Hi Sasha,
try:
tkmedit 2332 orig/001.mgz
On Mon, 29 Aug 2005, Sasha Wolosin wrote:
Sorry to send this twice, but I should have elaborated:
I am trying to convert files to mgz format. I was able to run mri_convert, but
when I run csurf and attempt to open the orig volume, I get the error:
"First orig image:
/freesurfer/subjects/2332/mri/orig/COR-001 not found"
Does anyone know why this may happen?
Here is the command and output:
[EMAIL PROTECTED] /freesurfer]# cd subjects/2332/mri/orig
[EMAIL PROTECTED] orig]# ls
2332_analyze 2332_crsg
[EMAIL PROTECTED] orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz
mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz
reading from 2332_crsg/001...
124 DICOM 3.0 files in list
Found 124 DICOM Files
WARNING: NumberOfFrames 0 != Found Count of slices 124.
reading DICOM image...
-------------------------------------------------
DICOM meta-header
file name 2332_crsg/001
Date and time
study date 20030630
study time 101639.0000
series time 104735.12
acquisition time 104735.12
Identification
patient name ...
manufacturer Philips Medical Systems
Dimensions
number of rows 256
number of columns 256
number of frames 124
pixel width 0.9375
pixel height 0.9375
slice thickness 1.5
field of view 240
image number 1 (might be not reliable)
Acquisition parameters
echo time 6.00003
repetition time 35
inversion time not found
echo number 1
flip angle 0.785398
bits allocated 16
Spatial information
first image position -114.756 -101.936 133.356
last image position -126.115 82.1994 135.698
image orientation 0.998088 0.0614863 0.00638348 0.00559035
0.0130627 -0.999899
-------------------------------------------------
TR=35.00, TE=6.00, TI=0.00, flip angle=45.00
i_ras = (-0.998088, -0.0614863, 0.00638348)
j_ras = (-0.00559035, -0.0130627, -0.999899)
k_ras = (0.0615663, -0.998022, 0.0126937)
writing to 001.mgz...
[EMAIL PROTECTED] orig]# csurf
Thanks,
Sasha
Sasha Wolosin
Research Assistant
Developmental Cognitive Neurology
Kennedy Krieger Institute
707 N. Broadway
Baltimore, MD 21205
ph: (443) 923-9270
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