Hello users, I am trying to get Freesurfer (5.2) working properly off-site and am encountering errors I did not have while working at the Martinos center. We use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data is similar to work with.
I have been using dcmunpack since unpacksdcmdir is not identifying the DICOM files properly. I have successfully unpacked the structural and bold scans using the command (entered from the raw scan data folder: dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2 MPRAGE nii struct (I also tried using mgz instead of nii, and also changed struct to other things as it appears to be a naming argument) dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast -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 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii (path) just being an abbreviate piece of the relevant pathway These generate the MPRAGE and bold folders in the subject folder as expected. I have difficulties with the next commands (environment has been set). I try: recon-all -i <path to structural data> -s <subject name> -force recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3 (I got an error about using -force so I omitted that from my command) and get the following Error ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. Yet when I omit -i and just use "recon-all -s unpack3", I get "ERROR: nothing to do" I tried a different tactic and used "recon-all -s unpack3 -autorecon1" as well as "recon-all -autorecon-all -s unpack3" which both created the various folders (bem, label, mri, surf, etc) but failed with "ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri. Make sure to have a volume called 001.mgz in (path)/FreesurferPractice/unpack3/mri/orig. If you have a second run of data call it 002.mgz, etc." I have tried these commands in both bash and tcsh shells with the same effect. So the problem, it seems, is that my "mri" file is blank, and this was not a problem I had running these commands at Martinos. Any idea what the issue might be? Best, Adam Nitenson Neuroscience Graduate Program Laboratory of Affective Neuroscience Brown University
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