Hi Akshay the -cs flag specifies the voxel size, not the field of view, so you are creating a volume with 256mm voxels! Try --cw256 instead.
cheers Bruce On Tue, 7 May 2013, Akshay wrote: > > mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256 > > On 5/7/13 2:55 PM, Bruce Fischl wrote: >> can you send me the full mri_convert command line that is run? >> On Tue, 7 May 2013, Akshay wrote: >> >>> Hi Bruce >>> >>> Please find the file attached >>> >>> Best, >>> >>> Akshay >>> >>> >>> On 5/7/13 2:40 PM, Bruce Fischl wrote: >>>> Hi Akshay >>>> >>>> is you send us that file we'll take a look. >>>> >>>> cheers >>>> Bruce >>>> On Tue, 7 May 2013, Akshay wrote: >>>> >>>>> Hi All, >>>>> >>>>> I am re-posting this question since there was no response to my >>>>> previous >>>>> attempt. >>>>> >>>>> I have a problem conforming certain nifti files, the following is the >>>>> log when i try to convert them, >>>>> >>>>> reading from >>>>> /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... >>>>> INFO: using NIfTI-1 qform >>>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>>>> i_ras = (0, -4.99113e-10, -1) >>>>> j_ras = (-4.99113e-10, -1, 4.99113e-10) >>>>> k_ras = (-1, 4.99113e-10, 0) >>>>> WARNING >>>>> ==================++++++++++++++++++++++++======================================= >>>>> The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot >>>>> fit in 256^3 mm^3 volume. >>>>> The resulting volume will have 282 slices. >>>>> If you find problems, please let us know >>>>> (freesurfer@nmr.mgh.harvard.edu). >>>>> ==================================================++++++++++++++++++++++++=============== >>>>> >>>>> Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, >>>>> 180) voxels. >>>>> Data is conformed to 1 mm size and 282 voxels for all directions >>>>> Reslicing using nearest >>>>> >>>>> >>>>> This is understood, however I want them to be conformed to 256^3 >>>>> mm. If >>>>> I use -cs 256 flag, it does resample the image to 256^3mm but the >>>>> image >>>>> is blank. >>>>> >>>>> Is there something wrong I am doing? How do I conform these files >>>>> to 256^3mm? >>>>> >>>>> Any help will be greatly appreciated. >>>>> >>>>> Best, >>>>> >>>>> Akshay >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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
