Re: [caret-users] projecting functional MRI to gii surfaces
On Mon, Sep 29, 2014 at 10:15 AM, Donna Dierker do...@brainvis.wustl.edu wrote: grep -a CIFTI my_file.nii That may not be particularly friendly to a terminal, and won't work on Windows. You can do it without -a, and if it says Binary file something matches, it is probably a CIFTI file. Another way is to do wb_command -nifti-information -print-header on the file (but requires having connectome workbench, while this list is meant for the older caret5 software, but if you are using HCP data, connectome workbench is required, more or less). If sizeof_hdr is 540, it is NIFTI-2, not NIFTI-1 (which would say 348), and most other software won't read it (yet). If it is NIFTI-2 and the intent code is in the range 3000-3099, it is a CIFTI file. Tim On Sep 28, 2014, at 5:07 PM, Tang, Yan yan.t...@ttu.edu wrote: yes, I also submit my question in website http://humanconnectome.org/contact/index.php. But nobody answer me. In question 3, the data's name is data.nii. So I think it is NIFTI. From: caret-users-boun...@brainvis.wustl.edu [ caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [ do...@brainvis.wustl.edu] Sent: Sunday, September 28, 2014 4:54 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, This question should be directed to hcp-users, rather than caret-users. But be warned that many of the HCP experts are tied up in meetings today and tomorrow. I'm not sure this is the issue with 3), but note that MRIcron probably can't read CIFTI files (composites of cortical surface and subcortical/cerebellar volumetric data). These are named like *.dscalar.nii, *.dlabel.nii, and several other flavors. These aren't NIFTI volumes like many software packages expect. For that matter, caret5 won't read them, either. You need workbench, which is supported by hcp-users. You're already on that list, no? Donna On Sep 27, 2014, at 10:25 AM, Tang, Yan yan.t...@ttu.edu wrote: hello, eveyone I am beginner. I want to download the DTI data in the Human Connectome Projet. But I are conflused by the processed data and unprocessed data. 1)The unprocessed data contains the NIFTI-formatted pairs (L-R, R-L) of diffusion scans for all directions (95,96,and 97). And processed data only include diffusion weighting (bvals), direction (bvecs), time series, brain mask, and a file (grad_dev.nii.gz). Why? what did you only keep? 2)In the processed data, whether the file of *_SBRef.nii describe the B0? 3)I download the processed data, but I couldn't use the Micron to open the data.nii. Why? I download two subjects. Both subjects couldn't be opened. From: caret-users-boun...@brainvis.wustl.edu [ caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [ do...@brainvis.wustl.edu] Sent: Thursday, August 28, 2014 3:47 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, There are lots of ways to split up the brain -- parcellations. For example, the Conte69 atlas ( http://brainvis.wustl.edu/wiki/index.php/Caret:Conte69_Atlas) comes with two label.gii files per hemisphere, e.g.: parcellations_VGD11b.R.164k_fs_LR.label.gii RSN-networks.R.164k_fs_LR.label.gii The first includes two parcellations: Composite Parcellation-rh (FRB08_OFP03_retinotopic) Brodmann rh (from colin.R via pals_R-to-fs_LR) The second includes four parcellations: 7 RSN Networks (YKS11 - Yeo et al., JNP, 2011) 17 RSN Networks (YKS11 - Yeo et al., JNP, 2011) RSN consensus communities (holes filled) (PCN11 - Power_Neuron11) RSN consensus communities (PCN11 - Power_Neuron11) And lots more have been published since, and will continue to be published. ;-) So you have to decide which one you want. Then you can either load that parcellation in wb_view (or caret5) and click on nodes interactively, or if you want to write a script that queries regions, there is a lookup table that maps the label key to a label name in the front of the label file, e.g.: Label Key=0 Red=0.667 Green=0.667 Blue=0.667 Alpha=0![CDATA[???]]