[iidaka]

This is a reply to the last mail.

1.
[1] TRUE

2.
svreg_label_surf_hemi D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\mri right -v1
svreg_label_surf_hemi D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\mri left -v1
register_cc_curve D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.svreg.tmp\2011101206.right.mid.cortex_smooth10.dfs
register_cc_curve D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.svreg.tmp\2011101206.left.mid.cortex_smooth10.dfs
volmap_ball D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.svreg.tmp\2011101206.target 1 -v1
volmap_ball D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 1 -v1
svreg_volreg D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.target -v1
refine_ROIs2 D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 left refine_ROIs2 D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 right -v1 -v1
svreg_refinements D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.target -v1
generate_stats_xls D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 -r

3.
[1] “C:/Program Files/BrainSuite17a”

4.
Error: Could not determine the BrainSuite atlas used for registration.
Please check the log file D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.

[iidaka]

Sorry, the results in previous mail was incorrect.

The first
[1] “D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC//2011101206/*.svreg.log”

The second
[1] “D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC//2011101206/2011101206.svreg.log”

The third
[1] TRUE

[iidaka]

Hi,

The first,
[1] “D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC//2011101206/*.svreg.log”
The second,
character(0)
The third,
[1] FALSE

[iidaka]

Hi,

This path really exists on my PC. It is working in previous directory.

I am afraid that “Yen mark” instead of “/” is used to separate directry in
Japanese PC and svreg.log file uses Yen mark.

*********************
> dir(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/”)
[1] “2011101206.air” “2011101206.bfc.nii.gz”
[3] “2011101206.brain.dfs” “2011101206.bse.nii.gz”
[5] “2011101206.bval” “2011101206.bvec”
[7] “2011101206.cerebrum.mask.nii.gz” “2011101206.cortex.dewisp.mask.nii.gz”
[9] “2011101206.cortex.scrubbed.mask.nii.gz” “2011101206.cortex.tca.mask.nii.gz”
[11] “2011101206.hemi.label.nii.gz” “2011101206.init.cortex.mask.nii.gz”
[13] “2011101206.inner.cortex.dfs” “2011101206.inner_skull.dfs”
[15] “2011101206.left.inner.cortex.dfs” “2011101206.left.inner.cortex.svreg.dfs”
[17] “2011101206.left.mapped.dfc” “2011101206.left.mid.cortex.svreg.dfs”
[19] “2011101206.left.mid.cortex.svreg.init.dfs” “2011101206.left.pial.cortex.dfs”
[21] “2011101206.left.pial.cortex.svreg.dfs” “2011101206.mask.nii.gz”
[23] “2011101206.nii” “2011101206.outer_skull.dfs”
[25] “2011101206.pial.cortex.dfs” “2011101206.pvc.frac.nii.gz”
[27] “2011101206.pvc.label.nii.gz” “2011101206.right.inner.cortex.dfs”
[29] “2011101206.right.inner.cortex.svreg.dfs” “2011101206.right.mapped.dfc”
[31] “2011101206.right.mid.cortex.svreg.dfs” “2011101206.right.mid.cortex.svreg.init.dfs”
[33] “2011101206.right.pial.cortex.dfs” “2011101206.right.pial.cortex.svreg.dfs”
[35] “2011101206.roiwise.stats.txt” “2011101206.roiwise.stats.xlsx”
[37] “2011101206.scalp.dfs” “2011101206.skull.label.nii.gz”
[39] “2011101206.svreg.init.label.nii.gz” “2011101206.svreg.inv.jacobian.nii.gz”
[41] “2011101206.svreg.inv.map.nii.gz” “2011101206.svreg.jacobian.nii.gz”
[43] “2011101206.svreg.label.nii.gz” “2011101206.svreg.log”
[45] “2011101206.svreg.map.nii.gz” “2011101206.warp”
[47] “2011101206diff.nii” “atlas.left.mid.cortex.jacobian.dfs”
[49] “atlas.left.mid.cortex.svreg.dfs” “atlas.right.mid.cortex.jacobian.dfs”
[51] “atlas.right.mid.cortex.svreg.dfs” “brainsuite_labeldescription.xml”
[53] “dicom”

> dir(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log”)
character(0)
>

[iidaka]

Hi,

Your script gives “character(0)”

If “&” was replaced by “and” the error message is the same as before.

**************************
Error: Could not determine the BrainSuite atlas used for registration.
Please check the log file D:/Tetsuya/All_data/MRI/DTIandMPRAGE/38NC/2011101206/2011101206.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument

[iidaka]

Hi,

Thank you for instruction for bssr. There is another error message like this.

****
Error: Could not determine the BrainSuite atlas used for registration.
Please check the log file D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.
****

In avreg.log file, there is a path to the atlas like this.
C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\mri

Best regards,

tetsuya

[iidaka]

Hi,

I have encountered following error.

Regards,

Tetsuya

*******************************
bss_cbm_anova.R –subjdir=D/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC –csv=D/Tetsuya/All_data/MRI/DTI&MPRAGE/NC38.csv –hemi=left –main_effect=gender –covariates=age –odir=D/Tetsuya/All_data/MRI/DTI&MPRAGE/NC38_gender_sex –smooth=2.5

Error: unexpected symbol in “bss_cbm_anova.R –subjdir=D/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC

[iidaka]

Hi, Shantanu

Thank you for response.

The installation has completed successfully.
I will try my data and report it.

Best regards,

tetsuya

[iidaka]

Hi, experts,

I am using BrainSuite 17a on Windows10 and still unable to install BSS.
There is no bss folder.

Best regards,

tetsuya

[iidaka]

Hi,

Let me post some additional information on this.
(BrainSuite 15c on windows7 64 bit machine)

Tractconnect.mat computed the results between ROIs whos id was between 611-641.
These ROIs are mostly subcortical structures. For the ROIs whose id is between 100-400,
which are mostly in cortical areas, no tract value is computed.

Best regards,

tetsuya

[iidaka]

Hi,

We have data on ROI#701 which is the left ventricle.
Thank you for responses.

tetsuya

[iidaka]

Hi,
Thank you for response.

Yes, this label description file is edited from the original one by excluding the ROIs that are not interested in our research and including only 92 cortical and subcortical ROIs. The file structure is not changed but some rows were deleted.

Regards,

Tetsuya

[iidaka]

I am using BrainSuite 15c on Windows7 64bit.

tetsuya

[iidaka]

Hi,

BrainSuite ends at *Time is 118846.479214 sec*
and probably following messages have been from matlab.

tetsuya

***********************************
Exception in thread “Timer-36505” java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.mathworks.mlwidgets.explorer.model.FileDecorationModel.<init>(FileDecorationModel.java:59)
at com.mathworks.mlwidgets.explorer.util.FileSystemUtils.getDecorationSynchronously(FileSystemUtils.java:113)
at com.mathworks.mlwidgets.explorer.model.table.FileSystemExpansionProvider.getDecoration(FileSystemExpansionProvider.java:124)
at com.mathworks.mlwidgets.explorer.model.table.FileSystemExpansionProvider.getDecoration(FileSystemExpansionProvider.java:131)
at com.mathworks.mlwidgets.explorer.model.table.PathAffordance.shouldEverShowAffordance(PathAffordance.java:330)
at com.mathworks.mlwidgets.e
**********************************

[iidaka]

Hi, BrainSuite

I need connectivity between 90 ROIs defined as ROI_ID from 120-641 by SurfReg.
This may create 90 x 90 = 8100 rows.

tetsuya

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