I'm not sure why the PD would be two frames -- the files were downloaded as dcm from the ADNI database. After looking through them though, there was a repeat of the slices, so I removed the second frame. Seems to have solved the problem, as the reslice is working now.
On Thu, Jun 23, 2011 at 09:28, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > p.s. also, why are you specifying --like and -rl? > > On Thu, 23 Jun 2011, G. William Chapman IV wrote: > > The files have been dropped.https://www.nmr.mgh.** >> harvard.edu/facility/filedrop/**showgroup/24787/1/** >> d2a16267b417faa9da6f7cff3c3622**8a<https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267b417faa9da6f7cff3c36228a> >> >> >> >> >> On Wed, Jun 22, 2011 at 13:21, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> if you file drop these volumes we'll take a look >> Bruce >> >> On Wed, 22 Jun 2011, G. William Chapman IV wrote: >> >> Hello all, >> I'm attempting to use mri_convert in order to match the slice size >> and >> thickness of T2 and PD images to the Freesurfer T1 images, after >> converting >> the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using: >> >> mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz >> --like >> ${SUBJECT}/mri/norm.nii.gz ${**SUBJECT}/T2/T2_like_norm.nii.**gz >> >> And having no problems. However, using the same code for the PD >> images I'm >> arriving at a bus error each time (output below). Is there any >> possible work >> around for this? >> >> (freesurfer-Darwin-leopard-**i686-stable-pub-v5.0.0) >> >> --- >> >> bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl >> ${SUBJECT}/mri/norm.nii.gz >> --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.** >> nii.gz >> >> mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl >> 003_S_0907_M00/mri/norm.nii.gz >> --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_** >> norm.nii.gz >> >> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ >> >> reading from 003_S_0907_M00/PD/PD.nii.gz... >> >> TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 >> >> i_ras = (-1, 2.05103e-10, 0) >> >> j_ras = (-2.05103e-10, -1, 0) >> >> k_ras = (-0, -0, 1) >> >> reading template info from volume 003_S_0907_M00/mri/norm.nii.** >> gz... >> >> INFO: transform src into the like-volume: >> 003_S_0907_M00/mri/norm.nii.gz >> >> Bus error >> >> >> >> >> >> >> >> 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<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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