/Label Label Key=1 Red=1 Green=1 Blue=1 Alpha=1![CDATA[u1_Unassigned]]/Label Label Key=2 Red=0.502 Green=0.502 Blue=0.502 Alpha=1![CDATA[u2_Ventral_frontal_temporal]]/Label Label Key=3 Red=1 Green=0 Blue=0 Alpha=1![CDATA[a3_Default_mode]]/Label Label Key=4 Red=0 Green=1 Blue=1 Alpha=1![CDATA[a4_Hand_somatosensory-motor]]/Label Label Key=5 Red=0 Green=0 Blue=1 Alpha=1![CDATA[a5_Visual]]/Label Label Key=6 Red=0.961 Green=0.961 Blue=0.059 Alpha=1![CDATA[a6_Fronto-parietal_task_control]]/Label Label Key=7 Red=0 Green=0.502 Blue=0.502 Alpha=1![CDATA[a7_Ventral_attention]]/Label Label Key=8 Red=0 Green=0.275 Blue
Re: [caret-users] projecting functional MRI to gii surfaces
Hi Yan, This question should be directed to hcp-users, rather than caret-users. But be warned that many of the HCP experts are tied up in meetings today and tomorrow. I'm not sure this is the issue with 3), but note that MRIcron probably can't read CIFTI files (composites of cortical surface and subcortical/cerebellar volumetric data). These are named like *.dscalar.nii, *.dlabel.nii, and several other flavors. These aren't NIFTI volumes like many software packages expect. For that matter, caret5 won't read them, either. You need workbench, which is supported by hcp-users. You're already on that list, no? Donna On Sep 27, 2014, at 10:25 AM, Tang, Yan yan.t...@ttu.edu wrote: hello, eveyone I am beginner. I want to download the DTI data in the Human Connectome Projet. But I are conflused by the processed data and unprocessed data. 1)The unprocessed data contains the NIFTI-formatted pairs (L-R, R-L) of diffusion scans for all directions (95,96,and 97). And processed data only include diffusion weighting (bvals), direction (bvecs), time series, brain mask, and a file (grad_dev.nii.gz). Why? what did you only keep? 2)In the processed data, whether the file of *_SBRef.nii describe the B0? 3)I download the processed data, but I couldn't use the Micron to open the data.nii. Why? I download two subjects. Both subjects couldn't be opened. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Thursday, August 28, 2014 3:47 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, There are lots of ways to split up the brain -- parcellations. For example, the Conte69 atlas (http://brainvis.wustl.edu/wiki/index.php/Caret:Conte69_Atlas) comes with two label.gii files per hemisphere, e.g.: parcellations_VGD11b.R.164k_fs_LR.label.gii RSN-networks.R.164k_fs_LR.label.gii The first includes two parcellations: Composite Parcellation-rh (FRB08_OFP03_retinotopic) Brodmann rh (from colin.R via pals_R-to-fs_LR) The second includes four parcellations: 7 RSN Networks (YKS11 - Yeo et al., JNP, 2011) 17 RSN Networks (YKS11 - Yeo et al., JNP, 2011) RSN consensus communities (holes filled) (PCN11 - Power_Neuron11) RSN consensus communities (PCN11 - Power_Neuron11) And lots more have been published since, and will continue to be published. ;-) So you have to decide which one you want. Then you can either load that parcellation in wb_view (or caret5) and click on nodes interactively, or if you want to write a script that queries regions, there is a lookup table that maps the label key to a label name in the front of the label file, e.g.: Label Key=0 Red=0.667 Green=0.667 Blue=0.667 Alpha=0![CDATA[???]]