Forum Replies Created
-
Posts
-
Hi Francois,
BrainSuite+SVReg is running fine on my computer so far. It has passed the stage where it showed error.
I am working with sample_auditory dataset. I downloaded it from brainstorm site, created a new subject in brainstorm and imported anatomy for sample_auditory there. Then I exported the mri as T1.nii
I ran brainsuite on this data with default parameters, except at skull extraction, I chose Edge constant=0.63 and Erosion Size=2.
Can you please make sure that this change was done when you ran the sequence? It could have caused bad extraction and then error later.The following was mentioned on the BrainSuite tutorial webpage on the BrainStorm site but now seems to be removed in the subsequent edits. I will reinsert it. Hope that it is fine.
For this tutorial data, the parameters for skull extraction need to be changed to get optimal results. Please set ‘Edge Constant=0.63’ and ‘Erosion Size=2’.
Thanks,
AnandHi Francois,
Thank you for reporting this. Did you get similar errors on other datasets (if you have processed other brains) with BrainSuite or only this one?
AnandHi Jon,
It is possible to create your own atlas using BrainSuite. Please check module 12 here:
http://brainsuite.org/processing/svreg/svreg_modules/
Please give it a try.
AnandI agree with David that the first issue related to time machine warning should be fixed by running Matlab using sudo as he explained. As such this should not affect the rest of the processing and you can safely ignore that warning.
Regarding the second issue related to the error during svreg processing, I think the surfaces are not probably extracted correctly. Before running SVReg, did the surfaces look like the ones shown in the screenshot below (right bottom windows)?
http://brainsuite.org/wp-content/uploads/2015/01/hemisplitpic.pngIf you can post or email me a screenshot that will help in addressing this.
Hi, It seems that the problems are fixed, but for the future, I recommend running
>conda update –all
after updating individual packages. This command will make sure that no dependencies are broken by the update.I tried it now but the stats.txt file was generated as expected. We will investigate it if we can reproduce the issue or if it reoccurs. Glad that things are working for you now.
Great! We will check if there is any issue in generating this file when the sequence is run through the gui and fix it. Thank you for reporting.
The file you are looking for is 20150427.roiwise.stats.txt right? fileprefix should be replaced by name of the subject. I am asking just to be sure.
Can you reproduce this error? Do you get the exact same error when you try again? Were there other programs running in the background as well? I recommend closing all programs and then running BrainSuite only to see how it works.
Hi Luca,
Yes, you need to install MCR for R2012a version of matlab. Higher or lower versions of MCR are not compatible. Once you install the correct MCR, and the VC++ 2010 redistributable, I think all the steps will work fine.
AnandBased on this, I think the SVReg sequence has not finished. There must be error. If you can try again and send us a screenshot of when the sequence stops, that will be helpful. When the SVReg sequence finishes (cmd line or gui) it generates the following outputs. SVReg generally takes 1-2 hrs.
http://brainsuite.org/processing/svreg/output/The file should have been generated. Which folder are you checking and can you please give me a list of files that are generated? Can you please give more information about version and platform that you are using? Also did you notice any error during the processing, did the sequence finish successfully?
You can use readdfs.m function available from http://brainsuite.org/processing/svreg/matlab/
to read your data into Matlab.I don’t think it is related to Matlab version as Matlab comes into play only later at the labeling step. Are you able to open the volume by opening brainsuite and then dragging and droppping nii volume into brainsuite interface?
Another alternative is to right click on the nii file in windows explorer, and then select open with-> BrainSuite15c.
Do any of these options work on your computer?
