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 <fis...@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.de...@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 <fis...@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 >> <gr...@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 >> <gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@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 >> > gr...@nmr.mgh.harvard.edu >> <mailto:gr...@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 >> 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 >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> >> > _______________________________________________ > 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. > >
_______________________________________________ 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.
