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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