Hi Freesufer developers
We are getting some errors in our resting state and ASL scans. Everything goes fine while we are scaning the subjects, but when we look at the data in BORGET, some of them come out with errors. I copied one of the scaninfo files, so you can see the errors. Is there anyway to not get errors? Or shall we just unpack the ok data and go on?
Thanks
1 localizer_64ch ok 512 512 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535 2 AAHead_Scout ok 160 160 128 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717 3 AAHead_Scout ok 162 162 5 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708 4 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712 5 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715 6 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274 7 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273 8 MEMPRAGE ok 256 256 176 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299 9 fMRI_DistortionMap_PA ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688 10 fMRI_DistortionMap_AP ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923 11 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295 12 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419 13 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555 14 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697 15 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838 16 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987 17 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134 18 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274 19 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422 20 tgse_pcasl_optBS_M0_PLD2000 ok 96 96 1 22 MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829 21 tgse_pcasl_optBS_M0_PLD2000 err 96 96 1 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101 22 HCP_CMRR_SpinEchoFieldMap_AP ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321 23 HCP_CMRR_SpinEchoFieldMap_PA ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977 24 HCP_CMRR_fMRI_rest_AP err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554 25 HCP_CMRR_fMRI_rest_AP err 104 104 72 216 MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992 26 HCP_CMRR_fMRI_rest_PA err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846 27 HCP_CMRR_fMRI_rest_PA ok 104 104 72 488 MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
Are the output volumes being created? Do they look ok? Sometimes unpacksdcmdir will print out an error when there is not actually an error there (eg, if it does not see the expected number of files, but some times its expectation is wrong). In dcmunpack (the replacement for unpacksdcmdir), I don't print out the ok/err because it it not always reliable.
On 06/28/2018 11:35 AM, Nasiriavanaki, Zahra wrote:
Hi Freesufer developers
We are getting some errors in our resting state and ASL scans. Everything goes fine while we are scaning the subjects, but when we look at the data in BORGET, some of them come out with errors. I copied one of the scaninfo files, so you can see the errors. Is there anyway to not get errors? Or shall we just unpack the ok data and go on?
Thanks 1 localizer_64ch ok 512 512 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535 2 AAHead_Scout ok 160 160 128 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717 3 AAHead_Scout ok 162 162 5 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708 4 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712 5 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715 6 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274 7 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273 8 MEMPRAGE ok 256 256 176 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299 9 fMRI_DistortionMap_PA ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688 10 fMRI_DistortionMap_AP ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923 11 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295 12 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419 13 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555 14 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697 15 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838 16 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987 17 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134 18 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274 19 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422 20 tgse_pcasl_optBS_M0_PLD2000 ok 96 96 1 22 MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829 21 tgse_pcasl_optBS_M0_PLD2000 err 96 96 1 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101 22 HCP_CMRR_SpinEchoFieldMap_AP ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321 23 HCP_CMRR_SpinEchoFieldMap_PA ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977 24 HCP_CMRR_fMRI_rest_AP err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554 25 HCP_CMRR_fMRI_rest_AP err 104 104 72 216 MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992 26 HCP_CMRR_fMRI_rest_PA err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846 27 HCP_CMRR_fMRI_rest_PA ok 104 104 72 488 MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248
*Zahra (Mona) Nasiriavanaki*
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug
Thanks for your reply.
I have not unpacked the error ones!
I will go for it and let you know if there was a problem.
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, June 28, 2018 9:57:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Errors in scans
Are the output volumes being created? Do they look ok? Sometimes unpacksdcmdir will print out an error when there is not actually an error there (eg, if it does not see the expected number of files, but some times its expectation is wrong). In dcmunpack (the replacement for unpacksdcmdir), I don't print out the ok/err because it it not always reliable.
On 06/28/2018 11:35 AM, Nasiriavanaki, Zahra wrote:
Hi Freesufer developers
We are getting some errors in our resting state and ASL scans. Everything goes fine while we are scaning the subjects, but when we look at the data in BORGET, some of them come out with errors. I copied one of the scaninfo files, so you can see the errors. Is there anyway to not get errors? Or shall we just unpack the ok data and go on?
Thanks 1 localizer_64ch ok 512 512 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535 2 AAHead_Scout ok 160 160 128 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717 3 AAHead_Scout ok 162 162 5 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708 4 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712 5 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715 6 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274 7 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273 8 MEMPRAGE ok 256 256 176 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299 9 fMRI_DistortionMap_PA ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688 10 fMRI_DistortionMap_AP ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923 11 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295 12 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419 13 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555 14 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697 15 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838 16 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987 17 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134 18 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274 19 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422 20 tgse_pcasl_optBS_M0_PLD2000 ok 96 96 1 22 MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829 21 tgse_pcasl_optBS_M0_PLD2000 err 96 96 1 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101 22 HCP_CMRR_SpinEchoFieldMap_AP ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321 23 HCP_CMRR_SpinEchoFieldMap_PA ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977 24 HCP_CMRR_fMRI_rest_AP err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554 25 HCP_CMRR_fMRI_rest_AP err 104 104 72 216 MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992 26 HCP_CMRR_fMRI_rest_PA err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846 27 HCP_CMRR_fMRI_rest_PA ok 104 104 72 488 MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248
*Zahra (Mona) Nasiriavanaki*
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Nasiriavanaki, Zahra