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Hello FreeSurfer experts,
May I ask how can I modify the surface-based fMRI data, such as combing two independent sessions into one or dividing one 4D into a series of 3D surface-based fMRI files in which each one denotes a single volume/TR? Thank you very much.
Best wishes,
Zhi
Are you using FSFAST? If you run the preprocessing (preproc-sess), then it will get you most of the way there.
On 11/05/2018 10:16 AM, Zhi Li wrote:
External Email - Use Caution
Hello FreeSurfer experts,
May I ask how can I modify the surface-based fMRI data, such as combing two independent sessions into one or dividing one 4D into a series of 3D surface-based fMRI files in which each one denotes a single volume/TR? Thank you very much.
Best wishes,
Zhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Dougles,
Thank your for your reply. Now I am using FSFAST, but I didn't find flags in prepro-sess which can be used in combing or dividing fMRI data. Using the following code I could get three files for each run (left cortical surface, right cortical surface and sub-cortical volume):
*preproc-sess -sf subjects -fsd task_name -sliceorder so -surface fsaverage lhrh -mni305 -fwhm 5 -per-session*
Can I use preproc-sess to combine files from different runs, and discard the first 4 time points of each run? If so, could you please give me a example?
Thanks and best,
Zhi
On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
Are you using FSFAST? If you run the preprocessing (preproc-sess), then it will get you most of the way there.
On 11/05/2018 10:16 AM, Zhi Li wrote:
External Email - Use CautionHello FreeSurfer experts,
May I ask how can I modify the surface-based fMRI data, such as combing two independent sessions into one or dividing one 4D into a series of 3D surface-based fMRI files in which each one denotes a single volume/TR? Thank you very much.
Best wishes,
Zhi
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
If you just want to concatenate you can use something like mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz 002/fmcpr.up.sm5.fsaverage.lh.nii.gz 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o all.fmcpr.up.sm5.fsaverage.lh.nii.gz
On 11/07/2018 12:30 PM, Zhi Li wrote:
External Email - Use Caution
Hi Dougles,
Thank your for your reply. Now I am using FSFAST, but I didn't find flags in prepro-sess which can be used in combing or dividing fMRI data. Using the following code I could get three files for each run (left cortical surface, right cortical surface and sub-cortical volume):
/preproc-sess -sf subjects -fsd task_name -sliceorder so -surface fsaverage lhrh -mni305 -fwhm 5 -per-session/
Can I use preproc-sess to combine files from different runs, and discard the first 4 time points of each run? If so, could you please give me a example?
Thanks and best,
Zhi
On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Are you using FSFAST? If you run the preprocessing (preproc-sess), then it will get you most of the way there. On 11/05/2018 10:16 AM, Zhi Li wrote: > > External Email - Use Caution > > Hello FreeSurfer experts, > > May I ask how can I modify the surface-based fMRI data, such as > combing two independent sessions into one or dividing one 4D into a > series of 3D surface-based fMRI files in which each one denotes a > single volume/TR? Thank you very much. > > Best wishes, > > Zhi > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
External Email - Use Caution
How can I discard the first 4 time points of each run during concatenating several runs? I know I can skip the first 4 time points with the flag *-nskip 4* in configuring a analysis, but this condition can be only applicable when each run is modelled into the GLM independently, right? If I feed the *mkanalysis-sess* with the concatenated file, it will only skip the first 4 time points of the 1st run in this file.
In addition, if my task design is event-related, do I need to set the duration of each stimulus as 0?
Thanks and best
On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
If you just want to concatenate you can use something like mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz 002/fmcpr.up.sm5.fsaverage.lh.nii.gz 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o all.fmcpr.up.sm5.fsaverage.lh.nii.gz
On 11/07/2018 12:30 PM, Zhi Li wrote:
External Email - Use CautionHi Dougles,
Thank your for your reply. Now I am using FSFAST, but I didn't find flags in prepro-sess which can be used in combing or dividing fMRI data. Using the following code I could get three files for each run (left cortical surface, right cortical surface and sub-cortical volume):
/preproc-sess -sf subjects -fsd task_name -sliceorder so -surface fsaverage lhrh -mni305 -fwhm 5 -per-session/
Can I use preproc-sess to combine files from different runs, and discard the first 4 time points of each run? If so, could you please give me a example?
