help > RE: subject's specific ROIs from freesurfer
Sep 9, 2015  04:09 AM | Alfonso Nieto-Castanon - Boston University
RE: subject's specific ROIs from freesurfer
Dear Jian,

The proper format of the .txt file will depend on how exactly you converted freesurfer's "aparc.a2009s+aseg.mgz" to your "APARCOhNine_ROI.nii" file, could you please give me a few more details (or just send me an example of your files)?

Alternatively, I would perhaps suggest to simply enter into CONN the original aparc.a2009s+aseg.mgz file (after first copying without any changes your system's FreeSurferColorLUT.txt file into the subject-specific folders renaming it as aparc.a2009s_aseg.txt). CONN should be able to then read that .mgz ROI file without a problem (and interpreting the associated *colorLUT.txt info as well)

Hope this helps
Alfonso
Originally posted by Jian Chen:
Dear Expert,

I have problems with using ROI from freesurfer. I try to define multiple ROI and subject's space. I have converted freesurfer aparc.a2009s+aseg.mgz to "APARCOhNine_ROI.nii" in each subject's freesurfer mri directory. I have also have a text "APARCOhNine_ROI.txt" in the same directory. Import of freesurfer's ROI don't have any error and warning. However when I try to preprocessing by press "Done", I have the error massage:

CONN: RUNNING SETUP STEP
Warning: file /home/jiancscratch/TWINS_PET/SPM_conn_freesurfer/freesurfer/twin00474/mri/APARCOhNine_ROI.txt format not recognized
Warning: file /home/jiancscratch/TWINS_PET/SPM_conn_freesurfer/freesurfer/twin00572/mri/APARCOhNine_ROI.txt format not recognized
Operation terminated by user during rex>rex_do (line 672)

In rex (line 155)
[params.ROIdata,params.ROInames,params.ROIinfo.basis,params.ROIinfo.voxels,params.ROIinfo.files,params.ROIinfo.select,params.ROIinfo.trans]=rex_do(params,1);
In conn_rex (line 8)
[varargout{1:nargout}]=rex(varargin{:});
In conn_process (line 677)
[data{nroi1},namesroi{nroi},params]=conn_rex(Vsourcethis,Vmask{nroi}{min(nses,nsesstemp)},'summary_measure','mean','conjunction_mask',mask,'level',level,'scaling',scalingl
In conn_process (line 12)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:5]);
In conn (line 2415)
conn_process('setup');
In conn_menumanager (line 112)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
Interrupt while evaluating uicontrol Callback.

my "APARCOhNine_ROI.txt" is formatted  as following:

ctx_lh_G_and_S_frontomargin
ctx_lh_G_and_S_occipital_inf
ctx_lh_G_and_S_paracentral
ctx_lh_G_and_S_subcentral
.....

Which is taken from FreeSurferColorLUT.txt. What is  the problem of my setup?

Thanks in advance from any help!

Jian

Threaded View

TitleAuthorDate
Jian Chen Sep 7, 2015
Kaitlin Cassady Mar 23, 2019
Kaitlin Cassady Mar 28, 2019
RE: subject's specific ROIs from freesurfer
Alfonso Nieto-Castanon Sep 9, 2015
Jian Chen Sep 18, 2015
Alfonso Nieto-Castanon Sep 18, 2015
Jian Chen Sep 18, 2015
Alfonso Nieto-Castanon Sep 25, 2015
Jian Chen Sep 18, 2015
Jian Chen Sep 9, 2015