Hi Michele,
It might not be the most direct way of converting your data to COR format, but AFNI has a good utility for dealing with GE data:
http://afni.nimh.nih.gov/pub/dist/doc/program_help/Ifile.html
Then you can use mri_convert to get from AFNI to COR format. Here's an example:
[antimony:07129] (nmr-dev-env) ls 008 I.001 I.014 I.027 I.040 I.053 I.066 I.079 I.092 I.105 I.118 I.002 I.015 I.028 I.041 I.054 I.067 I.080 I.093 I.106 I.119 I.003 I.016 I.029 I.042 I.055 I.068 I.081 I.094 I.107 I.120 I.004 I.017 I.030 I.043 I.056 I.069 I.082 I.095 I.108 I.121 I.005 I.018 I.031 I.044 I.057 I.070 I.083 I.096 I.109 I.122 I.006 I.019 I.032 I.045 I.058 I.071 I.084 I.097 I.110 I.123 I.007 I.020 I.033 I.046 I.059 I.072 I.085 I.098 I.111 I.124 I.008 I.021 I.034 I.047 I.060 I.073 I.086 I.099 I.112 SERHDR.008 I.009 I.022 I.035 I.048 I.061 I.074 I.087 I.100 I.113 I.010 I.023 I.036 I.049 I.062 I.075 I.088 I.101 I.114 I.011 I.024 I.037 I.050 I.063 I.076 I.089 I.102 I.115 I.012 I.025 I.038 I.051 I.064 I.077 I.090 I.103 I.116 I.013 I.026 I.039 I.052 I.065 I.078 I.091 I.104 I.117
[antimony:07129] (nmr-dev-env) Ifile 008/I.* ++ using time stamp. ++ using slice pattern alt+z ++ using output directory afni ++ Expanding file list ... ++ found 124 '*/I.*' files ++ Scanning GE headers ++ 124 files are good images ++ File time threshold = 10 s
RUN 01: 008/I.001 .. 008/I.124 124 images 1 Volume(s)
Found 1 complete scans. Run GERT_Reco to create AFNI bricks.
[antimony:07129] (nmr-dev-env) ./GERT_Reco Will use OutBrick_r1 for this data set. Forming image list ...
From 008/I.001 ...
to 008/I.124 Done with File List. on to To3D ...
Now Running: to3d -save_outliers OutBrick_r1_Outliers.1D -epan -prefix OutBrick_r1 -time:zt 124 1 0 alt+z -@ < ./PangaList
to3d: 2D slices into 3D datasets for AFNI, by RW Cox ++ WARNING: TR expressed in milliseconds will be converted to TR=0.000000s Illegal value of nt after -time: option Counting images: total=124 2D slices Reading images: ......................................... 3D dataset written to disk Done with To3D.
READY. \012Either execute:
cd afni afni &
Or <rescan this> in afni
[antimony:07129] (nmr-dev-env) ls afni/ OutBrick_r1+orig.BRIK OutBrick_r1+orig.HEAD
[antimony:07129] (nmr-dev-env) mkdir COR
[antimony:07129] (nmr-dev-env) mri_convert afni/OutBrick_r1+orig.BRIK COR/ mri_convert afni/OutBrick_r1+orig.BRIK COR/ reading from afni/OutBrick_r1+orig.BRIK... AFNI Header Information ============================================ DATASET_RANK : spatial dims 3, sub-bricks 1 DATASET_DIMENSIONS: (256, 256, 124) TYPESTRING : 3DIM_HEAD_ANAT SCENE_DATA : view type 0, func type 2, verify 0 ORIGIN : (-126.031197, -122.851402, -46.322140) DELTA : (0.937500, 0.937500, 1.000000) IDCODE_STRING : XYZ_2zCmhd23DSvVbCOGq0klwg BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.000000 max 668.000000 BRICK_TYPES : short BRICK_FLOAT_FACS : 0.000000 ==================================================================== BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 668.000000 <--> actual max = 668.000000 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) Original Data has (0.9375, 0.9375, 1) mm size and (256, 256, 124) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to COR/... [antimony:07129] (nmr-dev-env)
Hope that helps, -a
--- Adam Thomas adamt@nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370
-----Original Message----- From: Michele Perry [mailto:mperry@ucsd.edu] Sent: Thursday, September 01, 2005 5:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_convert with *.IMG
Hi, I was given some MRI structural data originally scanned on a GE Signa 5. It was converted from Genesis to 8-bit *.tif's and 16-bit *.IMG's (with corresponding *.HDR files). The raw data is 256 pixels x 256 pixels x 2 bytes, little endian Intel. There are 124 .TIF, .IMG and .HDR files I have tried to convert from .IMG to COR using mri_convert -it <see below> -ot cor /path/001.IMG $SUBJECTS_DIR/subjid/mri/orig
Here's what I get...
-it anaylze -ot cor (I get errors if I don't give an output type) (result: reading from /path/001.IMG... analyzeRead(): cannot find any files for /path/001.IMG)
-it ge -ot cor (result: reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG)
-it gelx -ot cor reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG
I have tried running this with the .IMG files in their own separate directory and in a directory with the .HDRs and .TIFs. I've also tried running it without specifing the .IMG file, just the directory.
Any ideas what I'm doing wrong? Michele
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