Error Importing T1 MRI BrainSuite Folder to Brainstorm

Bugs
1

Dear Experts,

After put the brainsuite_labeldescriptions.xml together with 8 segmented MRI images from Brainsuite, I still get this problem. I can’t use FreeSurfer right now, because the files is too big and need high speed RAM to segmented the MRI Images. Hopefully, at this time I can use Brainsuite first to see the difference between two these kinds of software.

Please help me to fix this problem as possible.

** Error: Line 17: fileparts at 17
** Input must be a row vector of characters.
**
** Call stack:
** >fileparts.m at 17
** >import_anatomy_bs.m>get_fileprefix at 437
** >import_anatomy_bs.m at 127
** >import_anatomy.m at 54
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@import_anatomy,iSubject) at 470
**

Thank you,
Elaina

2

Dear Elaine,

Does it mean that BrainSuite generated this brainsuite_labeldescriptions.xml file, but you moved it somewhere else before importing in Brainstorm?
When you use the menu “Import anatomy folder”, you should select the entire folder generated by BrainSuite.

I cannot reproduce your error, I need some test data.
Can you please send me your BrainSuite segmentation folder?
Zip the output of BrainSuite (the entire folder), upload it somewhere (ex. www.dropbox.com) and send me the link in a separate email (click on my username on this forum).

Thanks,
Francois

3

Hi Elaine,

Apparently the BrainSuite developers made some changes to the organization of the output data. They will look into this in more details.
For now, I fixed the error that was stopping the import.
You can update Brainstorm and try again (menu Help > Update Brainstorm).

To import the anatomy:

  1. Right-click on the subject > Import anatomy folder
  2. Select the “Patient1” folder (not “Test data”)
  3. Yes, apply the transformation to the MRI
  4. Select the NAS/LPA/RPA points (and try to guess where the AC/PC points would be in a healthy brain)
  5. It should create all the surfaces correctly, but without the SVReg atlas.
    => To get the atlas, copy the file brainsuite_labeldescriptions_14May2014.xml into the folder “Patient1” before importing the folder.

Cheers,
Francois

1 Like
4

Dear Francois,

Thank you very much! Its works properly… I am so happy and can proceed my data analysis.

Thanks again,

Best,
Elaine

5

Hello,
I think I have a problem in the same area :
Whenever I try the MRI Segnmentation with Brainsuite, I get this message :

** Error: BrainSuite failed at step 2/2 (SVREG).

** Check the Matlab command window for more information.

Plus, I added the Brainsuite2021a in the Brainstorm Preferences, but it stills send me an error message that says that it is not downloaded whenever I try to import a CTnii file.

Thank you !

6

If you are using BrainSuite21a, you would need Matlab MCR for 2021a. You can download and install it from here.

Please make sure to install MCR for 2021a (version has to be exact). Also please install at the default location. Hope this works. Thank you for using BrainStorm and BainSuite.

1 Like