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, thenrun 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 greve@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.htmlhttp://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.
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, thenrun 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 greve@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
freesurfer@nmr.mgh.harvard.edu
-
Aloi, Joseph -
Douglas N Greve