When you were getting the error message, was the program continuing? It should have continued normally (though it is not good practice to have big ERROR messages scrolling across the screen:)
On 03/01/2017 02:58 PM, Gustav Mårtensson wrote:
Hi,
Yes, the buildstamp says freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c and running Ubuntu 16.04.1 LTS:
$ lsb_release -a LSB Version: core-9.20160110ubuntu0.2-amd64:core-9.20160110ubuntu0.2-noarch:security-9.20160110ubuntu0.2-amd64:security-9.20160110ubuntu0.2-noarch Distributor ID: Ubuntu Description: Ubuntu 16.04.1 LTS Release: 16.04 Codename: xenial
Running it on another computer with Ubuntu 14.04 and FS 6.0 produces the same error.
*Gustav Mårtensson* | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet
On 2017-03-01 19:00, Douglas N Greve wrote:
And this is in version 6? What platform are you using?
On 03/01/2017 12:07 PM, Gustav Mårtensson wrote:
Hi,
Yes, running mri_convert ADNI_032_S_0187_MR____________MPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm dummy.mgh still produces the error
ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /home/gustav/Desktop/0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MR____________MPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm break DICOMRead.c:5228
regardless of if the dicom file is in its own directory or not.
Best, Gustav
On 2017-03-01 17:47, Douglas N Greve wrote:
Yes. I cannot replicate the error on my end. If you copy that dicom file to its own directory and try to convert it, do you get the same error?
doug
ps. Please include previous correspondence.
On 03/01/2017 02:54 AM, Gustav Mårtensson wrote:
Hi Douglas,
Thank you for your reply! I've attached one of the dicoms that fails.
setenv FS_LOAD_DWI 0 removes the error. Would you recommend doing this over replacing the mri_convert binary in FS 6.0 with the one from FS 5.3.0.
Best regards, Gustav It looks like it found something that it thinks is a DWI parameter butisn't, and it is causing it to fail. Can you send me one of the dicoms?In the mean time, if yousetenv FS_LOAD_DWI 0 then the error should go away
On 2/28/17 8:33 AM, Gustav Mårtensson wrote:
Hi, I have a problem when executing the following command on imagesscanned on 1.5T Philips (Intera) in FS 6.0:recon-all -i0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MR____________MPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm-subjid 4450a7a0-27e9-42bc-99ab-1c15519ad9a4 -all -mprage -qcache-hippocampal-subfields-T1 -brainstem-structures -cw256 which during mri_convert produces the error: ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOMs from other scanners works fine as far as we know. Whenprocessing them through 5.3.0 we didn't get any errors like this,regardless of scanner If we just copy the mri_convert binary file fromFS 5.3.0 to FS 6.0 the errors disappears. Would this be the recommendapproach to solve our issues?We are running on Ubuntu 16.04 LTS with FS versionfreesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I'veincluded recon-all.log case it is of interest. Thank you for your help! -- *Gustav Mårtensson* | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing listFreesurfer@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. -- *Gustav Mårtensson* | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet
Karolinska Institutet – a medical university
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve