Dear Fellow Freesurfers,
I am trying to display HDR waveforms (time courses) for group level FIR analyses in tksurfer.
When opening the group analysis data with tkmedit and a functional overlay, obviously some sort of time course data is loaded, because I can scroll back and forth between the different time points/frames of the functional overlay (for the specific contrast that I loaded).
However the load timecourse function does not seem to be working.
When attempting to load a hemodynamic waveform, I receive either an error (func_load_timecourse: error in FunD_New) without opening the HDR window, or then the time course volume is "interpreted as encoded scalar volume" and only one time point, of only one contrast, is shown in the HDR window.
I have tried downloading all possible and impossible files related to the group analysis (.hdr/.bhdr/.bfloat/.dat/.mat/.w) from both within the specific contrast directory or the one higher level, but they all fail in either of the two ways above. The wiki, in this case, was not very helpful in trying to discover which file to load: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization
Is this function currently functional? If so, which file should I load?
Details: group brain = fsaverage STUDY_DIR = /space/cognito/21/users/raij/avml_fmri_mctogether/ SUBJECTS_DIR = /space/cognito/5/users/raij/subjects_mri/ environment = nmr-std-env on machine ai (FreeSurfer vs >3) group analysis name = fegroup, analysis = ISI1TR_BERT_ERFIRsm5pf5tpefsub example contrast: AV-REST
Thanks for your help!
Tommi
--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
It is definitely possible to display time courses in tksurfer, but I usually load them from the cmd line with -timecourse. I don't think I've ever done it from the gui. Kevin will have to look into that error.
If you'd like to try loading from the cmd line then:
cd fegroup/bold/ISI1TR_BERT_ERFIRsm5pf5tpefsub/sph
You will need to paint the HDRs onto fsaverage:
mri_surf2surf --hemi lh --sval h-lh.bhdr --tval h-lh-fsaverage.mgh --srcsubject ico --trgsubject fsaverage --noreshape
Do the same thing for sig: cd AV-REST
mri_surf2surf --hemi lh --sval sig-lh.bhdr --tval sig-lh-fsaverage.mgh --srcsubject ico --trgsubject fsaverage --noreshape
This will create: h-lh-fsaverage.mgh
You can then:
tksurfer fsaverage lh inflated -overlay AV-REST/sig-lh-fsaverage.bhdr -timecourse h-lh-fsaverage.mgh
doug
raij@nmr.mgh.harvard.edu wrote:
Dear Fellow Freesurfers,
I am trying to display HDR waveforms (time courses) for group level FIR analyses in tksurfer.
When opening the group analysis data with tkmedit and a functional overlay, obviously some sort of time course data is loaded, because I can scroll back and forth between the different time points/frames of the functional overlay (for the specific contrast that I loaded).
However the load timecourse function does not seem to be working.
When attempting to load a hemodynamic waveform, I receive either an error (func_load_timecourse: error in FunD_New) without opening the HDR window, or then the time course volume is "interpreted as encoded scalar volume" and only one time point, of only one contrast, is shown in the HDR window.
I have tried downloading all possible and impossible files related to the group analysis (.hdr/.bhdr/.bfloat/.dat/.mat/.w) from both within the specific contrast directory or the one higher level, but they all fail in either of the two ways above. The wiki, in this case, was not very helpful in trying to discover which file to load: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization
Is this function currently functional? If so, which file should I load?
Details: group brain = fsaverage STUDY_DIR = /space/cognito/21/users/raij/avml_fmri_mctogether/ SUBJECTS_DIR = /space/cognito/5/users/raij/subjects_mri/ environment = nmr-std-env on machine ai (FreeSurfer vs >3) group analysis name = fegroup, analysis = ISI1TR_BERT_ERFIRsm5pf5tpefsub example contrast: AV-REST
Thanks for your help!
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If you're still having trouble with the time course loading, can you send me the command line you're using and the data you are trying to load?
On Wed, Jun 07, 2006 at 07:35:49PM -0400, Doug Greve wrote:
It is definitely possible to display time courses in tksurfer, but I usually load them from the cmd line with -timecourse. I don't think I've ever done it from the gui. Kevin will have to look into that error.
If you'd like to try loading from the cmd line then:
cd fegroup/bold/ISI1TR_BERT_ERFIRsm5pf5tpefsub/sph
You will need to paint the HDRs onto fsaverage:
mri_surf2surf --hemi lh --sval h-lh.bhdr --tval h-lh-fsaverage.mgh --srcsubject ico --trgsubject fsaverage --noreshape
Do the same thing for sig: cd AV-REST
mri_surf2surf --hemi lh --sval sig-lh.bhdr --tval sig-lh-fsaverage.mgh --srcsubject ico --trgsubject fsaverage --noreshape
This will create: h-lh-fsaverage.mgh
You can then:
tksurfer fsaverage lh inflated -overlay AV-REST/sig-lh-fsaverage.bhdr -timecourse h-lh-fsaverage.mgh
doug
raij@nmr.mgh.harvard.edu wrote:
Dear Fellow Freesurfers,
I am trying to display HDR waveforms (time courses) for group level FIR analyses in tksurfer.
When opening the group analysis data with tkmedit and a functional overlay, obviously some sort of time course data is loaded, because I can scroll back and forth between the different time points/frames of the functional overlay (for the specific contrast that I loaded).
However the load timecourse function does not seem to be working.
When attempting to load a hemodynamic waveform, I receive either an error (func_load_timecourse: error in FunD_New) without opening the HDR window, or then the time course volume is "interpreted as encoded scalar volume" and only one time point, of only one contrast, is shown in the HDR window.
I have tried downloading all possible and impossible files related to the group analysis (.hdr/.bhdr/.bfloat/.dat/.mat/.w) from both within the specific contrast directory or the one higher level, but they all fail in either of the two ways above. The wiki, in this case, was not very helpful in trying to discover which file to load: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization
Is this function currently functional? If so, which file should I load?
Details: group brain = fsaverage STUDY_DIR = /space/cognito/21/users/raij/avml_fmri_mctogether/ SUBJECTS_DIR = /space/cognito/5/users/raij/subjects_mri/ environment = nmr-std-env on machine ai (FreeSurfer vs >3) group analysis name = fegroup, analysis = ISI1TR_BERT_ERFIRsm5pf5tpefsub example contrast: AV-REST
Thanks for your help!
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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