Re: [HCP-Users] Mapping NIFTI to CIFTI

2018-06-01 Thread Seyedehrezvan Farahibozorg 
Perfect, thanks so much!

Best,
Rezvan

From: Glasser, Matthew 
Sent: 01 June 2018 19:38:53
To: Seyedehrezvan Farahibozorg; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Mapping NIFTI to CIFTI

For that you should probably follow the same steps as the fMRISurface pipeline 
with the exception of using the precomputed goodvoxels mask rather than 
recomputing that.

This code also provides a synopsis:

 
roiVolume="${AtlasResultsFolder}/RibbonVolumeToSurfaceMapping/goodvoxels.nii.gz"
  Flag="-fix-zeros"
  VolROI="-volume-roi $roiVolume"

if [ 1 -eq `echo "$BrainOrdinatesResolution == $FinalfMRIResolution" | bc 
-l` ] ; then
   #If using the same fMRI and grayordinates space resolution, use the simple 
algorithm to project bias field into subcortical CIFTI space like fMRI
   volumeIn="${AtlasResultsFolder}/${fMRIName}_${File}.nii.gz"
   currentParcel="${ROIFolder}/ROIs.${BrainOrdinatesResolution}.nii.gz"
   newParcel="${ROIFolder}/Atlas_ROIs.${BrainOrdinatesResolution}.nii.gz"
   kernel="${Sigma}"
   volumeOut="${AtlasResultsFolder}/${File}_AtlasSubcortical.nii.gz"
   $Caret7_Command -volume-parcel-resampling $volumeIn $currentParcel 
$newParcel $kernel $volumeOut ${Flag}
else
   #If using different fMRI and grayordinates space resolutions, use the 
generic algorithm to project bias field into subcortical CIFTI space like fMRI
   volumeIn="${AtlasResultsFolder}/${fMRIName}_${File}.nii.gz"
   currentParcel="${AtlasResultsFolder}/ROIs.${FinalfMRIResolution}.nii.gz"
   newParcel="${ROIFolder}/Atlas_ROIs.${BrainOrdinatesResolution}.nii.gz"
   kernel="${Sigma}"
   volumeOut="${AtlasResultsFolder}/${File}_AtlasSubcortical.nii.gz"
   $Caret7_Command -volume-parcel-resampling-generic $volumeIn $currentParcel 
$newParcel $kernel $volumeOut ${Flag}
fi

for Hemisphere in L R ; do
   #Map bias field volume to surface using the same approach as when fMRI data 
are projected to the surface
   volume="${AtlasResultsFolder}/${fMRIName}_${File}.nii.gz"
   
surface="${NativeFolder}/${Subject}.${Hemisphere}.midthickness.native.surf.gii"
   metricOut="${AtlasResultsFolder}/${File}.${Hemisphere}.native.func.gii"
   ribbonInner="${NativeFolder}/${Subject}.${Hemisphere}.white.native.surf.gii"
   ribbonOutter="${NativeFolder}/${Subject}.${Hemisphere}.pial.native.surf.gii"
   $Caret7_Command -volume-to-surface-mapping $volume $surface $metricOut 
-ribbon-constrained $ribbonInner $ribbonOutter ${VolROI}

  if [ ! ${File} = "dropouts" ] ; then
 #Fill in any small holes with dilation again as is done with fMRI
  metric="${AtlasResultsFolder}/${File}.${Hemisphere}.native.func.gii"
  
surface="${NativeFolder}/${Subject}.${Hemisphere}.midthickness.native.surf.gii"
  distance="20"
  metricOut="${AtlasResultsFolder}/${File}.${Hemisphere}.native.func.gii"
  $Caret7_Command -metric-dilate $metric $surface $distance $metricOut 
-nearest
  fi

  #Mask out the medial wall of dilated file
   metric="${AtlasResultsFolder}/${File}.${Hemisphere}.native.func.gii"
   mask="${NativeFolder}/${Subject}.${Hemisphere}.roi.native.shape.gii"
   metricOut="${AtlasResultsFolder}/${File}.${Hemisphere}.native.func.gii"
   $Caret7_Command -metric-mask $metric $mask $metricOut
   for RegName in ${RegNames} ; do
 if [ ! ${RegName} = "NONE" ] ; then
  RegString="_${RegName}"
else
  RegString=""
  RegName="MSMSulc"
fi
 #Resample the surface data from the native mesh to the standard mesh
 metricIn="${AtlasResultsFolder}/${File}.${Hemisphere}.native.func.gii"
 
currentSphere="${NativeFolder}/${Subject}.${Hemisphere}.sphere.${RegName}.native.surf.gii"
 
