21 Aug
2014
21 Aug
'14
10:25 a.m.
Hi Francesco
if you upload one of the dicom series that causes the problems we will take a look. If you can also send us the rawavg.mgz after your successful recon-all from the .nii that would also help
cheers Bruce On Wed, 20 Aug 2014, Francesco Deleo wrote:
Hi all! Sorry for my late answer but I went on holiday and I didn't have access to my mail.
The background is normal in original dicoms and it is not an avarage of more than one run.
The problem I reported was solved in all cases converting dicoms to nifti with dcm2nii and using the oriented volume. I don't know why but it functioned
Is there a bug in freesurfer using directly dicoms?
Thank you all for attention and advice.
Francesco
2014-08-08 19:53 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: can you tar and gzip the dicoms and send them to us? Is there a high background level in them as well? Is this the average of more than one run? You should check the mri/orig/00?.mgz volume(s) as well On Fri, 8 Aug 2014, Francesco Deleo wrote:
---------- Forwarded message ---------- From: Francesco Deleo <franc.deleo@gmail.com> Date: 2014-08-08 18:06 GMT+02:00 Subject: Re: [Freesurfer] mpr2mni305 failed error To: freesurfer <freesurfer@nmr.mgh.harvard.edu> It is not ok... It seems to have a contrast problem... I can send a snapshot, or if you want I can send the rawavg.mgz Francesco 2014-08-08 17:53 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: what does the rawavg.mgz look like? If it is ok, can you email it to us? On Fri, 8 Aug 2014, Francesco Deleo wrote: Thank you all for attention and help! Maybe we're finding the problem: in cases I received the mpr2mni305 error the orig.mgz is unintelligible (it is white with some black point). But my dicoms are ok (I've checked!). I've already tried converting dicom to tiff but I got the same error message and the same unintelligible orig.mgz (and the tiff are ok too!). So I think the likely problem is in the recon-all -i command! Any idea? It remains a mistery for me why I have this problem only in some (and not in every one) MRI scans even if all the parameters are the same. thanks again Francesco 2014-08-07 17:16 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Have you looked in transforms/talairach_avi.log? On 08/07/2014 07:57 AM, Francesco Deleo wrote: > Thank you Doug! > but i tried it in many cases but I've always received the same error > message... > Is there something else I can try? > > Francesco > > > 2014-08-07 0:46 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > Try it with -notal-check > doug > > On 08/06/2014 04:39 PM, Francesco Deleo wrote: > > I all! > > > > I am a new freesurfer user. > > I have a problem when I perform the recon-all -all, in about 15% of > > MRI scans, all made with the same scanning protocol (T1 MPRAGE in a > > SIEMENS Avanto 1,5 T). > > > > I can't recognize any difference between those scans which work > > correctly and those not. > > I have never found the same error on 3T MRI scans. > > > > I've already tried to add these flags to the recon-all -all command: > > -use-mritotal > > -talairach -use-mritotal > > -notalairach > > but I've always received an error message > > > > Thank you very much > > > > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log > > Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version > 13.3.0: > > Tue Jun 3 21:27:35 PDT 2014; > root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 > > > > Thanks very much for your attention > > > > Francesco > > Milan, Italy > > > > > --------------------------------------------------------------------- > > > > FREESURFER_HOME: /Applications/freesurfer > > > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > > > Kernel info: Darwin 13.3.0 x86_64 > > > > > --------------------------------------------------------------------- > > > > > > LAST LINES IN TALAIRACH_AVI.LOG > > > > parameters > > 9.0270 134.9373 110.8627 -84.3566 -7.5458 -11.3475 > > eta,q 0.95791 3.72402 > > 0.0485 0.0470 0.0477 0.0513 0.0470 0.0452 > > 0.0475 0.0471 0.0478 0.0513 0.0457 0.0435 > > 0.0472 0.0472 0.0476 0.0428 0.0434 0.0415 > > 0.0471 0.0471 0.0476 0.0435 0.0430 0.0415 > > 0.0470 0.0478 0.0457 0.0525 0.0415 0.0430 > > 0.0473 0.0511 0.0430 0.0548 0.0442 0.0453 > > 0.0486 0.0426 0.0406 0.0672 0.0431 0.0503 > > niter,ni,del,rscale 7 3 12.0000 1.2000 > > imgrege: no voxels in register > > ERROR: 'imgreg_4dfp > > /Applications/freesurfer/average/711-2C_as_mni_average_305 > > /Applications/freesurfer/average/711-2B_as_mni_average_305_mask > > talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' > > failed! status=254 > > ERROR: mpr2mni305 execution aborted > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:greve@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> > 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > _______________________________________________ > 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 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 _______________________________________________ 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.
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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.