/Label Label Key=1 Red=1 Green=1 Blue=1 Alpha=1![CDATA[u1_Unassigned]]/Label Label Key=2 Red=0.502 Green=0.502 Blue=0.502 Alpha=1![CDATA[u2_Ventral_frontal_temporal]]/Label Label Key=3 Red=1 Green=0 Blue=0 Alpha=1![CDATA[a3_Default_mode]]/Label Label Key=4 Red=0 Green=1 Blue=1 Alpha=1![CDATA[a4_Hand_somatosensory-motor]]/Label Label Key=5 Red=0 Green=0 Blue=1 Alpha=1![CDATA[a5_Visual]]/Label Label Key=6 Red=0.961 Green=0.961 Blue=0.059 Alpha=1![CDATA[a6_Fronto-parietal_task_control]]/Label Label Key=7 Red=0 Green=0.502 Blue=0.502 Alpha=1![CDATA[a7_Ventral_attention]]/Label Label Key=8 Red=0 Green=0.275 Blue=0.157 Alpha=1![CDATA[a8_Caudate_putamen]]/Label Label Key=9 Red=1 Green=0.722 Blue=0.831 Alpha=1![CDATA[a9_Superior_temporal_gyrus]]/Label Label Key=10 Red=0.675 Green=0.675 Blue=0.675 Alpha=1![CDATA[u10_Inferior_temporal_pole]]/Label You can also export the label table as ASCII text. But each vertex is associated with one of these keys in the label.gii file. Donna On Aug 28, 2014, at 2:27 PM, Tang, Yan yan.t...@ttu.edu wrote: I still have problem. How can I know which brain region is every vertex belonged to? From: Tang, Yan Sent: Friday, August 15, 2014 12:27 PM To: Caret, SureFit, and SuMS software users Subject: RE: [caret-users] projecting functional MRI to gii surfaces Thank all of you. Thank you very much. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Wednesday, August 13, 2014 2:27 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, I'm not sure about wb_import, but I know it won't downsample for you. This will, I hope: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/FSLR/downsample164_to_32k.zip login pub password download There is a script
Re: [caret-users] projecting functional MRI to gii surfaces
yes, I also submit my question in website http://humanconnectome.org/contact/index.php. But nobody answer me. In question 3, the data's name is data.nii. So I think it is NIFTI. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Sunday, September 28, 2014 4:54 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, This question should be directed to hcp-users, rather than caret-users. But be warned that many of the HCP experts are tied up in meetings today and tomorrow. I'm not sure this is the issue with 3), but note that MRIcron probably can't read CIFTI files (composites of cortical surface and subcortical/cerebellar volumetric data). These are named like *.dscalar.nii, *.dlabel.nii, and several other flavors. These aren't NIFTI volumes like many software packages expect. For that matter, caret5 won't read them, either. You need workbench, which is supported by hcp-users. You're already on that list, no? Donna On Sep 27, 2014, at 10:25 AM, Tang, Yan yan.t...@ttu.edu wrote: hello, eveyone I am beginner. I want to download the DTI data in the Human Connectome Projet. But I are conflused by the processed data and unprocessed data. 1)The unprocessed data contains the NIFTI-formatted pairs (L-R, R-L) of diffusion scans for all directions (95,96,and 97). And processed data only include diffusion weighting (bvals), direction (bvecs), time series, brain mask, and a file (grad_dev.nii.gz). Why? what did you only keep? 2)In the processed data, whether the file of *_SBRef.nii describe the B0? 3)I download the processed data, but I couldn't use the Micron to open the data.nii. Why? I download two subjects. Both subjects couldn't be opened. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Thursday, August 28, 2014 3:47 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, There are lots of ways to split up the brain -- parcellations. For example, the Conte69 atlas (http://brainvis.wustl.edu/wiki/index.php/Caret:Conte69_Atlas) comes with two label.gii files per hemisphere, e.g.: parcellations_VGD11b.R.164k_fs_LR.label.gii RSN-networks.R.164k_fs_LR.label.gii The first includes two parcellations: Composite Parcellation-rh (FRB08_OFP03_retinotopic) Brodmann rh (from colin.R via pals_R-to-fs_LR) The second includes four parcellations: 7 RSN Networks (YKS11 - Yeo et al., JNP, 2011) 17 RSN Networks (YKS11 - Yeo et al., JNP, 2011) RSN consensus communities (holes filled) (PCN11 - Power_Neuron11) RSN consensus communities (PCN11 - Power_Neuron11) And lots more have been published since, and will continue to be published. ;-) So you have to decide which one you want. Then you can either load that parcellation in wb_view (or caret5) and click on nodes interactively, or if you want to write a script that queries regions, there is a lookup table that maps the label key to a label name in the front of the label file, e.g.: Label Key=0 Red=0.667 Green=0.667 Blue=0.667 Alpha=0![CDATA[???]]