newSphere="${DownsampleFolder}/${Subject}.${Hemisphere}.sphere.${LowResMesh}k_fs_LR.surf.gii"
 method="ADAP_BARY_AREA"
 
metricOut="${AtlasResultsFolder}/${File}${RegString}.${Hemisphere}.${LowResMesh}k_fs_LR.func.gii"
 
currentArea="${NativeFolder}/${Subject}.${Hemisphere}.midthickness.native.surf.gii"
 
newArea="${DownsampleFolder}/${Subject}.${Hemisphere}.midthickness.${LowResMesh}k_fs_LR.surf.gii"
 roiMetric="${NativeFolder}/${Subject}.${Hemisphere}.roi.native.shape.gii"
 $Caret7_Command -metric-resample $metricIn $currentSphere $newSphere 
$method $metricOut -area-surfs $currentArea $newArea -current-roi $roiMetric
 #Make sure the medial wall is zeros
 
metric="${AtlasResultsFolder}/${File}${RegString}.${Hemisphere}.${LowResMesh}k_fs_LR.func.gii"
 
mask="${DownsampleFolder}/${Subject}.${Hemisphere}.atlasroi.${LowRe

Re: [HCP-Users] Mapping NIFTI to CIFTI

2018-06-01 Thread Glasser, Matthew 
ias field the same as the fMRI
 
surface="${DownsampleFolder}/${Subject}.${Hemisphere}.midthickness.${LowResMesh}k_fs_LR.surf.gii"
 
metricIn="${AtlasResultsFolder}/${File}${RegString}.${Hemisphere}.${LowResMesh}k_fs_LR.func.gii"
 smoothingKernel="${Sigma}"
 
metricOut="${AtlasResultsFolder}/${File}${RegString}.${Hemisphere}.${LowResMesh}k_fs_LR.func.gii"
 
roiMetric="${DownsampleFolder}/${Subject}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.shape.gii"
 $Caret7_Command -metric-smoothing $surface $metricIn $smoothingKernel 
$metricOut -roi $roiMetric
  done
done

 for RegName in ${RegNames} ; do
   if [ ! ${RegName} = "NONE" ] ; then
RegString="_${RegName}"
  else
RegString=""
RegName="MSMSulc"
  fi
  #Create CIFTI file of bias field as was done with fMRI
  
ciftiOut="${AtlasResultsFolder}/${fMRIName}_Atlas${RegString}_${File}.dscalar.nii"
  volumeData="${AtlasResultsFolder}/${File}_AtlasSubcortical.nii.gz"
  labelVolume="${ROIFolder}/Atlas_ROIs.${BrainOrdinatesResolution}.nii.gz"
  
lMetric="${AtlasResultsFolder}/${File}${RegString}.L.${LowResMesh}k_fs_LR.func.gii"
  
lRoiMetric="${DownsampleFolder}/${Subject}.L.atlasroi.${LowResMesh}k_fs_LR.shape.gii"
  
rMetric="${AtlasResultsFolder}/${File}${RegString}.R.${LowResMesh}k_fs_LR.func.gii"
  
rRoiMetric="${DownsampleFolder}/${Subject}.R.atlasroi.${LowResMesh}k_fs_LR.shape.gii"
  $Caret7_Command -cifti-create-dense-scalar $ciftiOut -volume $volumeData 
$labelVolume -left-metric $lMetric -roi-left $lRoiMetric -right-metric $rMetric 
-roi-right $rRoiMetric

  rm ${lMetric} ${rMetric}
done
rm ${volumeData}

Matt.

From: Seyedehrezvan Farahibozorg 
mailto:rezvan.farahiboz...@ndcn.ox.ac.uk>>
Date: Friday, June 1, 2018 at 1:29 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Mapping NIFTI to CIFTI

Hi Matt,
Thanks very much.
I'm trying to evaluate an RS connectivity method by checking spatial 
similarities/differences of when it's applied to volumetric vs. cifti data. I 
won't be comparing the original timeseries...

Many thanks
Rezvan

From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: 01 June 2018 19:09:03
To: Seyedehrezvan Farahibozorg; 
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Mapping NIFTI to CIFTI

That process does not replicate how the timeseries data were gotten on the 
surface to begin with.  What is it that you are trying to accomplish with this?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Seyedehrezvan Farahibozorg 
mailto:rezvan.farahiboz...@ndcn.ox.ac.uk>>
Date: Friday, June 1, 2018 at 1:05 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Mapping NIFTI to CIFTI


Hi all,

I have results of a subject-specific connectivity analysis on a) volumetric 
(.nii.gz) and b) CIFTI grayordinates (.dtseries.nii) data for a subset of 3T 
rfMRI HCP1200 subjects. In order to check the spatial correspondence, I am 
trying to map the former onto the space of the latter.



