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 

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!

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