/Label Label Key=1 Red=1 Green=1 Blue=1 Alpha=1![CDATA[u1_Unassigned]]/Label Label Key=2 Red=0.502 Green=0.502 Blue=0.502 Alpha=1![CDATA[u2_Ventral_frontal_temporal]]/Label Label Key=3 Red=1 Green=0 Blue=0 Alpha=1![CDATA[a3_Default_mode]]/Label Label Key=4 Red=0 Green=1 Blue=1 Alpha=1![CDATA[a4_Hand_somatosensory-motor]]/Label Label Key=5 Red=0 Green=0 Blue=1 Alpha=1![CDATA[a5_Visual]]/Label Label Key=6 Red=0.961 Green=0.961 Blue=0.059 Alpha=1![CDATA[a6_Fronto-parietal_task_control]]/Label Label Key=7 Red=0 Green=0.502 Blue=0.502 Alpha=1![CDATA[a7_Ventral_attention]]/Label Label Key=8 Red=0 Green=0.275 Blue=0.157 Alpha=1![CDATA[a8_Caudate_putamen]]/Label Label Key=9 Red=1 Green=0.722 Blue=0.831 Alpha=1![CDATA[a9_Superior_temporal_gyrus]]/Label Label Key=10 Red=0.675 Green=0.675 Blue=0.675 Alpha=1![CDATA[u10_Inferior_temporal_pole]]/Label You can also export the label table as ASCII text. But each vertex is associated with one of these keys in the label.gii file. Donna On Aug 28, 2014, at 2:27 PM, Tang, Yan yan.t...@ttu.edu wrote: I still have problem. How can I know which brain region is every vertex belonged to? From: Tang, Yan Sent: Friday, August 15, 2014 12:27 PM To: Caret, SureFit, and SuMS software users Subject: RE: [caret-users] projecting functional MRI to gii surfaces Thank all of you. Thank you very much. From: caret-users-boun
Re: [caret-users] projecting functional MRI to gii surfaces
hello, eveyone I am beginner. I want to download the DTI data in the Human Connectome Projet. But I are conflused by the processed data and unprocessed data. 1)The unprocessed data contains the NIFTI-formatted pairs (L-R, R-L) of diffusion scans for all directions (95,96,and 97). And processed data only include diffusion weighting (bvals), direction (bvecs), time series, brain mask, and a file (grad_dev.nii.gz). Why? what did you only keep? 2)In the processed data, whether the file of *_SBRef.nii describe the B0? 3)I download the processed data, but I couldn't use the Micron to open the data.nii. Why? I download two subjects. Both subjects couldn't be opened. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Thursday, August 28, 2014 3:47 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, There are lots of ways to split up the brain -- parcellations. For example, the Conte69 atlas (http://brainvis.wustl.edu/wiki/index.php/Caret:Conte69_Atlas) comes with two label.gii files per hemisphere, e.g.: parcellations_VGD11b.R.164k_fs_LR.label.gii RSN-networks.R.164k_fs_LR.label.gii The first includes two parcellations: Composite Parcellation-rh (FRB08_OFP03_retinotopic) Brodmann rh (from colin.R via pals_R-to-fs_LR) The second includes four parcellations: 7 RSN Networks (YKS11 - Yeo et al., JNP, 2011) 17 RSN Networks (YKS11 - Yeo et al., JNP, 2011) RSN consensus communities (holes filled) (PCN11 - Power_Neuron11) RSN consensus communities (PCN11 - Power_Neuron11) And lots more have been published since, and will continue to be published. ;-) So you have to decide which one you want. Then you can either load that parcellation in wb_view (or caret5) and click on nodes interactively, or if you want to write a script that queries regions, there is a lookup table that maps the label key to a label name in the front of the label file, e.g.: Label Key=0 Red=0.667 Green=0.667 Blue=0.667 Alpha=0![CDATA[???]]