[carnico]

Dear Anand,

i’ve already done, actually.

And if i load my modified mri label file, BS load the default brainsuite_labeldescription.xml, despite the fact it is in my custom atlas folder. In this folder, that contains modified label file previously mentioned, there is only the modified brainsuite_labeldescription.xml.

Best Regards

[carnico]

Dear sychoi,

thanks for the answer. The ROIs I would include are from the Juelich Atlas, in particular the visual pathways, listed below.

Lateral_geniculate_body_L
Lateral_geniculate_body_R
Optic_radiation_L
Optic_radiation_R
Visual_cortex_V1_BA17_L
Visual_cortex_V1_BA17_R
Visual_cortex_V2_BA18_L
Visual_cortex_V2_BA18_R
Visual_cortex_V3V_L
Visual_cortex_V3V_R
Visual_cortex_V4_L
Visual_cortex_V4_R
Visual_cortex_V5_L
Visual_cortex_V5_R

The lateral geniculate nucleus are already in the BrainSuiteAtlas1, but I would include the Juelich atlas ones because they’re a little bigger and positioned slightly different.
Some ROIs are pure white matter (optic radiation), others grey matter or, at least, they should be, since V1 ROI, for example, included also some white matter portion.

By the way, I’ve managed to draw these ROIs in the BrainSuiteAtlas1 (briefly: Juelich 1 mm Atlas previously registered to the BrainSuiteAtlas1 > extraction of the ROIs of interest > binary transformation > loading in BS > mask transformation > draw the ROIs inside the masks > save the new atlas with the descriptions > copy the atlas in BS svreg directory > modify the svregmanifest xml file) but the process halted during svreg.

I think there is a problem with these ROIs.

Another strange thing that happens is the following. If I load my custom atlas (which is BSatlas1 with added ROIs) an then load the mri label file, when I go to label tool in label description tab, I found the description of the original labels, not the modified description whit added labels, despite in my custom atlas folder there is the modified description file. To see them, i’ve to load the labeldescription file manually.

Thanks a lot for the support.

Best Regards

[carnico]

Hi Anand,

actually there was a problem in skull stripping step, it was not so precise. Once manually corrected it ran correctly also without the flag.

Thanks

[carnico]

Hi to all,

I think I’ve the same problem.

The <fileprefix>.dwi.RSA.nii.gz to me looks reasonable. (https://www.dropbox.com/s/fdhhn9l1futgst9/Screen%20Shot%202017-04-08%20at%2010.22.02.png?dl=0)

I try to run the command line with a mask defined by me:

/Applications/BrainSuite16a1/bdp/bdp.sh t1.bfc.nii.gz –dwi-mask dti_brain_mask.nii.gz –tensor –FRT –FRACT –nii dti.nii -g dti.bvec -b dti.bval

and changing the dwi masking method:

/Applications/BrainSuite16a1/bdp/bdp.sh t1.bfc.nii.gz –dwi-masking-method intensity –tensor –FRT –FRACT –nii dti.nii -g dti.bvec -b dti.bval

but same error appear.

This is the outputlog link:

log

Do you have any suggestion?

Best Regards

Nicolò

[carnico]

Thanks Anand.

I solved the problem re-installing brainsuite.

The svreg runs fine with my data with the flag “refine sulcal curves”, otherwise it give me an error.

Thanks a lot and Best Regards

[carnico]

Ok, I’ve manage to install MCR runtime 2015b, but the error is still the same.

MCR is in the /Applications/MATLAB/MATLAB_Runtime/v90, but BS can’t load it.

[Author]

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