[Freesurfer] Fwd: mpr2mni305 failed error
I all! I have the same problem in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T) during the recon-all -all process. 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 for your attention Francesco Deleo 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 73 12.1.2000 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 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] mpr2mni305 failed
I all! I have the same problem in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T) during the recon-all -all process. 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 for your attention Francesco Deleo 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 73 12.1.2000 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 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] mpr2mni305 failed error
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 73 12.1.2000 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 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.
Re: [Freesurfer] mpr2mni305 failed error
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 : > 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 73 12.1.2000 > > 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 > > 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 > > > 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.
Re: [Freesurfer] mpr2mni305 failed error
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 : > 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 > <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 73 12.1.2000 > > > 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 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >
[Freesurfer] Fwd: mpr2mni305 failed error
-- Forwarded message -- From: Francesco Deleo Date: 2014-08-08 18:06 GMT+02:00 Subject: Re: [Freesurfer] mpr2mni305 failed error To: freesurfer 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 : 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 : >> 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 >> > > <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 73 12.1.2000 >> > > imgrege: no vox
Re: [Freesurfer] Fwd: mpr2mni305 failed error
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 : > 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 >> Date: 2014-08-08 18:06 GMT+02:00 >> Subject: Re: [Freesurfer] mpr2mni305 failed error >> To: freesurfer >> >> >> 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 : >> 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 >> : >> 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 >> > > <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 >> > > >
