mri_surf2vol error: mri_read(): code inconsistency (file type recognized but not caught)
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Dear all,
I am trying to convert label files into volume ROI masks.
This is my command below:
mri_surf2vol --surfval /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --o /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/fonctional_vol_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz --identity sub-NSxLxYKx1964 --hemi lh --fillribbon --template /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/mri/brain.mgz
I get this error:
Reading surface /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.white
Done reading source surface
Reading thickness /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.thickness
Done
INFO: reading /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown
mri_read(): type = 32
error: mri_read(): code inconsistency (file type recognized but not caught)
ERROR: could not read /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown
Any idea what would cause this? Is it because the labels weren't saved in the correct format?
Thanks,
Best,
-Loïc
surf2vol does not take labels as an input. Instead, use mri_label2label to convert it to a mask, then use mri_surf2vol on the mask
On 4/18/2025 11:39 AM, Loïc Daumail wrote:
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Dear all,
I am trying to convert label files into volume ROI masks.
This is my command below:
mri_surf2vol --surfval /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --o /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/fonctional_vol_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz --identity sub-NSxLxYKx1964 --hemi lh --fillribbon --template /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/mri/brain.mgz
I get this error:
Reading surface /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.white
Done reading source surface
Reading thickness /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.thickness
Done
INFO: reading/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown
mri_read(): type = 32
error: mri_read(): code inconsistency (file type recognized but not caught)
ERROR: could not read /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown
Any idea what would cause this? Is it because the labels weren't saved in the correct format?
Thanks,
Best,
-Loïc
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug,
I see thanks! Would --srclabel and --trglabel be identical in my case? i.e., something like this: freesurferCommand = f'mri_label2label --srclabel {surf_label_file} --trglabel {surf_label_file} --outmask {out_mask_file} --hemi {hID} --s { participant} --regmethod surface'
Corresponding bash code:
mri_label2label --srclabel /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --trglabel /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --outmask /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz --hemi lh --s sub-NSxLxYKx1964 --regmethod surface
Thanks, Best, -Loïc
Le ven. 18 avr. 2025 à 11:47, Douglas N. Greve dgreve@mgh.harvard.edu a écrit :
surf2vol does not take labels as an input. Instead, use mri_label2label to convert it to a mask, then use mri_surf2vol on the mask
On 4/18/2025 11:39 AM, Loïc Daumail wrote:
External Email - Use CautionDear all,
I am trying to convert label files into volume ROI masks.
This is my command below:
mri_surf2vol --surfval /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --o /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/fonctional_vol_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz --identity sub-NSxLxYKx1964 --hemi lh --fillribbon --template /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/mri/brain.mgz
I get this error:
Reading surface /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.white
Done reading source surface
Reading thickness /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.thickness
Done
INFO: reading /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown
mri_read(): type = 32
error: mri_read(): code inconsistency (file type recognized but not caught)
ERROR: could not read /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown
Any idea what would cause this? Is it because the labels weren't saved in the correct format?
Thanks,
Best,
-Loïc
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1WpCYYm_WtYez_u1EclgrVwSlzpDJe01Q-qxSRJJHCaLM0i... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1kP5fi20l4rf8hCuPDnNgJglp5Yvbx4AdSQtiLusAmD6p5R... < https://secure-web.cisco.com/1kP5fi20l4rf8hCuPDnNgJglp5Yvbx4AdSQtiLusAmD6p5R... .
you can set the target label to a junk file because you won't need it.