/Label Label Key=1 Red=1 Green=1 Blue=1 Alpha=1![CDATA[u1_Unassigned]]/Label Label Key=2 Red=0.502 Green=0.502 Blue=0.502 Alpha=1![CDATA[u2_Ventral_frontal_temporal]]/Label Label Key=3 Red=1 Green=0 Blue=0 Alpha=1![CDATA[a3_Default_mode]]/Label Label Key=4 Red=0 Green=1 Blue=1 Alpha=1![CDATA[a4_Hand_somatosensory-motor]]/Label Label Key=5 Red=0 Green=0 Blue=1 Alpha=1![CDATA[a5_Visual]]/Label Label Key=6 Red=0.961 Green=0.961 Blue=0.059 Alpha=1![CDATA[a6_Fronto-parietal_task_control]]/Label Label Key=7 Red=0 Green=0.502 Blue=0.502 Alpha=1![CDATA[a7_Ventral_attention]]/Label Label Key=8 Red=0 Green=0.275 Blue=0.157 Alpha=1![CDATA[a8_Caudate_putamen]]/Label Label Key=9 Red=1 Green=0.722 Blue=0.831 Alpha=1![CDATA[a9_Superior_temporal_gyrus]]/Label Label Key=10 Red=0.675 Green=0.675 Blue=0.675 Alpha=1![CDATA[u10_Inferior_temporal_pole]]/Label You can also export the label table as ASCII text. But each vertex is associated with one of these keys in the label.gii file. Donna On Aug 28, 2014, at 2:27 PM, Tang, Yan yan.t...@ttu.edu wrote: I still have problem. How can I know which brain region is every vertex belonged to? From: Tang, Yan Sent: Friday, August 15, 2014 12:27 PM To: Caret, SureFit, and SuMS software users Subject: RE: [caret-users] projecting functional MRI to gii surfaces Thank all of you. Thank you very much. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Wednesday, August 13, 2014 2:27 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, I'm not sure about wb_import, but I know it won't downsample for you. This will, I hope: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/FSLR/downsample164_to_32k.zip login pub password download There is a script in there you will need to tweak to put in your pathnames and subject list. I tried it on some freesurfer_to_fs_LR output I had lying around, and it worked. The zip file also contains the spheres you need: ExtractDir=/home/donna/downsample164_to_32k SubjectDir=/mnt/myelin/donna/SUBJ/fs_LR_output_directory ResamplingMethod=BARYCENTRIC for Subject in $SubjList do for Hemisphere in L R do CoordInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.coord.gii TopoInput=$SubjectDir/$Subject/$Subject.$Hemisphere.164k_fs_LR.topo.gii SurfaceInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.surf.gii caret_command -file-convert -sc -is CARET $CoordInput $TopoInput -os GS
Re: [caret-users] projecting functional MRI to gii surfaces
I still have problem. How can I know which brain region is every vertex belonged to? From: Tang, Yan Sent: Friday, August 15, 2014 12:27 PM To: Caret, SureFit, and SuMS software users Subject: RE: [caret-users] projecting functional MRI to gii surfaces Thank all of you. Thank you very much. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Wednesday, August 13, 2014 2:27 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, I'm not sure about wb_import, but I know it won't downsample for you. This will, I hope: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/FSLR/downsample164_to_32k.zip login pub password download There is a script in there you will need to tweak to put in your pathnames and subject list. I tried it on some freesurfer_to_fs_LR output I had lying around, and it worked. The zip file also contains the spheres you need: ExtractDir=/home/donna/downsample164_to_32k SubjectDir=/mnt/myelin/donna/SUBJ/fs_LR_output_directory ResamplingMethod=BARYCENTRIC for Subject in $SubjList do for Hemisphere in L R do CoordInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.coord.gii TopoInput=$SubjectDir/$Subject/$Subject.$Hemisphere.164k_fs_LR.topo.gii SurfaceInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.surf.gii caret_command -file-convert -sc -is CARET $CoordInput $TopoInput -os GS $SurfaceInput CurrentSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.164k_fs_LR.surf.gii NewSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.32k_fs_LR.surf.gii SurfaceOutput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.32k_fs_LR.surf.gii wb_command -surface-resample \ $SurfaceInput \ $CurrentSphere \ $NewSphere \ $ResamplingMethod \ $SurfaceOutput done done Donna On Aug 13, 2014, at 10:42 AM, Tang, Yan yan.t...