Hi I think i understood it. Should i use mri_convert -rl template input output
from mri_convert.c printf("reading template info from volume %s...\n", reslice_like_name); template = MRIreadInfo(reslice_like_name); if(template == NULL) { fprintf(stderr, "error reading from volume %s\n", reslice_like_name); exit(1); Knut J On 10/15/2012 02:22 PM, Knut J Bjuland wrote: > I am able to convert using mri_convert, but when I try to reslice with > mri_convert -rl input output. I get the error message shown below. I > according to the documentation I could use mri_convert to reslice, but > it does not mention how I should set an vaule for the -rl input. Should > I use matlab instead please? > > http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert > > > mri_convert -rl 001.mgz 001t.mgz > mri_convert -rl 001.mgz 001t.mgz > > mri_convert: missing output volume name > > type mri_convert -u for usage > > > Knut J > > > On 10/15/2012 01:23 PM, Bruce Fischl wrote: >> Don't use the -I, just give it an input (the dicoms) and and output >> >> >> >> On Oct 15, 2012, at 1:23 AM, Knut J Bjuland <knut...@hotmail.com> wrote: >> >>> Hi Bruce >>> >>> I converted the dicom into 001.mgz. Then I tried to reslice. >>> >>> mri_convert -rl -i orig/001.mgz -o orig/001.mgz >>> mri_convert -rl -i orig/001.mgz -o orig/001.mgz >>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>> reading from orig/001.mgz... >>> TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00 >>> i_ras = (-0, -1, 0) >>> j_ras = (-0, -0, -1) >>> k_ras = (-1, 0, 0) >>> reading template info from volume -i... >>> >>> mri_read(): couldn't determine type of file >>> /home/knutjb/freesurfer/expo/test/mri/-i >>> error reading from volume -i >>> >>> Could you please give me an example on how to use mri_convert to reslice >>> please? >>> >>> >>> Knut J >>> >>> >>> >>> On 10/15/2012 12:43 AM, Bruce Fischl wrote: >>>> Hi Knut >>>> >>>> you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing >>>> the 125 into the 128 geometry (-rl) and go from there. >>>> >>>> cheers >>>> Bruce >>>> >>>> On Sun, 14 Oct 2012, Knut J Bjuland wrote: >>>> >>>>> Hi, >>>>> >>>>> When I import one subject with recon -i dicom -i dicom -s subjec, I get >>>>> this error message ERROR: inputs have mismatched dimensions! I think it >>>>> is caused by the fact that there is a different number of slices into >>>>> the two series. One series has 256x256x125 white the other has >>>>> 256x256x128. How can I detect if there is missing slices in the series >>>>> with 125 slices? What would you recommend me to do? Is is possible to >>>>> ask recon-all to bypass this error message and import both series? >>>>> >>>>> Knut J >>>>> >>>>> output >>>>> >>>>> k_ras = (-1, 0, 0) >>>>> writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... >>>>> ERROR: inputs have mismatched dimensions! >>>>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 >>>>> is >>>>> 256 x 256 x 125 while >>>>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 >>>>> is >>>>> 256 x 256 x 128 >>>>> Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC >>>>> 2012 x86_64 x86_64 x86_64 GNU/Linux >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> 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 Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer