Re: [HCP-Users] map data between FreeSurfer and HCP
Dear Matt, Thank you very much. Here you have the output of mri_info brain.finalsurfs.mgz: Volume information for brain.finalsurfs.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r =-0.5000 : x_a = 0., y_a = 0., z_a = 1., c_a =26. : x_s = 0., y_s = -1., z_s = 0., c_s = 1. talairach xfm : /Volumes/data3/sz/sort/x50001/FS/x50001/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 127.5000 0. 0. 1. -102. 0. -1. 0. 129. 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 127.5000 -0. -0. -1. 129. -0. 1. -0. 102. 0. 0. 0. 1. On 1/16/17, 12:07 AM, "Glasser, Matthew" wrote: Can you post the output of the mri_info command without the grep and such? Peace, Matt. On 1/15/17, 10:11 PM, "Leah Moreno" wrote: >Dear Matt and experts, > >Thank you for your help. Here you have the code from 1 subject and left >hemisphere: > >MatrixX=`mri_info brain.finalsurfs.mgz | grep "c_r" | cut -d "=" -f 5 | >sed s/" "/""/g` >MatrixY=`mri_info brain.finalsurfs.mgz | grep "c_a" | cut -d "=" -f 5 | >sed s/" "/""/g` >MatrixZ=`mri_info brain.finalsurfs.mgz | grep "c_s" | cut -d "=" -f 5 | >sed s/" "/""/g` >echo "1 0 0 ""$MatrixX" > c_ras.mat >echo "0 1 0 ""$MatrixY" >> c_ras.mat >echo "0 0 1 ""$MatrixZ" >> c_ras.mat >echo "0 0 0 1" >> c_ras.mat > >mris_convert lh.pial lh.pial.native.surf.gii >mris_convert lh.white lh.white.native.surf.gii >wb_command -set-structure lh.pial.native.surf.gii CORTEX_LEFT >-surface-type ANATOMICAL -surface-secondary-type PIAL >wb_command -set-structure lh.white.native.surf.gii CORTEX_LEFT >-surface-type ANATOMICAL -surface-secondary-type GRAY_WHITE >wb_command -surface-apply-affine lh.pial.native.surf.gii ../mri/c_ras.mat >lh.pial.native.surf.gii >wb_command -surface-apply-affine lh.white.native.surf.gii >../mri/c_ras.mat lh.white.native.surf.gii >wb_command -surface-average LH.midthickness.native.surf.gii -surf >lh.white.native.surf.gii -surf lh.pial.native.surf.gii >wb_command -set-structure LH.midthickness.native.surf.gii CORTEX_LEFT >-surface-type ANATOMICAL -surface-secondary-type MIDTHICKNESS > >wb_command -volume-to-surface-mapping zstat1.nii.gz >/Volumes/data3/sz/sort/x50001/FS/x50001/surf/LH.midthickness.native.surf.g >ii LH_zstat1.func.gii –trilinear > >Please find attached the image of the FCmap -volume-to-surface following >these steps. The FCmap is an individual z-map in mni space. > >Any help would be really appreciated. > >-L > > > > >On 1/15/17, 2:09 PM, "Glasser, Matthew" wrote: > >If you try with the beta version of FreeSurfer the mris_convert >command >may take care of what Donna was concerned about automatically or with >an >optional flag. That said, I asked you multiple times to provide the >exact >commands you were running and any error messages and you have not done >that. It is hard to provide support without knowing those kind of >details. > >Peace, > >Matt. > >On 1/15/17, 1:06 PM, "hcp-users-boun...@humanconnectome.org on behalf >of >Marta Moreno" mmorenoort...@icloud.com> wrote: > >>Thank you, Dona. I tried that too but I am getting similar pictures. >Any >>other recommendation? I got very nice results from analyses and need >nice >>pictures. >> >>Thanks, >>-L >> >> >>> On Jan 15, 2017, at 10:40 AM, Dierker, Donna >wrote: >>> >>> Hi Leah, >>> >>> I wonder if you need to apply an affine transform to your >white/pial >>>surfaces to adjust for the offset between Freesurfer¹s origin and >your >>>orig.mgz volume¹s origin. See this script: >>> >>> > >>>https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1 >>>a > >>>7ab9c6dd48a25de9be9bae7/PostFreeSurfer/script
Re: [HCP-Users] map data between FreeSurfer and HCP
Can you post the output of the mri_info command without the grep and such? Peace, Matt. On 1/15/17, 10:11 PM, "Leah Moreno" wrote: >Dear Matt and experts, > >Thank you for your help. Here you have the code from 1 subject and left >hemisphere: > >MatrixX=`mri_info brain.finalsurfs.mgz | grep "c_r" | cut -d "=" -f 5 | >sed s/" "/""/g` >MatrixY=`mri_info brain.finalsurfs.mgz | grep "c_a" | cut -d "=" -f 5 | >sed s/" "/""/g` >MatrixZ=`mri_info brain.finalsurfs.mgz | grep "c_s" | cut -d "=" -f 5 | >sed s/" "/""/g` >echo "1 0 0 ""$MatrixX" > c_ras.mat >echo "0 1 0 ""$MatrixY" >> c_ras.mat >echo "0 0 1 ""$MatrixZ" >> c_ras.mat >echo "0 0 0 1" >> c_ras.mat > >mris_convert lh.pial lh.pial.native.surf.gii >mris_convert lh.white lh.white.native.surf.gii >wb_command -set-structure lh.pial.native.surf.gii CORTEX_LEFT >-surface-type ANATOMICAL -surface-secondary-type PIAL >wb_command -set-structure lh.white.native.surf.gii CORTEX_LEFT >-surface-type ANATOMICAL -surface-secondary-type GRAY_WHITE >wb_command -surface-apply-affine lh.pial.native.surf.gii ../mri/c_ras.mat >lh.pial.native.surf.gii >wb_command -surface-apply-affine lh.white.native.surf.gii >../mri/c_ras.mat