Thanks and best,
Zhi
On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Are you using FSFAST? If you run the preprocessing (preproc-sess), then it will get you most of the way there. On 11/05/2018 10:16 AM, Zhi Li wrote: > > External Email - Use Caution > > Hello FreeSurfer experts, > > May I ask how can I modify the surface-based fMRI data, such as > combing two independent sessions into one or dividing one 4D into a > series of 3D surface-based fMRI files in which each one denotes a > single volume/TR? Thank you very much. > > Best wishes, > > Zhi > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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First run mri_convert --nskip 4 fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz then concat the skip files
On 11/07/2018 01:42 PM, Zhi Li wrote:
External Email - Use Caution
How can I discard the first 4 time points of each run during concatenating several runs? I know I can skip the first 4 time points with the flag /-nskip 4/ in configuring a analysis, but this condition can be only applicable when each run is modelled into the GLM independently, right? If I feed the /mkanalysis-sess/ with the concatenated file, it will only skip the first 4 time points of the 1st run in this file.
In addition, if my task design is event-related, do I need to set the duration of each stimulus as 0?
Thanks and best
On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
If you just want to concatenate you can use something like mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz 002/fmcpr.up.sm5.fsaverage.lh.nii.gz 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o all.fmcpr.up.sm5.fsaverage.lh.nii.gz On 11/07/2018 12:30 PM, Zhi Li wrote: > > External Email - Use Caution > > Hi Dougles, > > Thank your for your reply. Now I am using FSFAST, but I didn't find > flags in prepro-sess which can be used in combing or dividing fMRI > data. Using the following code I could get three files for each run > (left cortical surface, right cortical surface and sub-cortical volume): > > /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface > fsaverage lhrh -mni305 -fwhm 5 -per-session/ > > Can I use preproc-sess to combine files from different runs, and > discard the first 4 time points of each run? If so, could you please > give me a example? > > Thanks and best, > > Zhi > > > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Are you using FSFAST? If you run the preprocessing > (preproc-sess), then > it will get you most of the way there. > > On 11/05/2018 10:16 AM, Zhi Li wrote: > > > > External Email - Use Caution > > > > Hello FreeSurfer experts, > > > > May I ask how can I modify the surface-based fMRI data, such as > > combing two independent sessions into one or dividing one 4D into a > > series of 3D surface-based fMRI files in which each one denotes a > > single volume/TR? Thank you very much. > > > > Best wishes, > > > > Zhi > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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Great! So I also need to subtract 8 seconds from the onset time of each stimulus when I make the *paradigm file*, right? If the duration of stimulus is smaller than 1 second, such as 0.05 second, do I need to change its duration to 0 in a event-related deign?
On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
First run mri_convert --nskip 4 fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz then concat the skip files
On 11/07/2018 01:42 PM, Zhi Li wrote:
External Email - Use CautionHow can I discard the first 4 time points of each run during concatenating several runs? I know I can skip the first 4 time points with the flag /-nskip 4/ in configuring a analysis, but this condition can be only applicable when each run is modelled into the GLM independently, right? If I feed the /mkanalysis-sess/ with the concatenated file, it will only skip the first 4 time points of the 1st run in this file.
In addition, if my task design is event-related, do I need to set the duration of each stimulus as 0?
Thanks and best
On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
If you just want to concatenate you can use something like mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz 002/fmcpr.up.sm5.fsaverage.lh.nii.gz 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o all.fmcpr.up.sm5.fsaverage.lh.nii.gz On 11/07/2018 12:30 PM, Zhi Li wrote: > > External Email - Use Caution > > Hi Dougles, > > Thank your for your reply. Now I am using FSFAST, but I didn't find > flags in prepro-sess which can be used in combing or dividing fMRI > data. Using the following code I could get three files for each run > (left cortical surface, right cortical surface and sub-cortical volume): > > /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface > fsaverage lhrh -mni305 -fwhm 5 -per-session/ > > Can I use preproc-sess to combine files from different runs, and > discard the first 4 time points of each run? If so, could you please > give me a example? > > Thanks and best, > > Zhi > > > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Are you using FSFAST? If you run the preprocessing > (preproc-sess), then > it will get you most of the way there. > > On 11/05/2018 10:16 AM, Zhi Li wrote: > > > > External Email - Use Caution > > > > Hello FreeSurfer experts, > > > > May I ask how can I modify the surface-based fMRI data, such as > > combing two independent sessions into one or dividing one 4D into a > > series of 3D surface-based fMRI files in which each one denotes a > > single volume/TR? Thank you very much. > > > > Best wishes, > > > > Zhi > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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are you trying to use FSFAST to do the entire fmri anlaysis? If so, then follow the tutorial as it will handle the skipped TRs and the concatenation for you. If not, then you don't need a paradigm file
On 11/07/2018 02:14 PM, Zhi Li wrote:
External Email - Use Caution
Great! So I also need to subtract 8 seconds from the onset time of each stimulus when I make the /paradigm file/, right? If the duration of stimulus is smaller than 1 second, such as 0.05 second, do I need to change its duration to 0 in a event-related deign?
