External Email - Use Caution
dear experts, I try to run FSFAST with a block design paradigm. there a few question i can figure out on my own. the 1st question: the directory structure was set as: -meridian --sess01 --bold -001 -002 --lpx (subjectname folder contian anatomical data run by "recon-all" previously) --subjectname (a file) Since there was only one subject, i didn't create sessid. then i run: preproc-sess -s sess01 -fsd bold -per-run -fwhm 5 -sliceorder odd -surface fsaverage lhrh -init-fsl but i got this warning (the full log is in the attachment):
if: Expression Syntax.
I wonder what's wrong with the command.
--------------------------------------------------
the 2nd question:
following the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastLinkAnatData
I create a subjectname file which contains:
cd $SUBJECTS_DIR/$SUBJECT
echo "$SUBJECT">>lpx
is it work? How to link the functional data to anatomical data?
--------------------------------------------------
the 3rd question:
i use a stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex. the design parameters: TR=2, 8hz flickering checkerbords, 16s fixation followed by 4 conditions（20s each）, each condition show a wedge in up, down, left and right meridian, 3 repetitions
the meridian.par was set as:
0.0 0 16.0 1.0 fix
17.0 1 20.0 1.0 up
37.0 2 20.0 1.0 down
57.0 3 20.0 1.0 left
77.0 4 20.0 1.0 right
97.0 1 20.0 1.0 up
117.0 2 20.0 1.0 down
137.0 3 20.0 1.0 left
157.0 4 20.0 1.0 right
177.0 1 20.0 1.0 up
197.0 2 20.0 1.0 down
217.0 3 20.0 1.0 left
237.0 4 20.0 1.0 right
my question is, in the first-level analysis, is right to write the command: mkanalysis-sess \ -analysis meridian \ -event-related -paradigm meridian.par \ -TR 2 -nconditions 4 \ -mcextreg
best,
star
On 1/3/19 5:07 AM, xi star wrote:
External Email - Use Caution
dear experts, I try to run FSFAST with a block design paradigm. there a few question i can figure out on my own. the 1st question: the directory structure was set as: -meridian --sess01 --bold -001 -002 --lpx (subjectname folder contian anatomical data run by "recon-all" previously) --subjectname (a file) Since there was only one subject, i didn't create sessid. then i run: preproc-sess -s sess01 -fsd bold -per-run -fwhm 5 -sliceorder odd -surface fsaverage lhrh -init-fsl but i got this warning (the full log is in the attachment):
if: Expression Syntax.
I wonder what's wrong with the command.
I'm not sure. What version of FS are you running? If version 6, then don't use -init-fsl. If the error persists, then run it with -debug as the first option and send the terminal output.
the 2nd question:
following the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastLinkAnatData
I create a subjectname file which contains:
cd $SUBJECTS_DIR/$SUBJECT
echo "$SUBJECT">>lpx
is it work? How to link the functional data to anatomical data?
I actually don't know what that refers to. That page is way out of date (I just deleted it). An "lpx" file is not needed.
the 3rd question:
i use a stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex. the design parameters: TR=2, 8hz flickering checkerbords, 16s fixation followed by 4 conditions（20s each）, each condition show a wedge in up, down, left and right meridian, 3 repetitions
the meridian.par was set as:
0.0 016.01.0fix
17.0120.01.0up
37.0220.01.0down
57.0320.01.0left
77.0420.01.0right
97.0120.01.0up
117.0220.01.0down
137.0320.01.0left
157.0420.01.0right
177.0120.01.0up
197.0220.01.0down
217.0320.01.0left
237.0420.01.0right
my question is, in the first-level analysis, is right to write the command:
mkanalysis-sess \ -analysis meridian \ -event-related -paradigm meridian.par \ -TR 2 -nconditions 4 \ -mcextreg
Yes, that looks correct
best,
star
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I've fix the three problems with your help. Thanks a lot Doug.
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年1月4日周五 上午2:55写道：
On 1/3/19 5:07 AM, xi star wrote:
External Email - Use Cautiondear experts, I try to run FSFAST with a block design paradigm. there a few question i can figure out on my own. the 1st question: the directory structure was set as: -meridian --sess01 --bold -001 -002 --lpx (subjectname folder contian anatomical data run by "recon-all" previously) --subjectname (a file) Since there was only one subject, i didn't create sessid. then i run: preproc-sess -s sess01 -fsd bold -per-run -fwhm 5 -sliceorder odd -surface fsaverage lhrh -init-fsl but i got this warning (the full log is in the attachment):
if: Expression Syntax.
I wonder what's wrong with the command.
I'm not sure. What version of FS are you running? If version 6, then don't use -init-fsl. If the error persists, then run it with -debug as the first option and send the terminal output.
the 2nd question:
following the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastLinkAnatData
I create a subjectname file which contains:
cd $SUBJECTS_DIR/$SUBJECT
echo "$SUBJECT">>lpx
is it work? How to link the functional data to anatomical data?
I actually don't know what that refers to. That page is way out of date (I just deleted it). An "lpx" file is not needed.
the 3rd question:
i use a stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex. the design parameters: TR=2, 8hz flickering checkerbords, 16s fixation followed by 4 conditions（20s each）, each condition show a wedge in up, down, left and right meridian, 3 repetitions
the meridian.par was set as:
0.0 016.01.0fix
17.0120.01.0up
37.0220.01.0down
57.0320.01.0left
77.0420.01.0right
97.0120.01.0up
117.0220.01.0down
137.0320.01.0left
157.0420.01.0right
177.0120.01.0up
197.0220.01.0down
217.0320.01.0left
237.0420.01.0right
my question is, in the first-level analysis, is right to write the command:
mkanalysis-sess \ -analysis meridian \ -event-related -paradigm meridian.par \ -TR 2 -nconditions 4 \ -mcextreg
Yes, that looks correct
best,
star
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
xi star