lh.white.native.surf.gii >wb_command -surface-average LH.midthickness.native.surf.gii -surf >lh.white.native.surf.gii -surf lh.pial.native.surf.gii >wb_command -set-structure LH.midthickness.native.surf.gii CORTEX_LEFT >-surface-type ANATOMICAL -surface-secondary-type MIDTHICKNESS > >wb_command -volume-to-surface-mapping zstat1.nii.gz >/Volumes/data3/sz/sort/x50001/FS/x50001/surf/LH.midthickness.native.surf.g >ii LH_zstat1.func.gii trilinear > >Please find attached the image of the FCmap -volume-to-surface following >these steps. The FCmap is an individual z-map in mni space. > >Any help would be really appreciated. > >-L > > > > >On 1/15/17, 2:09 PM, "Glasser, Matthew" wrote: > >If you try with the beta version of FreeSurfer the mris_convert >command >may take care of what Donna was concerned about automatically or with >an >optional flag. That said, I asked you multiple times to provide the >exact >commands you were running and any error messages and you have not done >that. It is hard to provide support without knowing those kind of >details. > >Peace, > >Matt. > >On 1/15/17, 1:06 PM, "hcp-users-boun...@humanconnectome.org on behalf >of >Marta Moreno" mmorenoort...@icloud.com> wrote: > >>Thank you, Dona. I tried that too but I am getting similar pictures. >Any >>other recommendation? I got very nice results from analyses and need >nice >>pictures. >> >>Thanks, >>-L >> >> >>> On Jan 15, 2017, at 10:40 AM, Dierker, Donna >wrote: >>> >>> Hi Leah, >>> >>> I wonder if you need to apply an affine transform to your >white/pial >>>surfaces to adjust for the offset between Freesurfer¹s origin and >your >>>orig.mgz volume¹s origin. See this script: >>> >>> > >>>https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1 >>>a > >>>7ab9c6dd48a25de9be9bae7/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAn >>>d >>>RegisterNonlinear.sh >>> >>> Search for c_ras.mat. This applies to surfaces in subject¹s volume >>>space. >>> >>> If you map MNI FCmaps onto MNI surfaces, I¹d expect better >alignment, >>>but if you use a nonlinear method to get FCmaps on MNI, but just >apply >>>the talairach.xfm to the surfaces (linear/affine), then that >alignment >>>won¹t be as good as if you used the same method for both. >>> >>> Donna >>> >>> >>>> On Jan 15, 2017, at 1:40 AM, Leah Moreno > >>>>wrote: >>>> >>>> Dear experts, >>>> >>>> I have individual FCmaps in mni & subject volume space (not using >HCP >>>>or FreeSurfer) and individual surface data from FreeSurfer. I want >to >>>>map data from individual volumes to individual surfaces to then >average >>>>across subjects on the surface and visualize with workbench. But >the >>>>volume data is not being well mapped to the surface, please see >>>>attachment. >>>> >>>> I have also tried section B. of document ³How do I map data >between >>>>FreeSurfer and HCP?², but either with or without resampling the >output >>>>does not look ok. >>>> >>>> Any help, please? >>>> >>>> Thank you, >>>> >>>> -L >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> ___ >>>> 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, b
[HCP-Users] QC of structural MR images - protocol and example data
Dear experts, we are working to implement robust quality control routines for the data analysis by using HCP pipelines in our institute. Reading the paper Human Connectome Project Informatics: quality control, database services, and data visualization, Markus et al, NeuroImage 2013 was very inspirative. I would like to ask, could you provide more detailed protocol guidelines for QC assessment of structural images? As I understood, this part of QC is based on subjective assessment by operator. Do you have detailed instructions how to categorize the images to 1-4 scale? Could you provide typical example datasets? In hummanconnectome.org I did not find the relevant SOP document. Regards, Antonin Skoch Institute for Clinical and Experimental Medicine National Institute for Mental Health Czech Republic ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] map data between FreeSurfer and HCP
If you try with the beta version of FreeSurfer the mris_convert command may take care of what Donna was concerned about automatically or with an optional flag. That said, I asked you multiple times to provide the exact commands you were running and any error messages and you have not done that. It is hard to provide support without knowing those kind of details. Peace, Matt. On 1/15/17, 1:06 PM, "hcp-users-boun...