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/${Subject}.${Hemis
>>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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