Hi,
I am using BrainVisa 4.1.1 under Linux Ubuntu 12.04 LTS 64bit.
I have a "subject" called "nema_2013_05_07" in the study folder "NEMA_phantom" and for a strange reason neither the study nor the subject appears in the BrainVisa database. I tried to move the "nema_2013_05_07" subject folder into another study folder renamed "phantom" containing other files, all the other files appear correctly in the database but the NEMA one is still not. I have been scratching my head about it for the past 2 hours and cannot find any explanation....
There are no space or special characters in the folders name nor in the file names (except a "." but this is also the case for another phantom and it works fine).
Any ideas?
Thanks
Rv
study/subject not appearing in database
study/subject not appearing in database
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
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Re: study/subject not appearing in database
Hi,
The study/subject names seem OK.
Have you updated the database ?
Denis
The study/subject names seem OK.
Have you updated the database ?
Denis
Re: study/subject not appearing in database
Hi,
Yes I did update the databases. I even tried to delete all the database files and update again. I also tried to copy just these folder on another disk and create a new database, it still does not work...
Cheers,
Rv
Yes I did update the databases. I even tried to delete all the database files and update again. I also tried to copy just these folder on another disk and create a new database, it still does not work...
Cheers,
Rv
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: study/subject not appearing in database
Then I guess something else is wrong in the files organization. How have the data of this subject been included in the brainvisa database ? Is there a T1 MRI, and has is been imported using the import process ?
The raw T1 MRI should be located like this:
Here "default_acquisition" may be a different directory, but the MRI file should have the same file name as the subject directory. The MRI file extension may be different if it is a different format (.ima+.dim, .nii.gz, .mnc, .img+.hdr etc).
You can also check things using the "database explorer", a process in "data management". It shows database directories trees like a file system browser, but shows files/directories which are recognized within BV databases or not: when clicking on a data or a directory, the right panel displays information like data type and database organization properties.
BrainVisa 4.1 is rather old but it should work...
Denis
The raw T1 MRI should be located like this:
Code: Select all
<database_dir>/NEMA_phantom/nema_2013_05_07/t1mri/default_acquisition/nema_2013_05_07.nii
You can also check things using the "database explorer", a process in "data management". It shows database directories trees like a file system browser, but shows files/directories which are recognized within BV databases or not: when clicking on a data or a directory, the right panel displays information like data type and database organization properties.
BrainVisa 4.1 is rather old but it should work...
Denis
Re: study/subject not appearing in database
Hi,
OK so, I checked the name of the files, there was a discrepancy, i.e. the folder name was in lower case and the file name in upper case... I changed this, no effect.
Just to clarify, I have only PET and CT files in each subject folders, there is no T1 MRI associated with this study. To avoid mistake when I copy files onto the hard disk, I use a template of folder and subfolder so that they are all identical.
I used the database browser as you suggested, and I can see the NEMA_2013_05_07 folder (subject) in the "Phantom" study. However, I am not too sure about what I should see or look for in the right panel of the database browser?
I have attached a screenshot of the database browser view for the Phantom study folder and sub-folders. All folders have a tag "identified=True" whereas all the pet.v files have the their tag "identified=False". Am I right in guessing that this is the culprit? If so, what's wrong? How to make those files identified by BV?
Cheers,
Rv
OK so, I checked the name of the files, there was a discrepancy, i.e. the folder name was in lower case and the file name in upper case... I changed this, no effect.
Just to clarify, I have only PET and CT files in each subject folders, there is no T1 MRI associated with this study. To avoid mistake when I copy files onto the hard disk, I use a template of folder and subfolder so that they are all identical.
I used the database browser as you suggested, and I can see the NEMA_2013_05_07 folder (subject) in the "Phantom" study. However, I am not too sure about what I should see or look for in the right panel of the database browser?
I have attached a screenshot of the database browser view for the Phantom study folder and sub-folders. All folders have a tag "identified=True" whereas all the pet.v files have the their tag "identified=False". Am I right in guessing that this is the culprit? If so, what's wrong? How to make those files identified by BV?
Cheers,
Rv
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- brainvisa_database_browser_screenshot.png (205.49 KiB) Viewed 7981 times
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: study/subject not appearing in database
Yes, the "identified=False" is the problem (or the "?" on the icon on the left panel of the database explorer).
Was the nuclear imaging toolbox in the standard brainvisa 4.1 ? I don't remember... and I guess it is not included in later releases (which perhaps explains why you are using version 4.1)
However, I had a look at the files organization: PET images have a prefix to distiguish betxween human/animal and type of camera:
humans:
- h* for HR+1 camera
- i* for HR+2 camera
- j* for HRRT camera
- T* or PET_* for Biograph
phantoms:
- f* for HR+1
- g* for HR+2
- k* for HRRT
- m* for FOCUS
animals:
- a* for HR+1
- b* for HR+2
- c* for HRRT
- u0* for FOCUS
- v0* for INVEON
Don't ask me why those prefixes, ar what they change in processings, I'm not a PET expert.
Anyway that explains why "brain_phantom..." is recognized: starting with "b" it is recognized as an animal, HR+2 camera PET dataset, but "NEMA..." is not, because it does not start with one of the listed prefixes.
So you should prepend the correct prefix in the filename.
Denis
Was the nuclear imaging toolbox in the standard brainvisa 4.1 ? I don't remember... and I guess it is not included in later releases (which perhaps explains why you are using version 4.1)
However, I had a look at the files organization: PET images have a prefix to distiguish betxween human/animal and type of camera:
humans:
- h* for HR+1 camera
- i* for HR+2 camera
- j* for HRRT camera
- T* or PET_* for Biograph
phantoms:
- f* for HR+1
- g* for HR+2
- k* for HRRT
- m* for FOCUS
animals:
- a* for HR+1
- b* for HR+2
- c* for HRRT
- u0* for FOCUS
- v0* for INVEON
Don't ask me why those prefixes, ar what they change in processings, I'm not a PET expert.
Anyway that explains why "brain_phantom..." is recognized: starting with "b" it is recognized as an animal, HR+2 camera PET dataset, but "NEMA..." is not, because it does not start with one of the listed prefixes.
So you should prepend the correct prefix in the filename.
Denis
Re: study/subject not appearing in database
Hi Denis,
Spot on! That was the culprit!! Changing the first characters of the PET file to "m_" solved the problem, I can now select the files in Brainvisa.
Thanks a lot!
Rv
Spot on! That was the culprit!! Changing the first characters of the PET file to "m_" solved the problem, I can now select the files in Brainvisa.
Thanks a lot!
Rv
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________