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/${Subject}.${Hemisph
>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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