Dear all,

I am trying "RecommendedReconstruction", following Wiki instruction. My problem is, after the first step of recon-all ("recon-all -autorecon1") when I try to check the talairach transform (by tkregister2 --mgz ... --fstal), I get an image incorrectly aligned ... image is displayed in quadrant (pls see ac_aft_reconall1_target.jpg). In this display, I cannot manually adjust it for coregistration. When I continue to run autorecon2, it crashes.

For checking skull strip, it is correctly displayed (ac_aft_reconall1_tkmedit.jpg).

I thought problem could be already present in converting from dicom to mgz, as there seems to be some missing info (message_conv.txt), though I am not sure whether it is really relevant. The image was obtained by 3T GE magnet with SPGR at BWH.

Any thoughts regarding above are greatly appreciated.

Thanks in advance for your help.

Ryu Hashimoto

mri_convert -it dicom -ot mgz 001/ 001.mgz reading from 001/... 256 DICOM 3.0 files in list Found 256 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 256. reading DICOM image... ------------------------------------------------- DICOM meta-header

file name 001/dspgr_wa_001.dcm Date and time study date not found study time not found series time acquisition time Identification patient name not found manufacturer not found Dimensions number of rows 256 number of columns 256 number of frames 256 pixel width 0.94 pixel height 0.94 slice thickness 0.94 field of view 240.64 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time not found repetition time not found inversion time not found echo number not found flip angle not found bits allocated 16 Spatial information first image position 0 0 0 last image position 0 0 239.7 image orientation -1 0 0 0 -1 0 -------------------------------------------------

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -0, 0) j_ras = (-0, 1, 0) k_ras = (0, 0, 1) writing to 001.mgz...