On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
First run mri_convert --nskip 4 fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz then concat the skip files On 11/07/2018 01:42 PM, Zhi Li wrote: > > External Email - Use Caution > > How can I discard the first 4 time points of each run during > concatenating several runs? I know I can skip the first 4 time points > with the flag /-nskip 4/ in configuring a analysis, but this condition > can be only applicable when each run is modelled into the GLM > independently, right? If I feed the /mkanalysis-sess/ with the > concatenated file, it will only skip the first 4 time points of the > 1st run in this file. > > In addition, if my task design is event-related, do I need to set the > duration of each stimulus as 0? > > Thanks and best > > On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > > If you just want to concatenate you can use something like > mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz > 002/fmcpr.up.sm5.fsaverage.lh.nii.gz > 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o > all.fmcpr.up.sm5.fsaverage.lh.nii.gz > > > > > On 11/07/2018 12:30 PM, Zhi Li wrote: > > > > External Email - Use Caution > > > > Hi Dougles, > > > > Thank your for your reply. Now I am using FSFAST, but I didn't find > > flags in prepro-sess which can be used in combing or dividing fMRI > > data. Using the following code I could get three files for each run > > (left cortical surface, right cortical surface and sub-cortical > volume): > > > > /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface > > fsaverage lhrh -mni305 -fwhm 5 -per-session/ > > > > Can I use preproc-sess to combine files from different runs, and > > discard the first 4 time points of each run? If so, could you > please > > give me a example? > > > > Thanks and best, > > > > Zhi > > > > > > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > Are you using FSFAST? If you run the preprocessing > > (preproc-sess), then > > it will get you most of the way there. > > > > On 11/05/2018 10:16 AM, Zhi Li wrote: > > > > > > External Email - Use Caution > > > > > > Hello FreeSurfer experts, > > > > > > May I ask how can I modify the surface-based fMRI data, > such as > > > combing two independent sessions into one or dividing one > 4D into a > > > series of 3D surface-based fMRI files in which each one > denotes a > > > single volume/TR? Thank you very much. > > > > > > Best wishes, > > > > > > Zhi > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
I see. Thank you very much.
On Wed, 7 Nov 2018 at 15:18, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
are you trying to use FSFAST to do the entire fmri anlaysis? If so, then follow the tutorial as it will handle the skipped TRs and the concatenation for you. If not, then you don't need a paradigm file
On 11/07/2018 02:14 PM, Zhi Li wrote:
External Email - Use CautionGreat! So I also need to subtract 8 seconds from the onset time of each stimulus when I make the /paradigm file/, right? If the duration of stimulus is smaller than 1 second, such as 0.05 second, do I need to change its duration to 0 in a event-related deign?
On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
First run mri_convert --nskip 4fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
then concat the skip files On 11/07/2018 01:42 PM, Zhi Li wrote: > > External Email - Use Caution > > How can I discard the first 4 time points of each run during > concatenating several runs? I know I can skip the first 4 time points > with the flag /-nskip 4/ in configuring a analysis, but this condition > can be only applicable when each run is modelled into the GLM > independently, right? If I feed the /mkanalysis-sess/ with the > concatenated file, it will only skip the first 4 time points of the > 1st run in this file. > > In addition, if my task design is event-related, do I need to set the > duration of each stimulus as 0? > > Thanks and best > > On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > > If you just want to concatenate you can use something like > mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz > 002/fmcpr.up.sm5.fsaverage.lh.nii.gz > 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o > all.fmcpr.up.sm5.fsaverage.lh.nii.gz > > > > > On 11/07/2018 12:30 PM, Zhi Li wrote: > > > > External Email - Use Caution > > > > Hi Dougles, > > > > Thank your for your reply. Now I am using FSFAST, but I didn't find > > flags in prepro-sess which can be used in combing or dividing fMRI > > data. Using the following code I could get three files for each run > > (left cortical surface, right cortical surface and sub-cortical > volume): > > > > /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface > > fsaverage lhrh -mni305 -fwhm 5 -per-session/ > > > > Can I use preproc-sess to combine files from different runs, and > > discard the first 4 time points of each run? If so, could you > please > > give me a example? > > > > Thanks and best, > > > > Zhi > > > > > > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > Are you using FSFAST? If you run the preprocessing > > (preproc-sess), then > > it will get you most of the way there. > > > > On 11/05/2018 10:16 AM, Zhi Li wrote: > > > > > > External Email - Use Caution > > > > > > Hello FreeSurfer experts, > > > > > > May I ask how can I modify the surface-based fMRI data, > such as > > > combing two independent sessions into one or dividing one > 4D into a > > > series of 3D surface-based fMRI files in which each one > denotes a > > > single volume/TR? Thank you very much. > > > > > > Best wishes, > > > > > > Zhi > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Greve, Douglas N.,Ph.D. -
Zhi Li