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Thank you for your response, I agree with you.
However I do need your help to come out of the problem. Are there advantages in the analysis of subcortical structures with brainsuite?
What makes Brainsuite a better solution, except for the time needed to analyse a patient?
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?
I run Brainsuite till the end (with registration and labeling and everything) and I get the excel files with the ROI volumes.
I afterwards divide the patients in 2 groups, those with the symptom and those without, and I compare their ROIs (the volumes of them).
I find significance in, for instance, 4 ROIs. That means that by the patients with the symptom these 4 regions are volumetric bigger than in the group without the symptom.
Normally, as a method, Brainsuite makes surface based morphometry, right? Just like freesurfer etc.
But in this case I compare ROIs (voxel numbers). Does it make my analysis a voxel based analysis or is it still a surface based analysis because of the software (Brainsuite)?
I ran all patients with brainsuite and did registration and labeling. Afterwards, I did a ROI comparison with SPSS, I found significance in 4 regions between the two groups of patients.
The question is : does brainsuite perform generally a surface based morphometry because of the method that is followed from svREG or is it voxel based morphometry when we compare just the ROIs produced through svREG?
- This reply was modified 2 years, 4 months ago by leonidastra86.
Do you have preinstalled any older version of brain suite? Try to radically remove everything and then re install it.
The 18a should work on Mac without using the above recommendation, just run it.
I have my results and started to write the paper. I have however two more questions:
1) The yellow/pink colours show an increase in cortical thickness and the blue colour a decrease, is it right?
2) Is there a way to press on the coloured region and see which structure it is? Some of them are easy to identify but some of them not.
I thank you so much for your help until now and I hope that sonn I will attend a Brain Suite course to learn much more about the software.November 21, 2017 at 8:02 am in reply to: How to perform comparision study from tractography and connectivity matrix data #958
Is there a guide for the comparison of the connectivity matrices?
Thats a good idea you gave me. Thank you!
I will use laterality as main effect and the symptom that I want to examine as a covariate!
I will tell you what I did and also a second idea, which I think won’t work.
What I did is : analysed the contralateral hemisphere for both and combined the results – the right hemisphere of the patients with a tumor on the left side and the left hemisphere of the patients with the tumor on the right side.
In this case, the results are accurate but not combined. I would rather be able to mirror the patients for example with tumor on the left side so that I would be able to do one analysis for all the patients.
Concerning the last sentence (just above this one) I had the following ideas:
To re-name the atlas.pvc-thickness_0-6mm.smooth2.5mm.left.mid.cortex.dfs
a)left to right (for the patients for example with left side tumors) so that all the tumors will be on the same side and the side analysed will be the one that I need (contralateral)
In this case, I am afraid that the volumetric results won’t be right, because the structures of the left side will have the values of the right side.
b)in place of left to write ipsilateral and in place of right to write contralateral (or reverse, according each time to each case).
In this case, I am afraid that bssr won’t even work.
What do you think?
I hope you can understand my thoughts.
I want to make a statistical analysis of the changes in cortex of the contralateral side in patients with infratentorial tumors.
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
So, I did it and played a little with the viewing options. It works really good.
However, I receive, after saving the new mask, 2 files (*.hdr and *.img) which cannot be opened as labels.
Is it normal?
I am really sorry, I didn’t see your message before. I will try it out and tell you.
I think it should be enough!
Warning: qform is already set. Nothing to do.
> In add_qform (line 69)
In load_nii_BIG_Lab (line 47)
In svreg_smooth_vol_function (line 34)