External Email - Use Caution First of all, thanks you Douglas for the support. As I said i run the mri_vol2surf and I obtained an error:
mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img srcvol = /home/neuroimage/fsl/FreeSurfer/AAL.nii srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/MNI/mri/orig.mgz as target reference. Reading surface /usr/local/freesurfer/subjects/MNI/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/MNI/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 104840 Writing to /home/neuroimage/fsl/FreeSurfer/AAL-lh.img Dim: 161783 1 1 ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768 However I noticed that if i use the format .guii or .mgh this error message doesn't appear. Could I continue with the image in this format? What's the difference that makes this error appear with .img format? El dom, 29 nov 2020 a las 18:26, Greve, Douglas N.,Ph.D. (< dgr...@mgh.harvard.edu>) escribió: > Can you send the full terminal output? > > On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote: > > External Email - Use Caution > I tried to run mri_vol2surf with the following command: mri_vol2surf --src > /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 > --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i > obtain an error ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768. > How can i fix it? > > El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve (< > dgr...@mgh.harvard.edu>) escribió: > >> Which MNI space? If mni152, then run recon-all on the mni152 template, >> then run mri_vol2surf with --regheader mni152subjectname; also include >> --projfrac 0.5. But before you do that , load the AAL atlas onto the >> mni152subject with the surfaces to make sure everything aligns. You might >> want to do this with the colin27 brain instead because I think that is what >> the AAL atlas is defined on. >> >> On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote: >> >> External Email - Use Caution >> Hello everyone, I tried to follow your instruction about how to get the >> fresurfer stats in AAL ROIs. I have an image .nii with the labels of the >> AAL in the MNI space (i submit this image in the e-mail). Can I use this >> image in the mri_vol2surf? If so, i suppose that this image would be the >> input one, but i don't know what is registration file in the syntax of >> mri_vol2surf >> >> Sorry for the inconvenience, Alberto >> >> _______________________________________________ >> 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/1Y4VfoEJxaSeEKStezPDZfMmHPpFXSk6S1kf2NxtLlVCFXkl8RdSa-f1nnr8Cydn9VB3GM8M1kmIcY7DgFo-GCfXnjKUJpHSmINuTp6bMYH9vhycZReIp_FthKrCXTSqanz-o7GCZnpy2W4Ue8xzDqeKHeNxCr_jPtbYEUNogqepmnzCe2Ct9lJkJrXimWJ8XIKpRKOwYxlu2jN0AvVoaS4BE9lsf4yekHwqaRRrw6KukThCmGo-sAiriQKAFFS2L7oXtfB7hPkBR2dQdYM_adQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/14IcDxKKGdMR7E66lqttkWYQlfL6BfoHtuNxe_57f-7SWwe5KfbEouUEpZiuVccd5SdT2HnGR55o6yQ2uHBPVToGgpu2n_SipDPGGYclm38rXtQ033FapCVLphv8P7caedqe4bjnpwCYYeNiaN7wR5m_f48m45xm3zmDjTEAwSaGjS8xhr6_dpSuo00tbSCSAChx4qSAIcbfHAflDo32LlIaEBwDPDOvNh6uFzJYHCvXvokGb0x9eyPjhrHfFZE_DMVozizVxfd-sWRnX0QxFwA/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/1Y4VfoEJxaSeEKStezPDZfMmHPpFXSk6S1kf2NxtLlVCFXkl8RdSa-f1nnr8Cydn9VB3GM8M1kmIcY7DgFo-GCfXnjKUJpHSmINuTp6bMYH9vhycZReIp_FthKrCXTSqanz-o7GCZnpy2W4Ue8xzDqeKHeNxCr_jPtbYEUNogqepmnzCe2Ct9lJkJrXimWJ8XIKpRKOwYxlu2jN0AvVoaS4BE9lsf4yekHwqaRRrw6KukThCmGo-sAiriQKAFFS2L7oXtfB7hPkBR2dQdYM_adQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/14IcDxKKGdMR7E66lqttkWYQlfL6BfoHtuNxe_57f-7SWwe5KfbEouUEpZiuVccd5SdT2HnGR55o6yQ2uHBPVToGgpu2n_SipDPGGYclm38rXtQ033FapCVLphv8P7caedqe4bjnpwCYYeNiaN7wR5m_f48m45xm3zmDjTEAwSaGjS8xhr6_dpSuo00tbSCSAChx4qSAIcbfHAflDo32LlIaEBwDPDOvNh6uFzJYHCvXvokGb0x9eyPjhrHfFZE_DMVozizVxfd-sWRnX0QxFwA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________ > 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/1Y4VfoEJxaSeEKStezPDZfMmHPpFXSk6S1kf2NxtLlVCFXkl8RdSa-f1nnr8Cydn9VB3GM8M1kmIcY7DgFo-GCfXnjKUJpHSmINuTp6bMYH9vhycZReIp_FthKrCXTSqanz-o7GCZnpy2W4Ue8xzDqeKHeNxCr_jPtbYEUNogqepmnzCe2Ct9lJkJrXimWJ8XIKpRKOwYxlu2jN0AvVoaS4BE9lsf4yekHwqaRRrw6KukThCmGo-sAiriQKAFFS2L7oXtfB7hPkBR2dQdYM_adQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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