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