You're using mrinfo incorrectly. in order to get the gradient information you need to use it with the dicoms not the nifti output from mrconvert. > mrinfo /dir/to/diffusion/dicoms/ -grad /output.txt This will give you the phase encoding info in a text file On 26/07/2014 6:42 pm, "Erdem Ergen" <[log in to unmask]> wrote: > No, I have not used it before, thank you for information. > I can not use it with -grad option. Without -grad option mrinfo's output > is; > *erdem@erdem-virtual-machine:~/Documents/mrtrix-read-only$* mrconvert > /home/erdem/Desktop/Test/DICOM/12032816 ./out_img.nii.gz > mrconvert: scanning DICOM set "/home/erdem/Desktop/Test/DICOM/12032816" - > ok > Select series ('q' to abort): > 0 - 176 MR images 16:21:28 t1_mpr_sag_iso (*tfl3d1_ns) [2] > 1 - 62 MR images 16:23:13 ep2d_diff_mddw_30_p2 (*ep_b1000#5) [3] > 2 - 45 MR images 16:29:31 ep2d_diff_mddw_30_p2_ADC (*ep_b0_1000) [4] > 3 - 45 MR images 16:29:31 ep2d_diff_mddw_30_p2_TRACEW (*ep_b1000t) [5] > 4 - 45 MR images 16:29:31 ep2d_diff_mddw_30_p2_FA (*ep_b0_1000) [6] > 5 - 45 MR images 16:29:32 ep2d_diff_mddw_30_p2_ColFA (?) [7] > 6 - 72 MR images 16:30:41 gre_field_mapping (*fm2d2r) [9] > 7 - 36 MR images 16:30:41 gre_field_mapping (*fm2d2r) [10] > 8 - 113 MR images 16:32:40 ep2d_pace_dynt_moco 103 (*epfid2d1_64) [11] > 9 - 113 MR images 16:32:40 act_MoCoSeries (*epfid2d1_64) [12] > 10 - 1 MR images 16:37:32 Design (*epfid2d1_64) [13] > 11 - 1 MR images 16:37:32 EvaSeries_GLM (*epfid2d1_64) [14] > 12 - 3 MR images 16:37:32 Mean_&_t-Maps (*epfid2d1_64) [15] > 13 - 179 MR images 16:39:53 ep2d_tra_pasl_p2 140 (*epfid2d1_64) [16] > 14 - 179 MR images 16:39:53 MoCoSeries (*epfid2d1_64) [17] > 15 - 1 MR images 16:46:17 Perfusion_Weighted (*epfid2d1_64) [18] > 16 - 1 MR images 16:46:17 relCBF (*epfid2d1_64) [19] > ? 1 > mrconvert: reading DICOM series "ep2d_diff_mddw_30_p2"... 100% > mrconvert: DICOM image contains multiple frames - reformating... 100% > mrconvert: copying data... 100% > *erdem@erdem-virtual-machine:~/Documents/mrtrix-read-only$* mrinfo -grad > out_img.nii.gz > mrinfo: expected at least 1 arguments (0 supplied) > *erdem@erdem-virtual-machine:~/Documents/mrtrix-read-only$ *mrinfo -grad > ./out_img.nii.gz > mrinfo: expected at least 1 arguments (0 supplied) > *erdem@erdem-virtual-machine:~/Documents/mrtrix-read-only$* mrinfo > ./out_img.nii.gz > ************************************************ > Image: "./out_img.nii.gz" > ************************************************ > Format: NIfTI-1.1 > Dimensions: 128 x 128 x 45 x 62 > Voxel size: 2 x 2 x 2 x ? > Dimension labels: 0. left->right (mm) > 1. posterior->anterior (mm) > 2. inferior->superior (mm) > 3. undefined (?) > Data type: unsigned 16 bit integer (little endian) > Data layout: [ +0 +1 +2 +3 ] > Data scaling: offset = 0, multiplier = 1 > Comments: Kirkar Ali Emir (2 > study: EGE BEYIN; DOB: 04/02/2003; DOS: 28/03/2012 > 16:23:13 > Transform: 0.9975 6.938e-08 -0.07125 -126.6 > -0.002623 0.9993 -0.03672 -142.7 > 0.0712 0.03681 0.9968 -41.47 > 0 0 0 1 > *erdem@erdem-virtual-machine:~/Documents/mrtrix-read-only$ * > So how should I progress? >