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