Got it, this is fantastic, thanks!
Emily
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Barbara Kreilkamp bakk.hbg@googlemail.com Sent: Sunday, September 18, 2016 5:54:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] Unpacking DWI Data
Hi Emily,
Yes, Osirix Lite should be sufficient, I think it works by picking File-import and then File-export-export DICOMs (decompression is sometimes helpful). It should be straightforward, just have a go at it.
Hope it helps.
Best wishes, Barbara
On 19/09/2016 00:36, Emily Louise Belleau wrote:
Hi Barbara,
Thank you so much! I have downloaded Osirix Lite, since regular Osirix costs a pretty penny!
So, once I have imported the dicoms, is it simply a matter of exporting them onto my hardrive where I would like them to be?
Thanks so much!
Emily
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Barbara Kreilkamp bakk.hbg@googlemail.commailto:bakk.hbg@googlemail.com Sent: Sunday, September 18, 2016 3:21:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] Unpacking DWI Data
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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