Hi Matt,
I thought I would be almost finish line.
But, it seems that my results from -volume-to-surface-mapping are not perfect.
What I did was,
1) I create bilateral midthickness surfaces (lh & rh.surf.gii) with -surface-average
2) then, the surface mapping of fMR data was performed to the midthickness surface like below;
wb_command -volume-to-surface-mapping fMRI.nii.gz lh.surf.gii lh.func.gii -ribbon-constrained lh.white.surf.gii lh.pial.surf.gii
3) resample to 32k
On the workbench, values of func.gii were zero on occipito-parietal area.
I send a figure via e-mail
I'll appreciate for any comment.
Thanks,
Jeong
On Wed, 14 May 2014 09:22:18 -0500, Matt Glasser <[log in to unmask]> wrote:
>1) Load in some matching GIFTI surfaces (i.e. On the 32k mesh). If you
>don’t have them, create them with wb_command -surface-resample from the
>native mesh surfaces in a similar way to how you did for the surface
>timeseries (but use the regular BARYCENTRIC algorithm).
>
>2) No, the matrix is 91282 x 195, which is too big for NIFTI-1 along one
>dimension, so it is wrapped to the dimensions you see.
>
>3) For your melodic output, I would set it to 1 and 1, as each map in the
>dtseries file is a component. Optionally you can convert the file to
>dscalar and give each map a name (e.g. Component 1, Component 2, etc).
>
>Peace,
>
>Matt.
>
>On 5/13/14, 10:35 PM, "SUBSCRIBE FSL B. Jeong" <[log in to unmask]>
>wrote:
>
>>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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