On 4/18/2025 12:31 PM, Loïc Daumail wrote:
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Hi Doug,
I see thanks! Would --srclabel and --trglabel be identical in my case? i.e., something like this: freesurferCommand = f'mri_label2label --srclabel {surf_label_file}--trglabel {surf_label_file}--outmask {out_mask_file}--hemi {hID}--s {participant}--regmethod surface'
Corresponding bash code:
mri_label2label --srclabel /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --trglabel /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --outmask /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz --hemi lh --s sub-NSxLxYKx1964 --regmethod surface
Thanks, Best, -Loïc
Le ven. 18 avr. 2025 à 11:47, Douglas N. Greve dgreve@mgh.harvard.edu a écrit :
surf2vol does not take labels as an input. Instead, use mri_label2label to convert it to a mask, then use mri_surf2vol on the mask On 4/18/2025 11:39 AM, Loïc Daumail wrote:External Email - Use Caution Dear all, I am trying to convert label files into volume ROI masks. This is my command below: mri_surf2vol --surfval /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --o /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/fonctional_vol_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz --identity sub-NSxLxYKx1964 --hemi lh --fillribbon --template /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/mri/brain.mgz I get this error: Reading surface /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.white Done reading source surface Reading thickness /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.thickness Done INFO: reading/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown mri_read(): type = 32 error: mri_read(): code inconsistency (file type recognized but not caught) ERROR: could not read /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown Any idea what would cause this? Is it because the labels weren't saved in the correct format? Thanks, Best, -Loïc _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1WpCYYm_WtYez_u1EclgrVwSlzpDJe01Q-qxSRJJHCaLM0iIJR_77Jfyo0bj_O3bbfaoD4T3UJRNC0ci3B-TSL51z1zQSt2zm0cVBfB9eCQR8f77hHv9uTH4E4PSVI7Oku1WlAXRYHVJu6Uq9UXhAOXIqnHUa-adK6EUIciAWHs-7uEvFQYeoDCGatqWpGLhZb6UDNwRUI0ubo-NY84qxfi_uJuDY2gYk44QYvUrlkVnOQRbJBR3oRyr_YuS2Au11sFjPUrR4pHxBIUHPdT4zcNH1fmTjmJoAixEpmysYSRA8FYOo8EzZMwJmVfgagvY9Viz1UqfDCEunAes3O3wO0Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1WpCYYm_WtYez_u1EclgrVwSlzpDJe01Q-qxSRJJHCaLM0iIJR_77Jfyo0bj_O3bbfaoD4T3UJRNC0ci3B-TSL51z1zQSt2zm0cVBfB9eCQR8f77hHv9uTH4E4PSVI7Oku1WlAXRYHVJu6Uq9UXhAOXIqnHUa-adK6EUIciAWHs-7uEvFQYeoDCGatqWpGLhZb6UDNwRUI0ubo-NY84qxfi_uJuDY2gYk44QYvUrlkVnOQRbJBR3oRyr_YuS2Au11sFjPUrR4pHxBIUHPdT4zcNH1fmTjmJoAixEpmysYSRA8FYOo8EzZMwJmVfgagvY9Viz1UqfDCEunAes3O3wO0Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1kP5fi20l4rf8hCuPDnNgJglp5Yvbx4AdSQtiLusAmD6p5RvAvG23qawYTNjPnnXsZB4HNYutjsBFGU2qYSRWNxXvGPRISwSrXABZG7VmNpRbJbtp0zC5ZnVgXyuSmG6wUnh7XHVCoNgW-Jk_Bj8HAckmlnMQO-KtMCmRZFfW3Xsj0IFpLb0dDLy6qWM3LkO8f-hgr5Btr6L1tS2anlBCAfGU0Rz7hRKgesU7Qi2JKS4K0PBzxxz6Bh6AD8mYCwTGbIkxvcl3gUwCylAN8GICPsmd-UNSOL-2s0sau8u8vdzG9ODsHLwMFCY96oaWWUlT/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1AuIopx2WXmlNEv1eSet-v_m-GyQnTgvkl_kcMV1aUAxfsziXGdU57WtYUNf6UrrS3Qcqn80CAm-OhHGTaJDxnQ0-WrAHCpB_Lqi-rCmYsssRQ1xX0lc_sNz6ZWMCqG25ubbOUVEdA0UiH2di43SbXZqaeUySZfEgZ8LiuSZMKe6LFNkfbUHItuP2Ut__BIHnU1DLSK2h_il1UYqpaMzG_fNDsy6NEC7zIPd7d6fNSvP7RQNa4zCOt0MNE42QtqTiPF2rOCe9VZiwXZjbXTEEH90TN7Lbt1h_56ahzvWzzGdfK4NcN1Vdj7RtIiTuk3Ft/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
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Douglas N. Greve -
Loïc Daumail