import DTI data from siemens machine

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tulu
Posts: 28
Joined: Sun Apr 04, 2004 6:34 am

import DTI data from siemens machine

Post by tulu »

Dear DTI experts,
I am newbie in DTI. I use FC4 and Brainvisa 3.0. I have a series of dicom files from siemens machine and I use MRIcro to convert it as one T2 analyze image and a 4D series DWI image in analyze format. than I use Aims converter to convert these images as two separated .ima files. Finally I manually edit the .minf file by add 'bvalues' and 'diffusion_gradient_orientation'. my questions is:

1. how to import these data (t2 and 4D dwi file) into database ? I check datamanagement, import diffusion part but I don't know how which one I can choice. also I read the "diffusion data importation in BrainVISA database file" but I find AimsFileInfo did not have -o option, so it is difficult for me to follow this instruction. Can anyone give me a detail instruction ?
thanks for your help
JL H
JLH
neurologist
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Yann Cointepas
Posts: 316
Joined: Tue Jan 20, 2004 2:56 pm
Location: Neurospin, Saint Aubin, France
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Post by Yann Cointepas »

You are right, there is a copy-paste bug in the document "Diffusion data importation in BrainVISA database", AimsFileInfo is used instead of AimsSubVolume. The following lines:

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AimsFileInfo -i dicom_raw_data -o volume_00.ima -x 0 -X 22
AimsFileInfo -i dicom_raw_data -o volume_01.ima -x 23 -X 45
AimsFileInfo -i dicom_raw_data -o volume_02.ima -x 46 -X 68
AimsFileInfo -i dicom_raw_data -o volume_03.ima -x 69 -X 91
AimsFileInfo -i dicom_raw_data -o volume_04.ima -x 92 -X 114
AimsFileInfo -i dicom_raw_data -o volume_05.ima -x 115 -X 137
AimsFileInfo -i dicom_raw_data -o volume_06.ima -x 138 -X 160
AimsFileInfo -i dicom_raw_data -o volume_07.ima -x 161 -X 183
AimsFileInfo -i dicom_raw_data -o volume_08.ima -x 184 -X 206
AimsFileInfo -i dicom_raw_data -o volume_09.ima -x 207 -X 229
AimsFileInfo -i dicom_raw_data -o volume_10.ima -x 230 -X 252
AimsFileInfo -i dicom_raw_data -o volume_11.ima -x 253 -X 275
AimsFileInfo -i dicom_raw_data -o volume_12.ima -x 276 -X 298
AimsFileInfo -i dicom_raw_data -o volume_13.ima -x 299 -X 321
sould be replaced by:

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AimsSubVolume -i dicom_raw_data -o volume_00.ima -x 0 -X 22
AimsSubVolume -i dicom_raw_data -o volume_01.ima -x 23 -X 45
AimsSubVolume -i dicom_raw_data -o volume_02.ima -x 46 -X 68
AimsSubVolume -i dicom_raw_data -o volume_03.ima -x 69 -X 91
AimsSubVolume -i dicom_raw_data -o volume_04.ima -x 92 -X 114
AimsSubVolume -i dicom_raw_data -o volume_05.ima -x 115 -X 137
AimsSubVolume -i dicom_raw_data -o volume_06.ima -x 138 -X 160
AimsSubVolume -i dicom_raw_data -o volume_07.ima -x 161 -X 183
AimsSubVolume -i dicom_raw_data -o volume_08.ima -x 184 -X 206
AimsSubVolume -i dicom_raw_data -o volume_09.ima -x 207 -X 229
AimsSubVolume -i dicom_raw_data -o volume_10.ima -x 230 -X 252
AimsSubVolume -i dicom_raw_data -o volume_11.ima -x 253 -X 275
AimsSubVolume -i dicom_raw_data -o volume_12.ima -x 276 -X 298
AimsSubVolume -i dicom_raw_data -o volume_13.ima -x 299 -X 321
Once you have obtained the T2 volume (T2) and the diffusion-weighted 4D volume (DW), they can be put in a BrainVISA database by following a directories and file name pattern for a given protocol and subject. The pattern for the T2 and DW are respectively:

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BrainVISA_database/<protocol>/<subject>/diffusion/<subject>_t2_diffusion
BrainVISA_database/<protocol>/<subject>/diffusion/<subject>_dw_diffusion
For example, if you have a protocol named "test", a subject named "myself" and you are using the GIS format (with extension *.dim, *.ima), you should have the four following files in your database:

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BrainVISA_database/test/myself/diffusion/myself_t2_diffusion.dim
BrainVISA_database/test/myself/diffusion/myself_t2_diffusion.ima
BrainVISA_database/test/myself/diffusion/myself_dw_diffusion.dim
BrainVISA_database/test/myself/diffusion/myself_dw_diffusion.ima
tulu
Posts: 28
Joined: Sun Apr 04, 2004 6:34 am

Post by tulu »

Dear DTI expert,
thanks replay. I still have problem in analysis DTI image. After I get t2 & dw GIS image from Aims convert, I use DTI pipline process. When whole process finish, the "eye icon" did not appear and I did not get any diffusion map image such as FA or others. I think it because I did not use BrainVIsa database. but I don't know how to do that.
since my diffusion image is siemens file, I try to type " AimsSubVolume -i dicom_raw_data -o volume_00.ima -x 0 -X 22 " on the terminal console but it can not run.
I also try to type "BrainVISA_database/<protocol>/<subject>/diffusion/<subject>_t2_diffusion" on the terminal but I also get error message.
sincerely
JL H
JLH
neurologist
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