External Email - Use Caution Thanks, that worked without error and the resampling looks correct.
Jim On Thu, May 12, 2022, 11:42 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Sorry, one more thing. Add --regheader to the command lien > > On 5/12/2022 5:12 PM, James Hengenius wrote: > > 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.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1EM4baxR8u3Q8gwbnuY9vttqG6xIZYi2LfAAzIEPwEpbPnahjbQXJ7B92U_Z17PBmB9vK56w1rG89cpVbyf-O5QpFN3aA59Jhr7a3gV2WlICJAf2wQ_gl1m0yKJX-lFXO2loCU5U7CjnO0mkr61YN5BXMkZ-92Hf2BI_0SZFVq-msu45VNA8rdN2HBKN4RXdVT7Ge62oWVdw7Gi6xz7oG_UJxkOaHHBnXTn6X6BeDHeEOatGygHHx9Sov6wjWpYqsQTP2KrJhAtsg0TOSKmrehFSR0vlnkd1JwE7MWjf5Ev58nhYQeQz8begZ9_uyJD3i/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <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> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1EM4baxR8u3Q8gwbnuY9vttqG6xIZYi2LfAAzIEPwEpbPnahjbQXJ7B92U_Z17PBmB9vK56w1rG89cpVbyf-O5QpFN3aA59Jhr7a3gV2WlICJAf2wQ_gl1m0yKJX-lFXO2loCU5U7CjnO0mkr61YN5BXMkZ-92Hf2BI_0SZFVq-msu45VNA8rdN2HBKN4RXdVT7Ge62oWVdw7Gi6xz7oG_UJxkOaHHBnXTn6X6BeDHeEOatGygHHx9Sov6wjWpYqsQTP2KrJhAtsg0TOSKmrehFSR0vlnkd1JwE7MWjf5Ev58nhYQeQz8begZ9_uyJD3i/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <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. 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Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> > > > -- > Jim Hengenius > Post-doctoral Researcher > Rosano and Huppert Groups > Department of Epidemiology > University of Pittsburgh > > My Google Calendar > <http://secure-web.cisco.com/1h3estQ2AU_P-QEYQ84cp30lfumtXqCRnjkcb5J0k9twnq4bpjMhkK8j_i4U34u7hk1jsno4tjtkzESQsvWRBPRzBWpRs8a-Tt9xh55_OQ_StvS2O2hBrTOPjdmuCyv4Nz6KqXPH_rn5QWrnh6EvmzI4ceXDKAP6Ic5-yJrxS6iSfLmalnh7MWQd-Y3w9BAwxaoO_ie2ZUzjsqYgO4SPcnveof3Q6ZK8LTaXzxPEdCV3LMJyIGy_N01Yaa4dOXKtnc5Ww3jiZJICJ-uK9yGWKw36xPd85HkMo5cy1L5_YDD8o-iwXrtG3Z25bZpP5SeDQ/http%3A%2F%2Fwww.google.com%2Fcalendar%2Fembed%3Fsrc%3Djames.hengenius%40gmail.com> > > _______________________________________________ > 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/1EM4baxR8u3Q8gwbnuY9vttqG6xIZYi2LfAAzIEPwEpbPnahjbQXJ7B92U_Z17PBmB9vK56w1rG89cpVbyf-O5QpFN3aA59Jhr7a3gV2WlICJAf2wQ_gl1m0yKJX-lFXO2loCU5U7CjnO0mkr61YN5BXMkZ-92Hf2BI_0SZFVq-msu45VNA8rdN2HBKN4RXdVT7Ge62oWVdw7Gi6xz7oG_UJxkOaHHBnXTn6X6BeDHeEOatGygHHx9Sov6wjWpYqsQTP2KrJhAtsg0TOSKmrehFSR0vlnkd1JwE7MWjf5Ev58nhYQeQz8begZ9_uyJD3i/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. 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