@humanconnectome.org on behalf of Marta Moreno" wrote: >Thank you, Dona. I tried that too but I am getting similar pictures. Any >other recommendation? I got very nice results from analyses and need nice >pictures. > >Thanks, >-L > > >> On Jan 15, 2017, at 10:40 AM, Dierker, Donna wrote: >> >> Hi Leah, >> >> I wonder if you need to apply an affine transform to your white/pial >>surfaces to adjust for the offset between Freesurfer¹s origin and your >>orig.mgz volume¹s origin. See this script: >> >> >>https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1a >>7ab9c6dd48a25de9be9bae7/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAnd >>RegisterNonlinear.sh >> >> Search for c_ras.mat. This applies to surfaces in subject¹s volume >>space. >> >> If you map MNI FCmaps onto MNI surfaces, I¹d expect better alignment, >>but if you use a nonlinear method to get FCmaps on MNI, but just apply >>the talairach.xfm to the surfaces (linear/affine), then that alignment >>won¹t be as good as if you used the same method for both. >> >> Donna >> >> >>> On Jan 15, 2017, at 1:40 AM, Leah Moreno >>>wrote: >>> >>> Dear experts, >>> >>> I have individual FCmaps in mni & subject volume space (not using HCP >>>or FreeSurfer) and individual surface data from FreeSurfer. I want to >>>map data from individual volumes to individual surfaces to then average >>>across subjects on the surface and visualize with workbench. But the >>>volume data is not being well mapped to the surface, please see >>>attachment. >>> >>> I have also tried section B. of document ³How do I map data between >>>FreeSurfer and HCP?², but either with or without resampling the output >>>does not look ok. >>> >>> Any help, please? >>> >>> Thank you, >>> >>> -L >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ___ >>> 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. > >___ >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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] map data between FreeSurfer and HCP
Thank you, Dona. I tried that too but I am getting similar pictures. Any other recommendation? I got very nice results from analyses and need nice pictures. Thanks, -L > On Jan 15, 2017, at 10:40 AM, Dierker, Donna wrote: > > Hi Leah, > > I wonder if you need to apply an affine transform to your white/pial surfaces > to adjust for the offset between Freesurfer’s origin and your orig.mgz > volume’s origin. See this script: > > https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1a7ab9c6dd48a25de9be9bae7/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh > > Search for c_ras.mat. This applies to surfaces in subject’s volume space. > > If you map MNI FCmaps onto MNI surfaces, I’d expect better alignment, but if > you use a nonlinear method to get FCmaps on MNI, but just apply the > talairach.xfm to the surfaces (linear/affine), then that alignment won’t be > as good as if you used the same method for both. > > Donna > > >> On Jan 15, 2017, at 1:40 AM, Leah Moreno wrote: >> >> Dear experts, >> >> I have individual FCmaps in mni & subject volume space (not using HCP or >> FreeSurfer) and individual surface data from FreeSurfer. I want to map data >> from individual volumes to individual surfaces to then average across >> subjects on the surface and visualize with workbench. But the volume data is >> not being well mapped to the surface, please see attachment. >> >> I have also tried section B. of document “How do I map data between >> FreeSurfer and HCP?”, but either with or without resampling the output does >> not look ok. >> >> Any help, please? >> >> Thank you, >> >> -L >> >> >> >> >> >> >> >> >> >> >> >> >> ___ >> 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] map data between FreeSurfer and HCP
Hi Leah, I wonder if you need to apply an affine transform to your white/pial surfaces to adjust for the offset between Freesurfer’s origin and your orig.mgz volume’s origin. See this script: https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1a7ab9c6dd48a25de9be9bae7/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh Search for c_ras.mat. This applies to surfaces in subject’s volume space. If you map MNI FCmaps onto MNI surfaces, I’d expect better alignment, but if you use a nonlinear method to get FCmaps on MNI, but just apply the talairach.xfm to the surfaces (linear/affine), then that alignment won’t be as good as if you used the same method for both. Donna > On Jan 15, 2017, at 1:40 AM, Leah Moreno wrote: > > Dear experts, > > I have individual FCmaps in mni & subject volume space (not using HCP or > FreeSurfer) and individual surface data from FreeSurfer. I want to map data > from individual volumes to individual surfaces to then average across > subjects on the surface and visualize with workbench. But the volume data is > not being well mapped to the surface, please see attachment. > > I have also tried section B. of document “How do I map data between > FreeSurfer and HCP?”, but either with or without resampling the output does > not look ok. > > Any help, please? > > Thank you, > > -L > > > > > > > > > > > > > ___ > 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
