Dear Matt,
Great!
Using -cifti-create-dense-timeseries, I got a CIFTI file "dtseries.nii" which looked similar to HCP subject dtseries file.
Thanks a lot.
I can find signals only at subcortical area via workbench.
I believe the dtseries.nii contains cortical signals.
Question 1: How can I see the cortical signals in surface using workbench?
Using -cifti-convert -to-nifti, the CIFTI file was converted to a nifti file.
The dimension of the nifti file was 32767 x 3 x 1 x 195.
Question 2: does 3 in y dimension mean left, right, and subcortex OR other?
Then, melodic command using 2 nifti files produced melodic_IC.nii.gz (32767 x 3 x 1 x no. of ICs).
To convert back first IC, -from-nifti option was used like below:
wb_command -cifti-convert -from-nifti /home/projects/bu/marek/New/test/tmp/test1.ica+/IC01.nii.gz AtlasDenseTimeseries.dtseries.nii IC_01.nii -reset-timepoints 3 0
Question 3: if TR is 3 sec, is 3 and 0 in -reset-timepoints correct?
My melodic output also showed in subcortical regions when I see it with workbench.
I appreciate if I can check my melodic output on surface with workbench.
Thanks,
Jeong
On Mon, 12 May 2014 13:18:51 +0100, SUBSCRIBE FSL B. Jeong <[log in to unmask]> wrote:
>Hi Matt,
>
>1. Thank you. I had to, but didn't, use a field map. I'll redo my preprocessing with a field map.
>2. I guess v3.2.0 is up-to-date(?) one to public (fsl 5.0.6). I'll appreciate any information about the latest version.
>3. In terms of my hurdle which -volume-parcel-resampling option produced 4D fMR volume having all 0 valued voxels, could you look at my data? (I'll send a email to you including a link for downloading 2mm MNI spaced subcortical ROI volume and 4D fMR data (just having 5 volumes (11.2Mb) for convenience)
>
>Thank you,
>
>Jeong
>
>On Fri, 9 May 2014 09:31:13 -0500, Matt Glasser <[log in to unmask]> wrote:
>
>>Did you correct your data for distortions with a field map?
>>
>>I believe the latest version of FSLView is 4.0.1, but Dave Flitney, the
>>author, could confirm. Old versions may not display NIFTI files produced
>>by Caret or Connectome Workbench correctly because of additional
>>information in the NIFTI header.
>>
>>Peace,
>>
>>Matt.
>>
>>On 5/9/14, 8:24 AM, "SUBSCRIBE FSL B. Jeong" <[log in to unmask]> wrote:
>>
>>>I believe fslview 3.2.0 is mostly recent one.
>>>
>>>bbregister was used to register from fMRI to freesurfer conformed space.
>>>It seemed be fine, but not perfect especially in the anterior margin of
>>>caudate.
>>>Which command do you recommend for registration from freesurfer spaced
>>>fMR data to 2mm MNI space?
>>>I did flirt.
>>>
>>>Thank you,
>>>
>>>Jeong
>>>
>>>
>>>On Thu, 8 May 2014 20:47:25 -0500, Matt Glasser <[log in to unmask]> wrote:
>>>
>>>>Are you looking at this with an old version of FSLView or something like
>>>>that? The images you sent me looked okay (though your EPI is poorly
>>>>aligned with your structural…).
>>>>
>>>>Peace,
>>>>
>>>>Matt.
>>>>
>>>>On 5/8/14, 8:10 PM, "SUBSCRIBE FSL B. Jeong" <[log in to unmask]>
>>>>wrote:
>>>>
>>>>>Not perfectly matched but mostly overlapped between my subcortical
>>>>>ROIs(2mm) and HCP Atlas_ROIs.2.
>>>>>I'll send figures to your MA-TEA.com email.
>>>>>
>>>>>Thanks,
>>>>>
>>>>>Jeong
>>>>>
>>>>>On Thu, 8 May 2014 11:33:35 -0500, Matt Glasser <[log in to unmask]> wrote:
>>>>>
>>>>>>I�m confused again as to where we are because the previous e-mails are
>>>>>>not
>>>>>>included. Do your ROIs and Atlas_ROIs look okay in FSLView?
>>>>>>
>>>>>>-roi-left and -roi-right you can get from an HCP subject�s
>>>>>>${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hem
>>>>>>is
>>>>>>ph
>>>>>>ere}.atlasroi.32k_fs_LR.shape.gii
>>>>>>
>>>>>>Peace,
>>>>>>
>>>>>>Matt.
>>>>>>
>>>>>>On 5/8/14, 8:07 AM, "SUBSCRIBE FSL B. Jeong" <[log in to unmask]>
>>>>>>wrote:
>>>>>>
>>>>>>>Hi Matt,
>>>>>>>
>>>>>>>Thank you for your comment.
