External Email - Use Caution Hi Douglas,
Thanks for the suggestion! However, using mri_vol2vol generates the error message: ERROR: SUBJECTS_DIR undefined. > If I set SUBJECTS_DIR to the study directory, I get the following error: movvol ICBM152_2009c_AtlasWhite.nii.gz > targvol T1w_MNI.nii.gz > outvol AtlasWhite_resampled.nii.gz > invert 0 > tal 0 > talres 2 > regheader 0 > noresample 0 > interp nearest (0) > precision float (3) > Gdiag_no -1 > Synth 0 > SynthSeed 1653169738 > ERROR: no registration (R) is specified > Invalid argument > mri_vol2vol --targ T1w_MNI.nii.gz --interp nearest --mov > ICBM152_2009c_AtlasWhite.nii.gz --o AtlasWhite_resampled.nii.gz : Signal > 124 Note that our participant directories aren't in the standard Freesurfer subject directory structure, if that matters. Is mri_vol2vol looking for a Freesurfer generated registration somewhere in the subject directory? Thanks! Jim H On Thu, May 12, 2022 at 3:43 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > try this > mri_vol2vol --targ T1w_MNI.nii.gz --interp nearest --mov > ICBM152_2009c_AtlasWhite.nii.gz --o WhiteAtlas_resampled.nii.gz > > > On 5/9/2022 11:58 AM, James Hengenius wrote: > > External Email - Use Caution > Hello FS experts, > > I'm trying to reslice a third-party atlas into the same resolution as my > data in MNI space. I am using the following command: > > mri_convert > --like T1w_MNI.nii.gz > --resample_type nearest > ICBM152_2009c_AtlasWhite.nii.gz > WhiteAtlas_resampled.nii.gz > > Output is: > > mri_convert --like T1w_MNI.nii.gz --resample_type nearest > ICBM152_2009c_AtlasWhite.nii.gz WhiteAtlas_resampled.nii.gz > reading from ICBM152_2009c_AtlasWhite.nii.gz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > INFO: transform src into the like-volume: T1w_MNI.nii.gz > writing to WhiteAtlas_resampled.nii.gz... > > In the resulting resampled atlas, the boundaries of the ROIs appear to use > an interpolation and not nearest neighbor (i.e., they take values other > than the ROI values in the atlas). Not sure if I can embed images - if so, > see the attached for an example: > > [image: image.png] > > The output is the same whether I include the --resample_type nearest flag > or leave it out, making me think that mri_convert is ignoring the flag and > using the default interp option. > > This can be replicated in the relatively current version > "freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b" as well as the > older "$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $" (which > we keep around for old pipeline compatibility). > > Any ideas on how to fix this so the ROI interfaces take appropriate > (nearest neighbor) values rather than interpolated values? > > Thanks all! > > Jim H. > > > _______________________________________________ > Freesurfer mailing > listfreesur...@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/1JIZT_Nfiv_O3V9Op5Rohp18FzwEzNqX9wj3wDmq3BJ0VxUxdjABcebZf1uYIt3Ykm3x4kBqIi_GgPXGGKj7_63Bh8EedMUsbYb9Eez_KBxhNIwuuImuYDR2KRT6ndOzwAh8AqcSf8esLY5ERtCzZl1cbgJmRLv5sT2uBp2GsEb0xwoLEV-jlsKLvNRpU-TYYTsotAtl_bx5qJc1fdZFGvDh7Vyq9adglfuWCEkV3z63Ld7RqTwFphZl6R_hYyUhknkNVzUpiTF7909fdWXaAS4bbBJ2qdJj1CVplEABNHWCaoUIxFVAgTYnO3UFJe53O/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 > https://secure-web.cisco.com/1y2kmJO_G-NY507NWtUnosin6IDNpUoIzwBGK1AUPUr47l-NRFXPoEwFm8cx3xl1LT4uNpx-aeidDAIp6p_QX2v1hJHflaZ6ihPkTyW_Ild0nFuUGtDnYl6Yo0joERw9VJl-bukSh9fjc3WFLMRSv4LpEpRbfbR-nI-sV6tjEoCji0ctBvTzdqqQIuyhWCmRl5_cLG3Y4PFgbFmd9Bs0ZGrL6_fGXRgyruCYttTIjk7St_0Igw5CE7m82B4ODQqYuIhiYDHN5c7jUi1bARAUBX9_nrv8qRUjQ1KxOGFyTSlOrcNHZ3ieljHuDB2QGaTO2/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1y2kmJO_G-NY507NWtUnosin6IDNpUoIzwBGK1AUPUr47l-NRFXPoEwFm8cx3xl1LT4uNpx-aeidDAIp6p_QX2v1hJHflaZ6ihPkTyW_Ild0nFuUGtDnYl6Yo0joERw9VJl-bukSh9fjc3WFLMRSv4LpEpRbfbR-nI-sV6tjEoCji0ctBvTzdqqQIuyhWCmRl5_cLG3Y4PFgbFmd9Bs0ZGrL6_fGXRgyruCYttTIjk7St_0Igw5CE7m82B4ODQqYuIhiYDHN5c7jUi1bARAUBX9_nrv8qRUjQ1KxOGFyTSlOrcNHZ3ieljHuDB2QGaTO2/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > Please note that this e-mail is not secure (encrypted). 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