> > Hi Doug, > > The command runs a bit further now but then exits with errors. > Unfortunately this time there is no specific stated error. The last few > lines of the log are: > > INFO: extension is mgz > #-------------------------------------------- > #@# Talairach Tue Jun 4 13:22:08 EDT 2013 > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack4/mri > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > Linux node271 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 01:55:29 UTC > 2012 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s unpack4 exited with ERRORS at Tue Jun 4 13:22:10 EDT 2013 > > > > The only other section of the log that seems like it could be related to > an error is: > > Can't locate MNI/Startup.pm in @INC (@INC contains: > /gpfs/runtime/opt/perl/5.16.0/lib > /gpfs/runtime/opt/perl/5.16.0/lib/site_perl /usr/local/lib64/perl5 > /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > BEGIN failed--compilation aborted at > /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > > So, I'm not sure what it's not liking here. > > Thanks again, > Adam > > > On Tue, Jun 4, 2013 at 11:44 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> That dcmunpack command will put the data into a file called >> unpack3/MPRAGE/002/struct.nii >> It needs to be put into upack3/mri/orig/002.mgz >> doug >> >> >> >> >> On 06/04/2013 11:22 AM, Nitenson, Adam wrote: >> >>> 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 >>> <mailto:gr...@nmr.mgh.harvard.**edu<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 >>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> > >>> >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >>> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> Fax: 617-726-7422 <tel:617-726-7422> >>> >>> Bugs: >>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: >>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>> >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> >>> Outgoing: >>> >>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >>> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >>> >>> >>> >> -- >> 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >
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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.
