External Email - Use Caution Then, now that I have the AAL in the surface I should make a label for every region in the AAL_surface image with mri_vol2label with surf option and run mri_label2label for every label and every subject in my study. Is this the correct workflow?
El lun, 30 nov 2020 a las 16:26, Greve, Douglas N.,Ph.D. (< dgr...@mgh.harvard.edu>) escribió: > Oh, don't use .img as it cannot handle the surface dimensions. > Technically, nifti cannot either, but I hacked our nifti version to > accommodate. Or use mgh as you have done. > > On 11/30/2020 8:31 AM, Alberto Del Cerro Leon wrote: > > 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/1nUf0Dtd9yocXIDY7ZxspoTQzocVAQ-7le5C-2zG2PyfEMcJ3oyHqH6DjIpvRTY2SjFwxlwhFq5OQrI9FwpqIClUxP7oOpJnUELDdmWnxD5ZIFQr_gZuwPkMd7_5LXWsgCcCx5CS85Hfk6jpW7jo43qNvDKtTJoJi7tMLRSl2538RIMAcp-FQcEZEVYJrwScRXGibi7X40V_xV32XPP98zeNOtSDd41_-VSxjauj66LDuLS6h4Yg_9xXQRAZHyAKV5frhm8xmqxqdk_X3fWvZjw/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/1nUf0Dtd9yocXIDY7ZxspoTQzocVAQ-7le5C-2zG2PyfEMcJ3oyHqH6DjIpvRTY2SjFwxlwhFq5OQrI9FwpqIClUxP7oOpJnUELDdmWnxD5ZIFQr_gZuwPkMd7_5LXWsgCcCx5CS85Hfk6jpW7jo43qNvDKtTJoJi7tMLRSl2538RIMAcp-FQcEZEVYJrwScRXGibi7X40V_xV32XPP98zeNOtSDd41_-VSxjauj66LDuLS6h4Yg_9xXQRAZHyAKV5frhm8xmqxqdk_X3fWvZjw/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.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1nUf0Dtd9yocXIDY7ZxspoTQzocVAQ-7le5C-2zG2PyfEMcJ3oyHqH6DjIpvRTY2SjFwxlwhFq5OQrI9FwpqIClUxP7oOpJnUELDdmWnxD5ZIFQr_gZuwPkMd7_5LXWsgCcCx5CS85Hfk6jpW7jo43qNvDKtTJoJi7tMLRSl2538RIMAcp-FQcEZEVYJrwScRXGibi7X40V_xV32XPP98zeNOtSDd41_-VSxjauj66LDuLS6h4Yg_9xXQRAZHyAKV5frhm8xmqxqdk_X3fWvZjw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1Y4VfoEJxaSeEKStezPDZfMmHPpFXSk6S1kf2NxtLlVCFXkl8RdSa-f1nnr8Cydn9VB3GM8M1kmIcY7DgFo-GCfXnjKUJpHSmINuTp6bMYH9vhycZReIp_FthKrCXTSqanz-o7GCZnpy2W4Ue8xzDqeKHeNxCr_jPtbYEUNogqepmnzCe2Ct9lJkJrXimWJ8XIKpRKOwYxlu2jN0AvVoaS4BE9lsf4yekHwqaRRrw6KukThCmGo-sAiriQKAFFS2L7oXtfB7hPkBR2dQdYM_adQ/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/1nUf0Dtd9yocXIDY7ZxspoTQzocVAQ-7le5C-2zG2PyfEMcJ3oyHqH6DjIpvRTY2SjFwxlwhFq5OQrI9FwpqIClUxP7oOpJnUELDdmWnxD5ZIFQr_gZuwPkMd7_5LXWsgCcCx5CS85Hfk6jpW7jo43qNvDKtTJoJi7tMLRSl2538RIMAcp-FQcEZEVYJrwScRXGibi7X40V_xV32XPP98zeNOtSDd41_-VSxjauj66LDuLS6h4Yg_9xXQRAZHyAKV5frhm8xmqxqdk_X3fWvZjw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1Y4VfoEJxaSeEKStezPDZfMmHPpFXSk6S1kf2NxtLlVCFXkl8RdSa-f1nnr8Cydn9VB3GM8M1kmIcY7DgFo-GCfXnjKUJpHSmINuTp6bMYH9vhycZReIp_FthKrCXTSqanz-o7GCZnpy2W4Ue8xzDqeKHeNxCr_jPtbYEUNogqepmnzCe2Ct9lJkJrXimWJ8XIKpRKOwYxlu2jN0AvVoaS4BE9lsf4yekHwqaRRrw6KukThCmGo-sAiriQKAFFS2L7oXtfB7hPkBR2dQdYM_adQ/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/1nUf0Dtd9yocXIDY7ZxspoTQzocVAQ-7le5C-2zG2PyfEMcJ3oyHqH6DjIpvRTY2SjFwxlwhFq5OQrI9FwpqIClUxP7oOpJnUELDdmWnxD5ZIFQr_gZuwPkMd7_5LXWsgCcCx5CS85Hfk6jpW7jo43qNvDKtTJoJi7tMLRSl2538RIMAcp-FQcEZEVYJrwScRXGibi7X40V_xV32XPP98zeNOtSDd41_-VSxjauj66LDuLS6h4Yg_9xXQRAZHyAKV5frhm8xmqxqdk_X3fWvZjw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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