[Freesurfer] Permutation with Non-Orthogonal Matrices
External Email - Use Caution Hi FreeSurfer Experts, Reposting this message. I am trying to correct for multiple comparisons by running a permutation for a non-orthogonal design. Based on reading through the blog, I came up with the following script: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --sim perm-resid 1000 3.0 --sim-sign abs --cwp 0.05 --2spaces I am getting the following error message: ERROR: Flag abs unrecognized. And when I tried to put the "abs" after "1000 3.0," I got the error message saying that I needed to specify the --sim-sign. Could you please let me know how I need to edit my script? I have already run mris_preproc and mri_glmfit. Thanks! Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Converting .mgz (or .nii) file to .hdr file (.hdr and .img)
Hi Kim are you really sure that you want to use analyze format? I doesn't keep track of the direction cosines properly so once you go to it it is hard to know left from right. SPM should be fine with nifti. In any case conversion should be something like: mri_convert file.mgz file.nii or mri_convert file.mgz file.img although again, I wouldn't recommend using analyze cheers Bruce On Sat, 4 Apr 2020, Kim, Gwang-Won wrote: Dear expert, I'd like to convert .mgz (or .nii) file to .hdr file (.hdr and .img) to use .hdr in SPM software. I tried to convert the file using "mri_convert". But, there were the error messages below. Please, let me know how to onvert .mgz (or .nii) file to .hdr file (.hdr and .img). 1) convert .nii file to .hdr file (.hdr and .img) [latifah:kim] (nmr-stable6-env) mri_convert -it nii -ot spm BB.nii RE mri_convert.bin -it nii -ot spm BB.nii RE $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from BB.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to RE... ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 2) convert .mgh file to .hdr file (.hdr and .img) [latifah:kim] (nmr-stable6-env) mri_convert -it mgh -ot spm AA.mgh RE.hdr mri_convert.bin -it mgh -ot spm AA.mgh RE.hdr $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from AA.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to RE.hdr... ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Converting .mgz (or .nii) file to .hdr file (.hdr and .img)
Dear expert, I'd like to convert .mgz (or .nii) file to .hdr file (.hdr and .img) to use .hdr in SPM software. I tried to convert the file using "mri_convert". But, there were the error messages below. Please, let me know how to onvert .mgz (or .nii) file to .hdr file (.hdr and .img). 1) convert .nii file to .hdr file (.hdr and .img) [latifah:kim] (nmr-stable6-env) mri_convert -it nii -ot spm BB.nii RE mri_convert.bin -it nii -ot spm BB.nii RE $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from BB.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to RE... ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 2) convert .mgh file to .hdr file (.hdr and .img) [latifah:kim] (nmr-stable6-env) mri_convert -it mgh -ot spm AA.mgh RE.hdr mri_convert.bin -it mgh -ot spm AA.mgh RE.hdr $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from AA.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to RE.hdr... ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfield volumes.
External Email - Use Caution Hi, I want to extract hippocampal subfield volume from longitudinal samples. I ran recon-all-all with longitudinal pipeline for all those samples in FreeSurfer 6.0. How I need to process further (Commands that I need to follow). Would you please help me out? Regards Devika K ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
