Hi All,
I'm trying to use recon-all on some structural data, and when I drop the command (specifically, recon-all -i /cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid SPAR_016_130708), I get this error message:
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 continuing an analysis of an existing subject, then omit all -i flags.
I have tried all the options suggested in the error message, and none work. I can't delete the subject folder, because no such folder exists. I tried running the command with a different subject name, and although the command appeared to complete without error, no folder with the new name was created, and no files were generated. I tried removing the -i flags, and I got this: ERROR: nothing to do.
Any suggestions?
Thanks, Joe Andreano
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Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________
are you looking in the right place? Look in $SUBJECTS_DIR, not the current directory doug
On 8/5/13 5:45 PM, Joseph Andreano wrote:
Hi All,
I'm trying to use recon-all on some structural data, and when I drop the command (specifically, recon-all -i /cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid SPAR_016_130708), I get this error message:
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 continuing an analysis of an existing subject, then omit all -i flags.
I have tried all the options suggested in the error message, and none work. I can't delete the subject folder, because no such folder exists. I tried running the command with a different subject name, and although the command appeared to complete without error, no folder with the new name was created, and no files were generated. I tried removing the -i flags, and I got this: ERROR: nothing to do.
Any suggestions?
Thanks, Joe Andreano
Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Joe
try adding -all to the end. You need to specify a directive for it to carry out
cheers Bruce On Mon, 5 Aug 2013, Joseph Andreano wrote:
Hi All,
I'm trying to use recon-all on some structural data, and when I drop the command (specifically, recon-all -i /cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid SPAR_016_130708), I get this error message:
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 continuing an analysis of an existing subject, then omit all -i flags.
I have tried all the options suggested in the error message, and none work. I can't delete the subject folder, because no such folder exists. I tried running the command with a different subject name, and although the command appeared to complete without error, no folder with the new name was created, and no files were generated. I tried removing the -i flags, and I got this: ERROR: nothing to do.
Any suggestions?
Thanks, Joe Andreano
Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Joseph Andreano