open-discussion > CONN automating
Showing 1-5 of 5 posts
Display:
Results per page:
Oct 9, 2018  06:10 AM | Abdullah BAS - Ercıyes
CONN automating
How can we automate setup process ?

How can we use wildcard adressing for CONN setup part ? It is very hard to prepare setup at CONN and it takes too much time..

Thanks.
Oct 9, 2018  01:10 PM | Gregory Bator
RE: CONN automating
I write here, cause I want to see the solution.
I've to agree and it's not as easy it should be.
Oct 10, 2018  12:10 AM | Abdullah BAS - Ercıyes
RE: CONN automating
I have found a code struct in conn toolbox and it was for automating all processes but it is independent of normal conn gui so it can be a problem so i modified it and it is just working for setup part and you can check the parameters from gui. It took just 5 minutes to prepare setup process.

Thanks.
Oct 10, 2018  12:10 AM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: CONN automating
Hi,

Using Conn GUI to quickly specify functional and structural images is easy. In the structural or functional tab, you will note on the right side that there is a list of folders in your present working directory. Further on the lower right side you will notice the following:

.img; *.nii; *.gz; *-1.dcm

Now, let us say that all your structural files are named as *T1w*.nii. Edit this location to read *T1w*.nii and click on "Find". Conn will list all the found files below the list of folders. You can select all your subjects on the left pane and all the found files in the right side and simply click on Select. This will assign one file per subject. You can similarly do this for the functional scans. If the ordering of subjects is not inconsistent, you can do this in less than a minute and finish most of the Setup. The GUI also supports using regular expressions in case the above does not solve your problem completely.

That said, if you prefer scripting, just make a Conn Batch file (see the batch manual on how to specify the Batch parameters). This is very efficient.

Hope this helps


Best
Pravesh

Originally posted by Abdullah BAS:
I have found a code struct in conn toolbox and it was for automating all processes but it is independent of normal conn gui so it can be a problem so i modified it and it is just working for setup part and you can check the parameters from gui. It took just 5 minutes to prepare setup process.

Thanks.
Oct 11, 2018  07:10 AM | Abdullah BAS - Ercıyes
RE: CONN automating
Hi Pravesh,

    I use the conn_batch function but it has all the analyses codes so i modified it to create just setup. I have looked to CONN manual for scripting.

    Simply, the setup takes too much time and it is easy to mix up at GUI.  I want to use something like that  'E:/Dataset/*(All Groups)/*(All Subjects)/*T1w*.nii. When you insert this string to Matlab function will assign all subject's files to all subject's fields so you can control setup fields from GUI and then you could just do analyses from GUI as you do. It is working correctly now and takes less than 5 mins for 36 subjects. 

I was asking the time and the mixing up problem but it has solved.

Thanks for replying I appreciated.

-Abdullah
Originally posted by Pravesh Parekh:
Hi,

Using Conn GUI to quickly specify functional and structural images is easy. In the structural or functional tab, you will note on the right side that there is a list of folders in your present working directory. Further on the lower right side you will notice the following:

.img; *.nii; *.gz; *-1.dcm

Now, let us say that all your structural files are named as *T1w*.nii. Edit this location to read *T1w*.nii and click on "Find". Conn will list all the found files below the list of folders. You can select all your subjects on the left pane and all the found files in the right side and simply click on Select. This will assign one file per subject. You can similarly do this for the functional scans. If the ordering of subjects is not inconsistent, you can do this in less than a minute and finish most of the Setup. The GUI also supports using regular expressions in case the above does not solve your problem completely.

That said, if you prefer scripting, just make a Conn Batch file (see the batch manual on how to specify the Batch parameters). This is very efficient.

Hope this helps


Best
Pravesh

Originally posted by Abdullah BAS:
I have found a code struct in conn toolbox and it was for automating all processes but it is independent of normal conn gui so it can be a problem so i modified it and it is just working for setup part and you can check the parameters from gui. It took just 5 minutes to prepare setup process.

Thanks.