Re: [HCP-Users] Standard to Native Applywarp Error
Thanks for getting back to me.
This is HCP data. Specifically, the social task. I am using FSL
(probtrackx) for tractography. I used the cifti-separate command and the
metric-resample command to extract the surface data. But I'm interested in
doing a whole-brain tractography with subcortical regions as well. So I
figured I could resample the surfaces to the fsaverage brain and then
combine them with the subcortical with vlrmerge. Do you have any other
recommendations on how I can get the output from cifti-separate into native
volume space?
Here are the commands I used:
# 1) Generate single-hemisphere gifti and volume nifti from cifti file
wb_command -cifti-separate-all ${contrast_dir}/zstat1.dtseries.nii \
-volume ${contrast_dir}/zstat.nii.gz \
-left ${contrast_dir}/zstat.L.func.gii \
-right ${contrast_dir}/zstat.R.func.gii
# 2) Map scalar data to fsaverage
for hemi in L R; do
wb_command -metric-resample \
${contrast_dir}/zstat.${hemi}.func.gii \
standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.${hemi}.sphere.32k_fs_LR.surf.gii
\
standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.${hemi}.164k_fsavg_${hemi}.surf.gii
ADAP_BARY_AREA \
${contrast_dir}/${hemi}.164k_fsavg_${hemi}.func.gii \
-area-metrics
standard_mesh_atlases/resample_fsaverage/fs_LR.${hemi}.midthickness_va_avg.32k_fs_LR.shape.gii
\
standard_mesh_atlases/resample_fsaverage/fsaverage.${hemi}.midthickness_va_avg.164k_fsavg_${hemi}.shape.gii
done
# Register subcortical data to MNI305
mri_vol2vol --mov ${contrast_dir}/zstat.nii.gz \
--targ
/usr/local/freesurfer/subjects/fsaverage/mri.2mm/mni305.cor.mgz \
--xfm $SUBJECTS_DIR/${SUB}/mri/transforms/talairach.xfm \
--o ${contrast_dir}/zstat.mni305.2mm.nii.gz
# Merge surface data with subcortical into one combined volume
vlrmerge --o ${contrast_dir}/zstat_combined.nii.gz \
--lh ${contrast_dir}/L.164k_fsavg_L.func.gii \
--rh ${contrast_dir}/R.164k_fsavg_R.func.gii \
--v ${contrast_dir}/zstat.mni305.2mm.nii.gz \
--scm /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz
On Thu, Apr 4, 2019 at 9:32 PM Glasser, Matthew wrote:
> Is this HCP data? What software are you using for tractography? If you
> want statistical maps in native volume space, it might be easiest to
> project them from the subject’s physical space surfaces in the
> T1w/fsaverage_LR32k or alternatively track the data to those surfaces.
>
> Matt.
>
> From: on behalf of Haroon Popal <
> tuk12...@temple.edu>
> Date: Wednesday, April 3, 2019 at 5:15 PM
> To: "hcp-users@humanconnectome.org"
> Subject: [HCP-Users] Standard to Native Applywarp Error
>
> Hello,
>
> I am trying to use the provided commands in the link below to transform a
> contrast from the social task to native space.
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-16.CanIgetthefMRIdatainasubject's'nativespace'?
>
> I used the pipeline in the second link to extract the surface and
> subcortical data from the original zstat.dtseries.nii file in one of the
> cope directories. I then used vlrmerge from FreeSurfer to combine the
> surface and volume data.
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?
>
> When I run the applywarp command, I'm getting a weird registration, where
> the brain is tilted up in the sagittal view, with the frontal lobe of the
> functional data pointing upwards.
>
> I am trying to do all of these because I need a volume for the contrast
> map, to compare to some DTI. I need my functional data and DTI data in the
> same space.
>
> Thanks for your help.
>
> --
> Haroon S. Popal
> Ph.D. Student
> Cognitive Neuroscience Laboratory
> Department of Psychology | Temple University
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
--
Haroon S. Popal
Ph.D. Student
Cognitive Neuroscience Laboratory
Department of Psychology | Temple University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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Re: [HCP-Users] Standard to Native Applywarp Error
I would recommend using probtrackx2 and tracking directly to the surface and
into the CIFTI space, rather than trying to go back to the volume.
Matt.
From: Haroon Popal mailto:tuk12...@temple.edu>>
Date: Thursday, April 4, 2019 at 8:49 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Standard to Native Applywarp Error
Thanks for getting back to me.
This is HCP data. Specifically, the social task. I am using FSL (probtrackx)
for tractography. I used the cifti-separate command and the metric-resample
command to extract the surface data. But I'm interested in doing a whole-brain
tractography with subcortical regions as well. So I figured I could resample
the surfaces to the fsaverage brain and then combine them with the subcortical
with vlrmerge. Do you have any other recommendations on how I can get the
output from cifti-separate into native volume space?
