NITRC Brainnetome Atlas Viewer Forum: open-discussion

AtlasViewer with MNI305 template

hanieh — Thu, 17 Oct 2019 15:51:51 GMT

Hello All,

I have the results of freesurfer segmentation (based on MNI305). MNI305 is not part of atlases that includes in AtlasViewr. Anybody has any idea what we can do?

Best

Where is Cortical LUT lookup table

Peter Jones — Mon, 19 Aug 2019 12:30:26 GMT

Thank you for making the BN_Atlas_freesurfer available to all.

I have been successfully using your script mapping_to_subjects.sh (with some edits). However, this does not make an aparc of the cortex, only an aseg of subcortical regions. I used the command
mri_aparc2aseg --s ${sub} --o ${SUBJECTS_DIR}/${sub}/mri/aseg.bn.mgz --annot BN_Atlas
to make an aseg. But the LUT is not correct. The file BN.mgz you provide reuses some values from the FreeSurferColorLUT, e.g. freesurfer value 173 (midbrain) is listed in the insula of BN. If I select the BN_Atlas_246_LUT then this is relabelled dig_L. But in my file created with the command above it has a value 1173. Where can I find the correct LUT for the aseg.bn that matches the --annot BN_Atlas? Then I could do the command,
mri_aparc2aseg --s ${sub} --o ${SUBJECTS_DIR}/${sub}/mri/aseg.bn.mgz --annot BN_Atlas --annot_table NEW_LUT

Thanks for your help.

Simon

cannot find the reverse inference results

Chenxi Zhao — Fri, 01 Dec 2017 5:07:40 GMT

Hi community,
I am recently trying to use the Behavioral Domain and Paradigm Class (BDPC) Analysis results to do some explanatory work , but I can't find the reverse inference results (e.g. P(domain|activation) or P(paradigm|activation) ) using DBPC utility (which has been explicitly showed in your recent manual on Page 15, Figure 12). Am I use the wrong version, or otherwise can I use the forward inferences instead (my result was attached) ?

Look forward to your reply!

subcortical in fsaverage space

Peter McColgan — Thu, 02 Nov 2017 5:56:51 GMT

Dear Brainnetome team,

Is it possible to get subcortical atlas in fsaverage space as I am hoping to use both cortical and sub-cortical brainnectome regions in native subject space?

Thanks

Peter

RE: Brainnetome Atlas error

lingzhong Fan — Thu, 08 Sep 2016 13:40:13 GMT

Hi, Aral
Please download the latest version. Then, the error can be solved.

Best
Lingzhong

Brainnetome Atlas error

aral ahmadi — Thu, 28 Jul 2016 15:24:44 GMT

I could open up the Brainnetome Atlas GUI on windows but it keeps on giving me an error when I am trying open it up using Matlab on Linux.

here is the Error it gives me:
Error using ==> fgetl at 44
Invalid file identifier. Use fopen to generate a
valid file identifier.
Error in ==> Brainnetome_Atlas at 57
s=fgetl(fid);rror
what could be the problem?
Thanks,
Aral

brainnetome gui error

aral ahmadi — Thu, 21 Jul 2016 13:46:55 GMT

I could open up the Brainnetome Atlas GUI on windows but it keeps on giving me an error when I am trying open it up using Matlab on Linux.

here is the Error it gives me:

Error using ==> fgetl at 44
Invalid file identifier. Use fopen to generate a
valid file identifier.

Error in ==> Brainnetome_Atlas at 57
s=fgetl(fid);rror

what could be the problem?
Thanks,
Aral

Welcome to Open-Discussion

lingzhong Fan — Tue, 15 Jul 2014 8:14:01 GMT

Welcome to Open-Discussion