Hi Doug, When I try the command as you suggested: recon-all -all -s unpack3 I get the following error:
ERROR: no run data found in /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. Make sure to have a volume called 001.mgz in /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/orig Do you know why I might be lacking that volume? This was not usually an issue after running the two unpacksdcmdir commands (for MPRAGE and bold runs). Thanks, Adam On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > 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. > >
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