Here are the commands I used:
# 1) Generate single-hemisphere gifti and volume nifti from cifti file
wb_command -cifti-separate-all ${contrast_dir}/zstat1.dtseries.nii \
-volume ${contrast_dir}/zstat.nii.gz \
-left ${contrast_dir}/zstat.L.func.gii \
-right ${contrast_dir}/zstat.R.func.gii
# 2) Map scalar data to fsaverage
for hemi in L R; do
wb_command -metric-resample \
${contrast_dir}/zstat.${hemi}.func.gii \
standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.${hemi}.sphere.32k_fs_LR.surf.gii
\
standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.${hemi}.164k_fsavg_${hemi}.surf.gii
ADAP_BARY_AREA \
${contrast_dir}/${hemi}.164k_fsavg_${hemi}.func.gii \
-area-metrics
standard_mesh_atlases/resample_fsaverage/fs_LR.${hemi}.midthickness_va_avg.32k_fs_LR.shape.gii
\
standard_mesh_atlases/resample_fsaverage/fsaverage.${hemi}.midthickness_va_avg.164k_fsavg_${hemi}.shape.gii
done
# Register subcortical data to MNI305
mri_vol2vol --mov ${contrast_dir}/zstat.nii.gz \
--targ
/usr/local/freesurfer/subjects/fsaverage/mri.2mm/mni305.cor.mgz \
--xfm $SUBJECTS_DIR/${SUB}/mri/transforms/talairach.xfm \
--o ${contrast_dir}/zstat.mni305.2mm.nii.gz
# Merge surface data with subcortical into one combined volume
vlrmerge --o ${contrast_dir}/zstat_combined.nii.gz \
--lh ${contrast_dir}/L.164k_fsavg_L.func.gii \
--rh ${contrast_dir}/R.164k_fsavg_R.func.gii \
--v ${contrast_dir}/zstat.mni305.2mm.nii.gz \
--scm /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz
On Thu, Apr 4, 2019 at 9:32 PM Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
Is this HCP data? What software are you using for tractography? If you want
statistical maps in native volume space, it might be easiest to project them
from the subject’s physical space surfaces in the T1w/fsaverage_LR32k or
alternatively track the data to those surfaces.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Haroon Popal mailto:tuk12...@temple.edu>>
Date: Wednesday, April 3, 2019 at 5:15 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Standard to Native Applywarp Error
Hello,
I am trying to use the provided commands in the link below to transform a
contrast from the social task to native space.
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-16.CanIgetthefMRIdatainasubject's'nativespace'?
I used the pipeline in the second link to extract the surface and subcortical
data from the original zstat.dtseries.nii file in one of the cope directories.
I then used vlrmerge from FreeSurfer to combine the surface and volume data.
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?
When I run the applywarp command, I'm getting a weird registration, where the
brain is tilted up in the sagittal view, with the frontal lobe of the
functional data pointing upwards.
I am trying to do all of these because I need a volume for the contrast map, to
compare to some DTI. I need my functional data and DTI data in the same space.
Thanks for your help.
--
Haroon S. Popal
Ph.D. Student
Cognitive Neuroscience Laboratory
Department of Psychology | Temple University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient,
Re: [HCP-Users] Standard to Native Applywarp Error
Is this HCP data? What software are you using for tractography? If you want statistical maps in native volume space, it might be easiest to project them from the subject’s physical space surfaces in the T1w/fsaverage_LR32k or alternatively track the data to those surfaces. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Haroon Popal mailto:tuk12...@temple.edu>> Date: Wednesday, April 3, 2019 at 5:15 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Standard to Native Applywarp Error Hello, I am trying to use the provided commands in the link below to transform a contrast from the social task to native space. https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-16.CanIgetthefMRIdatainasubject's'nativespace'? I used the pipeline in the second link to extract the surface and subcortical data from the original zstat.dtseries.nii file in one of the cope directories. I then used vlrmerge from FreeSurfer to combine the surface and volume data. https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP? When I run the applywarp command, I'm getting a weird registration, where the brain is tilted up in the sagittal view, with the frontal lobe of the functional data pointing upwards. I am trying to do all of these because I need a volume for the contrast map, to compare to some DTI. I need my functional data and DTI data in the same space. Thanks for your help. -- Haroon S. Popal Ph.D. Student Cognitive Neuroscience Laboratory Department of Psychology | Temple University ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Standard to Native Applywarp Error
Hello, I am trying to use the provided commands in the link below to transform a contrast from the social task to native space. https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-16.CanIgetthefMRIdatainasubject's'nativespace'? I used the pipeline in the second link to extract the surface and subcortical data from the original zstat.dtseries.nii file in one of the cope directories. I then used vlrmerge from FreeSurfer to combine the surface and volume data. https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP? When I run the applywarp command, I'm getting a weird registration, where the brain is tilted up in the sagittal view, with the frontal lobe of the functional data pointing upwards. I am trying to do all of these because I need a volume for the contrast map, to compare to some DTI. I need my functional data and DTI data in the same space. Thanks for your help. -- Haroon S. Popal Ph.D. Student Cognitive Neuroscience Laboratory Department of Psychology | Temple University ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