>>>>>>>
>>>>>>>1) Could you any comment in terms of "mostly" correct?
>>>>>>>
>>>>>>>2) Unfortunately, the command below produced a 4D volume which have
>>>>>>>all
>>>>>>>zero value:
>>>>>>>
>>>>>>>wb_command -volume-parcel-resampling fMRI.2mm.MNI.nii.gz ROIs.2.nii.gz
>>>>>>>Atlas_ROIs.2.nii.gz 2.12 fMRI.subcortex.2.nii.gz
>>>>>>>
>>>>>>>(fMRI.2mm.MNI, ROIs.2, Atlas_ROIs.2 files have same dimension
>>>>>>>(2*2*2mm)
>>>>>>>and same orientation (LAS))
>>>>>>>
>>>>>>>
>>>>>>>3) I can not fully understand the -cifti-create-dense-timeseries
>>>>>>>command.
>>>>>>>what should be placed in -roi-left? How can I make it?
>>>>>>>
>>>>>>>wb_command -cifti-create-dense-timeseries
>>>>>>>AtlasDenseTimeseries.dtseries.nii -volume fMRI.subcortex.2.nii.gz
>>>>>>>Atlas_ROIs.2.nii.gz -left-metric lh.32k.func.gii -roi-left ?
>>>>>>>-right-metric rh.32k.func.gii -roi-right ? -timestep $TR
>>>>>>>
>>>>>>>Thanks,
>>>>>>>
>>>>>>>Jeong
>>>>>
>>>>>——————
>>>>>That seems mostly correct. You¹ll want to download one of our HCP
>>>>>subjects and use
>>>>>${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz as
>>>>>new-parcels and your extracted subcortical labels as cur-parcels.
>>>>>
>>>>>Peace,
>>>>>
>>>>>Matt.
>>>>>
>>>>>On 5/7/14, 5:02 AM, "SUBSCRIBE FSL B. Jeong" <[log in to unmask]>
>>>>>wrote:
>>>>>
>>>>>>Hi Matt,
>>>>>>
>>>>>>1) I started from freesurfer results.
>>>>>>change FS surface and volume to gii or nii
>>>>>>2) create the white and pial surfaces with -surface-average
>>>>>>rh.white.gii lh.white.gii
>>>>>>3) surface mapping of fMR data with -volume-to-surface-mapping with
>>>>>>-ribbon-constrained option (lh.white.gii lh.pial.gii)
>>>>>>4) make new surface (32k: Sphere.32k.L.surf.gii) with
>>>>>>-surface-create-sphere
>>>>>>5) resampling to a lower resolution (32k) standard mesh with
>>>>>>-metric-resample lh.func.gii lh.sphere.reg.surf.gii
>>>>>>Sphere.32k.L.surf.gii
>>>>>>ADAP_BARY_AREA lh.32k.func.gii
>>>>>>
>>>>>>Then, I did subcortical process.
>>>>>>1) wmparc mgz (1*1*1mm) was resampled to MNI 2*2*2mm space
>>>>>>2) fMR volume also was resampled to this space
>>>>>>3) extracted subcortical labels from wmparc.2.nii.gz with
>>>>>>-volume-label-import
>>>>>>
>>>>>>Now I faced on difficulty in -volume-parcel-resampling
>>>>>>In wb_command -volume-parcel-resampling
>>>>>>I thought cur-parcels may be wmparc.2.nii.gz and new-parcels is the
>>>>>>extracted subcortical labels from wmparc.2.nii.gz
>>>>>>
>>>>>>But I faced on error message like below:
>>>>>>
>>>>>>parcel volumes are not of type label
>>>>>>
>>>>>>Could you check my process?
>>>>>>
>>>>>>Thanks,
>>>>>>
>>>>>>Jeong
>>>>>>
>>>>>>----------------------------
>>>>>>You need to resample wmparc.nii.gz to whatever resolution you want the
>>>>>>subcortical data modeled at and then run this command:
>>>>>>
>>>>>>wb_command -volume-label-import wmparc.${FinalfMRIResolution}.nii.gz
>>>>>>FreeSurferSubcorticalLabelTableLut.txt
>>>>>>ROIs.${FinalfMRIResolution}.nii.gz
>>>>>>-discard-others
>>>>>>
>>>>>>If you want to use the HCP standard 91282 grayordinates space, you
>>>>>>should
>>>>>>download one of our subjects and use
>>>>>>${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz
>>>>>>
>>>>>>You don¹t want to use any -subvolume flag. Use the individual
>>>>>>parcellation (from the command above) as cur-parcels and the file I
>>>>>>mention from the HCP subject as new-parcels.
>>>>>>
>>>>>>How did you downsample and achieve alignment on the surface? It might
>>>>>>be
>>>>>>good to recount your steps so I can check them.
>>>>>>
>>>>>>Peace,
>>>>>>
>>>>>>Matt.
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