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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:
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
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
| Title | Author | Date |
|---|---|---|
| Jian Chen | Sep 7, 2015 | |
| Kaitlin Cassady | Mar 23, 2019 | |
| Kaitlin Cassady | Mar 28, 2019 | |
| 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 | |
