Got it, this is fantastic, thanks!
Emily ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Barbara Kreilkamp <bakk....@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Barbara Kreilkamp <bakk....@googlemail.com><mailto:bakk....@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
