Hi Adam, if the subject folder exists and you pass recon-all a -i flag, then it will exit with error saying that the data exist (otherwise it would overwrite what is there). However, just because the subject folder exists does not mean that there is any data sitting in subject/mri/orig. Then it will tell you that it cannot find any data.
Note that when you run recon-all, you need to tell it to do something (eg, add the "-all" flag to do everything) doug On 06/03/2013 03:21 PM, Nitenson, Adam wrote: > 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
