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 >>>>> listfreesur...@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 > -- 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