To do so, I used the following steps using wb command line:



1- Mapped the volumetric data to subject-specific surface using 
-volume-to-surface-mapping:

wb_command -volume-to-surface-mapping $input_nii $subject_gifti_left 
$output_gifti_left -trilinear

wb_command -volume-to-surface-mapping $input_nii 
$subject_gifti_right $output_gifti_right -trilinear

2- Combined these mapped cortical responses and subcortical grey matter voxel 
responses in one CIFTI file using -cifti-create-dense-from-template:

wb_command -cifti-create-dense-from-template  $template_cifti  
$output_cifti -series 1 0 -volume-all $input_nii -metric CORTEX_LEFT $ 
output_gifti_left -metric CORTEX_RIGHT $output_gifti_right



where $template_cifti is a group average of the aforementioned analysis on 
CIFTI data.



I was wondering if this way of mapping is correct? I would very much appreciate 
your feedback...



So many thanks,

Rezvan

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Mapping NIFTI to CIFTI

2018-06-01 Thread Seyedehrezvan Farahibozorg 
Hi Matt,
Thanks very much.
I'm trying to evaluate an RS connectivity method by checking spatial 
similarities/differences of when it's applied to volumetric vs. cifti data. I 
won't be comparing the original timeseries...

Many thanks
Rezvan

From: Glasser, Matthew 
Sent: 01 June 2018 19:09:03
To: Seyedehrezvan Farahibozorg; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Mapping NIFTI to CIFTI

That process does not replicate how the timeseries data were gotten on the 
surface to begin with.  What is it that you are trying to accomplish with this?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Seyedehrezvan Farahibozorg 
mailto:rezvan.farahiboz...@ndcn.ox.ac.uk>>
Date: Friday, June 1, 2018 at 1:05 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Mapping NIFTI to CIFTI


Hi all,

I have results of a subject-specific connectivity analysis on a) volumetric 
(.nii.gz) and b) CIFTI grayordinates (.dtseries.nii) data for a subset of 3T 
rfMRI HCP1200 subjects. In order to check the spatial correspondence, I am 
trying to map the former onto the space of the latter.



To do so, I used the following steps using wb command line:



1- Mapped the volumetric data to subject-specific surface using 
-volume-to-surface-mapping:

wb_command -volume-to-surface-mapping $input_nii $subject_gifti_left 
$output_gifti_left -trilinear

wb_command -volume-to-surface-mapping $input_nii 
$subject_gifti_right $output_gifti_right -trilinear

2- Combined these mapped cortical responses and subcortical grey matter voxel 
responses in one CIFTI file using -cifti-create-dense-from-template:

wb_command -cifti-create-dense-from-template  $template_cifti  
$output_cifti -series 1 0 -volume-all $input_nii -metric CORTEX_LEFT $ 
output_gifti_left -metric CORTEX_RIGHT $output_gifti_right



where $template_cifti is a group average of the aforementioned analysis on 
CIFTI data.



I was wondering if this way of mapping is correct? I would very much appreciate 
your feedback...



So many thanks,

Rezvan

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Mapping NIFTI to CIFTI

2018-06-01 Thread Glasser, Matthew 
That process does not replicate how the timeseries data were gotten on the 
surface to begin with.  What is it that you are trying to accomplish with this?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Seyedehrezvan Farahibozorg 
mailto:rezvan.farahiboz...@ndcn.ox.ac.uk>>
Date: Friday, June 1, 2018 at 1:05 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Mapping NIFTI to CIFTI

Hi all,
I have results of a subject-specific connectivity analysis on a) volumetric 
(.nii.gz) and b) CIFTI grayordinates (.dtseries.nii) data for a subset of 3T 
rfMRI HCP1200 subjects. In order to check the spatial correspondence, I am 
trying to map the former onto the space of the latter.

To do so, I used the following steps using wb command line:

1- Mapped the volumetric data to subject-specific surface using 
-volume-to-surface-mapping:
wb_command -volume-to-surface-mapping $input_nii $subject_gifti_left 
$output_gifti_left -trilinear
wb_command -volume-to-surface-mapping $input_nii 
$subject_gifti_right $output_gifti_right -trilinear
2- Combined these mapped cortical responses and subcortical grey matter voxel 
responses in one CIFTI file using -cifti-create-dense-from-template:
wb_command -cifti-create-dense-from-template  $template_cifti  
$output_cifti -series 1 0 -volume-all $input_nii -metric CORTEX_LEFT $ 
output_gifti_left -metric CORTEX_RIGHT $output_gifti_right

where $template_cifti is a group average of the aforementioned analysis on 
CIFTI data.

I was wondering if this way of mapping is correct? I would very much appreciate 
your feedback...

So many thanks,
Rezvan

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users