Hi,
I need to import large numbers of freesurfer datasets (5 x ~400). I have already managed to import single subjects but cannot see how to automatise this process so that the import pipeline automatically imports all subjects in one directory.
Could you please point me in the right direction.
Thanks
parallel importation from freesurfer
Re: parallel importation from freesurfer
Hi,
It seems not very clear what you mean by "the import pipeline automatically imports all subjects in one directory". I guess that you want to import each data into only one brainvisa database. But in this case, each data will be imported into directory something like that : "Database->proto-> sujet->T1mri'
(see http://brainvisa.info/doc/axon-4.2/bv_m ... /ch04.html)
Have you ever used the iteration mode in BrainVISA ? This mode allows to iterate the same process on several data.
Here are the main steps in few words:
1) open the "Import From FreeSrufer to T1 pipeline"
2) set the "use_t1pipeline" to "don't used it'
3) click on "Iterate" -> a new window is opening
4) From this new window, click on the green button on the "T1_orig"
-> Select (the inputs) many T1 from your freesurfer database by clicking on the left button and Ctrl key
5) Click on the red button on the "T1_output"
-> you have to create the subjects for the brainvisa database (database with the brainvisa 3.1.0 ontology)
-> for more visibility, select attributes like this: 'database='<select one database>, 'data type = raw t1 mri', 'file format=NIFTI-1 format'
-> select or create a protocol
-> in the subject field, type the output names with a space between them, for example, you can type : "subj1 subj2". if you do this, 2 outputs will be created and you will see them on the right panel. The number of outputs must be the same than the number of inputs.
6) Click OK, and now you obtain a tree of iterations
7) Take a look at the tree to check the process parameters of some of process. All parameters must be filled out and the "use_t1pipeline" is always set to "don't used it'
(more details on http://brainvisa.info/doc/axon-4.2/bv_m ... 03s07.html)
Once you have imported data, you can use Morphologist (T1 pipeline) as usual. Have you ever processed data with Morphologist ?
If you can access to parallel computing resources (multiple core machines, clusters or grids), do you know that yo can use Soma-workflow by choosing "Run in parallel" ?
For more information, please take a look at http://brainvisa.info/doc/axon-4.2/bv_m ... /ch06.html
Isabelle
Note = you can use "use_t1pipeline = in batch" but in this case it takes a long time because the process will launch some steps of Morphologist
It seems not very clear what you mean by "the import pipeline automatically imports all subjects in one directory". I guess that you want to import each data into only one brainvisa database. But in this case, each data will be imported into directory something like that : "Database->proto-> sujet->T1mri'
(see http://brainvisa.info/doc/axon-4.2/bv_m ... /ch04.html)
Have you ever used the iteration mode in BrainVISA ? This mode allows to iterate the same process on several data.
Here are the main steps in few words:
1) open the "Import From FreeSrufer to T1 pipeline"
2) set the "use_t1pipeline" to "don't used it'
3) click on "Iterate" -> a new window is opening
4) From this new window, click on the green button on the "T1_orig"
-> Select (the inputs) many T1 from your freesurfer database by clicking on the left button and Ctrl key
5) Click on the red button on the "T1_output"
-> you have to create the subjects for the brainvisa database (database with the brainvisa 3.1.0 ontology)
-> for more visibility, select attributes like this: 'database='<select one database>, 'data type = raw t1 mri', 'file format=NIFTI-1 format'
-> select or create a protocol
-> in the subject field, type the output names with a space between them, for example, you can type : "subj1 subj2". if you do this, 2 outputs will be created and you will see them on the right panel. The number of outputs must be the same than the number of inputs.
6) Click OK, and now you obtain a tree of iterations
7) Take a look at the tree to check the process parameters of some of process. All parameters must be filled out and the "use_t1pipeline" is always set to "don't used it'
(more details on http://brainvisa.info/doc/axon-4.2/bv_m ... 03s07.html)
Once you have imported data, you can use Morphologist (T1 pipeline) as usual. Have you ever processed data with Morphologist ?
If you can access to parallel computing resources (multiple core machines, clusters or grids), do you know that yo can use Soma-workflow by choosing "Run in parallel" ?
For more information, please take a look at http://brainvisa.info/doc/axon-4.2/bv_m ... /ch06.html
Isabelle
Note = you can use "use_t1pipeline = in batch" but in this case it takes a long time because the process will launch some steps of Morphologist
Re: parallel importation from freesurfer
Thank you very much Isabelle, this was very helpful particularly because it was not clear to me that I could type in "subj1 subj2" to create the subjects in the brainvisa ontology.
All the rest seems to be working fine although I have only tested that with 2 subjects and I now need to see if all is ok with 400....
Cheers
All the rest seems to be working fine although I have only tested that with 2 subjects and I now need to see if all is ok with 400....
Cheers
Re: parallel importation from freesurfer
Hi,
Yes, I think it's a good practice to try only some data from the importation to the last step (do you want to use the sulci recognition ?), perhaps with many groups of 10, to be sure to set correct options/parameters in order to process really what you want and to trace back potential problems.
Isa
Yes, I think it's a good practice to try only some data from the importation to the last step (do you want to use the sulci recognition ?), perhaps with many groups of 10, to be sure to set correct options/parameters in order to process really what you want and to trace back potential problems.
Isa