[leonidastra86]

I am trying to make a cortical thickness analysis with BSSR but it doesn’t really work.

1)I made folder with the patients, smoothed atlas.pvc-thickness_0-6mm.smooth2.5mm.right/left.mid.cortex.dfs files for both sides.
2)Smoothing for the abc.svreg.inv.jacobian.nii.gz files didn’t really work
3)After installing R, R Suite and the BSSR through R Suite I am trying with the following path to start but comes always to an error :

bss_data <- load_bss_data (type=”cbm”,
subjdir = /Users/leonidastra86/Desktop/ICBM25
csv = “/Users/leonidastra86/Desktop/ICBM25/ABC_demographics_tbm.csv – sample_demographics_tbm.csv”, hemi=”left”, smooth=2,5)

and the error:
Error: unexpected ‘,’ in ” csv = “/Users/leonidastra86/Desktop/ICBM25/ABC_demographics_tbm.csv – sample_demographics_tbm.csv”,”

Error: unexpected ‘/’ in:
“bss_data <- load_bss_data (type=”cbm”,
subjdir = /”

I have no idea from programming and I need your help to analyse my data.

Thank you in advance and thumbs up for your work on the program.

[yeunkim]

Hi,

In this command:

bss_data <- load_bss_data (type=”cbm”,
subjdir = /Users/leonidastra86/Desktop/ICBM25
csv = “/Users/leonidastra86/Desktop/ICBM25/ABC_demographics_tbm.csv – sample_demographics_tbm.csv”, hemi=”left”, smooth=2,5)

Could you try putting quotation marks around:
/Users/leonidastra86/Desktop/ICBM25

Could you also put just one csv file for the csv argument?
“/Users/leonidastra86/Desktop/ICBM25/sample_demographics_tbm.csv”

And use “.” for 2.5 for the smoothing level.

So the command would be something like:
bss_data <- load_bss_data (type=”cbm”,
subjdir = “/Users/leonidastra86/Desktop/ICBM25”,
csv = “/Users/leonidastra86/Desktop/ICBM25/sample_demographics_tbm.csv”, hemi=”left”, smooth=2.5)

Hope this helps.

Best,
Yeun

[leonidastra86]

Hi Yeun and thank you very much for your help.
After some changes that you suggested and some mistakes that I found in my data, I could form the right pathway.
It asks about the atlas, although I used the Brainsuite atlas.

Error: Could not determine the BrainSuite atlas used for registration.
Please check the log file /Users/leonidastra86/Desktop/ICBM25/1001/1001.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.

Any ideas?

[yeunkim]

Hi,

Could you open the /Users/leonidastra86/Desktop/ICBM25/1001/1001.svreg.log file and look at the second line and see if the path to your atlas exists? You may have to edit the path to the atlas folder in the *.svreg.log files.

I hope this made sense.

Best,
Yeun

[leonidastra86]

Oh God, I now know the problem. I analysed the Data with 2 Computers, half on a Windows computer (C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\) and half with a MacOs Computer (so the path is not the same).
Is there a solution for this? Do I need the svreg. files for all of the patients and edit the path every time or is it just for the first case? Because in the ICBM25 folder that I downloaded from the Brainsuite page was only on the first patient present.

[leonidastra86]

Problem was fixed, analysis was performed without any problems.
Thank you all so much for your help!

[leonidastra86]

Could I make the same thing but without covariates?
I am trying following command but without any success:
bss_model <- bss_anova(main_effect= “disease”, bss_data)

and I receive

Error in bss_anova(main_effect = “tinnitus”, bss_data) :
argument “bss_data” is missing, with no default

[fproessl]

Hey leonidastra86 –

I am running into a similar issue you did when trying to run the bssr:

Error: Could not determine the BrainSuite atlas used for registration.
Please check the log file C:/Users/Fproessl/Desktop/BACL_Visual/4010WK/4010WK.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.

Do you remember how you solved this? I tried to rename the filepath of the .log file but it did not work…

Thanks,
Felix

[leonidastra86]

The path to the atlas is in the .svreg text file.

However, I am trying to do the same analysis in windows and I get an error that the csv command is either wrong or not found.
I am using exactly the same command as before and it used to work…
What is the problem?

[astrologerdevanand]

The forum topic on BrainSuite discussing “Problem with BSSR” addresses issues related to BrainSuite’s BSSR (BrainSuite Spatial Registration) tool. Users often report challenges with the accuracy of spatial registration, which involves aligning brain images for analysis. Common problems include misalignment of brain structures, errors in transforming images to a common space, and software compatibility issues. Solutions typically involve troubleshooting software settings, ensuring accurate input data, and consulting user guides or community forums for advice on resolving specific issues related to BSSR.

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