
would not work in my situation where all scans are in one folder?
The runs that say "err" which typically indicated something is missing
in the scan appear to be unpacking. However, it does say on the
terminal that there is an error but attempting to unpack anyway.
Some of the runs that say "ok" in the scan log are not unpacking
properly. Additionally, we are finding that when we unpack on of the
DWI sequences we used, we get bvec and bval files. However, we do not
when we unpack a different DWI sequence we also ran we do not get the
corresponding bvec and bval files.
The command I am using, where I put related runs into related folders:
unpacksdcmdir -src dicomdir -targ targetdir -fsfast \
-run 2 bold nii f.nii \
-run 3 bold nii f.nii \
-run 4 bold nii f.nii \
-run 5 bold nii f.nii \
-run 6 bold nii f.nii \
-run 8 3danat mgz 001.mgz \
-run 9 3danat mgz 001.mgz
Any help would be great appreciated! Thanks!
Rmily
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