yea, can you post the log file of both the successful and failing runs? On 05/19/2016 11:28 AM, Aloi, Joseph wrote: > > Hi Doug, > > No that’s not how I usually store my files- I have a folder for the > particular study that I am working on then the dicoms for each subject > in that study are stored in individual subject folders within the > study folder. > > I got a chance to look around the recon-all logs this morning for a > subject that I had successfully processed in the past (but that I get > the error when I try to process this same dataset now). From > comparing the recon-all log from when recon-all ran successfully > versus now, things are running fine up until it gets to MRI_convert. > However, it looks like things are actually starting to go haywire > during MRI_convert even before I get the warning about the ASCII > header and recon-all exits. It appears that MRI_convert is having > some trouble with extracting some of the information it needs from the > dicom file, resulting in the error that I posted. I know you guys are > busy, but would you be able to take a look at the log files? I’ve > only been using freesurfer a few weeks, so I would definitely > appreciate any insights you might have from looking at the log files. > > Thank you! > > I don't have any idea what is going wrong. I noticed that the file > that it is having problems with is here > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm > Do you really keep all your dicom files in that location? > > > > On 05/17/2016 11:47 PM, Aloi, Joseph wrote: > > Hi Doug, > > Sorry- I've added entire correspondence onto the end of this > e-mail. I don't think the disk filled up as I am on a 3 TB hard drive > and I still have ~2 TB of free space on my disk. Anything else you > think it could be? > > Thanks! > > Joseph Aloi > > Please remember to include previous correspondence otherwise we can't > > keep track of the problem! > > Eg, I don't have the previous email to see what the error was. Is it > > possible that the disk filled up? > > On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > > > Hi Doug, > > > > > > Yes, you are correct- data I have previously processed without any > > > problems is no longer being processed. > > > > > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > > > ago so I have not changed my freesurfer version recently. > > > > > > Thanks! > > > > > > Joseph Aloi > > > Graduate Student, MD/PhD Scholars Program > > > Department of Pharmacology and Experimental Neuroscience > > > University of Nebraska Medical Center > > > > > > Neurobehavioral Research Assistant, Center For Neurobehavioral > Research > > > Boys Town National Research Hospital > > So the exact same data set is now generating an error whereas it ran > > smoothly before? What version of FS are you using? Did you change > versions? > > doug > > On 05/16/2016 09:49 AM, Aloi, Joseph wrote: > > > > > > Hi freesurfer experts, > > > > > > I have recently begun to use freesurfer to do structural MRI > > > analyses. I have been able to successfully process about 40 > > > structural scans with recon-all thus far, but starting a few days ago, > > > I started getting this error whenever I run recon-all: > > > > > > WARNING: file > > > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not > > > contain a Siemens ASCII header > > > > > > has this file been anonymized? > > > > > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan > > > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 > > > > > > recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 > CDT 2016 > > > > > > Here are a few of the troubleshooting steps I’ve tried to track down > > > the cause of the error: > > > > > > -- Re-run recon-all with a couple of scans from my dataset that I have > > > already successfully processed > > > > > > - - Re-run recon-all the same datasets but on a different computer > > > > > > - - Re-convert the scans from .ima files to dicoms in osirix, then > > > run recon-all > > > > > > > > > For all of these steps, I have gotten the exact same error message. > > > The files should be anonymized, since I used osirix’s “anonymize and > > > convert” function to generate the dicom files (the scans were given to > > > me as .ima files). > > > > > > Any suggestions on what to try next? > > > > > > Thank you! > > > > > > > > > Joseph Aloi > > > > > > The information in this e-mail may be privileged and confidential, > > > intended only for the use of the addressee(s) above. Any unauthorized > > > use or disclosure of this information is prohibited. If you have > > > received this e-mail by mistake, please delete it and immediately > > > contact the sender. > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > The information in this e-mail may be privileged and confidential, > > intended only for the use of the addressee(s) above. Any unauthorized > > use or disclosure of this information is prohibited. If you have > > received this e-mail by mistake, please delete it and immediately > > contact the sender. > > > > > > _______________________________________________ > > 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 > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <file://localhost/transfer/outgoing/flat/greve> > > > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > 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.
