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. >>> >> >>
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