@ttu.edu wrote: You means I can finish this work by using the Connectome Workbench. So, the first thing I need to do is to convert all files to Workbench format by using wb_import. Is it true? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Tuesday, August 12, 2014 7:16 PM To: Caret, SureFit, and SuMS software users; Donna Dierker Subject: Re: [caret-users] projecting functional MRI to gii surfaces -spec-file-change-resolution will not get you to the fs_LR 32k atlas from fs_LR 164k (but it may get you deceptively close, making it even more treacherous). Those messages aren't errors, and the reasons behind them are better left alone, as this isn't the command you want. What you need to do is to use the fs_LR atlas files for resampling the surface. In caret5, this requires deformation map files, which we have probably already made for going between fs_LR 32k and 164k (Donna, do you know if these are available?), with the -deformation-map-apply command. However, we now do this in Connectome Workbench using atlas spheres directly with the -surface-resample command (the fs_LR 32k and 164k spheres are aligned by definition, but going to or from other atlases will need a cross-atlas registered sphere). Tim On Tue, Aug 12, 2014 at 4:33 PM, Tang, Yan yan.t...@ttu.edu wrote: Sorry, I meet another problem. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. I think the vertex too much. So I want to down-sampled to a 32,492 vertex surface. I used the caret_command -spec-file-change-resolution. But, the error was followed: Nonstandard resolution specified... Using closest divided icosahedron, with 32492 nodes. Can you explain it? if I change the number, I find only a few files be created such as def_sphere.coord, def_sphere.deform_map,study1.R.2k_fs_LR.topo.gii and study1.R.mini+orig.2k_fs_LR.spc. Many files such as curvature.shape.gii, inflated.coord.gii, midthickness.coord.gii, pial.coord.gii, thickness.shape.gii and white.coord.gii all aren't changed. So, I do some wrong steps. How should I do it? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Monday, August 11, 2014 3:54 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan yan.t...@ttu.edu wrote: Yes，I have a lot of volumes which need be projected to surface. I only know how to use the 'map volume to surface '. I don't know how to use the command. Could you give me an example? Can the file of *.coord.gii be thought as the coordinate-file-name file? But I only found
Re: [caret-users] projecting functional MRI to gii surfaces
Hi Yan, There are lots of ways to split up the brain -- parcellations. For example, the Conte69 atlas (http://brainvis.wustl.edu/wiki/index.php/Caret:Conte69_Atlas) comes with two label.gii files per hemisphere, e.g.: parcellations_VGD11b.R.164k_fs_LR.label.gii RSN-networks.R.164k_fs_LR.label.gii The first includes two parcellations: Composite Parcellation-rh (FRB08_OFP03_retinotopic) Brodmann rh (from colin.R via pals_R-to-fs_LR) The second includes four parcellations: 7 RSN Networks (YKS11 - Yeo et al., JNP, 2011) 17 RSN Networks (YKS11 - Yeo et al., JNP, 2011) RSN consensus communities (holes filled) (PCN11 - Power_Neuron11) RSN consensus communities (PCN11 - Power_Neuron11) And lots more have been published since, and will continue to be published. ;-) So you have to decide which one you want. Then you can either load that parcellation in wb_view (or caret5) and click on nodes interactively, or if you want to write a script that queries regions, there is a lookup table that maps the label key to a label name in the front of the label file, e.g.: Label Key=0 Red=0.667 Green=0.667 Blue=0.667 Alpha=0![CDATA[???]]/Label Label Key=1 Red=1 Green=1 Blue=1 Alpha=1![CDATA[u1_Unassigned]]/Label Label Key=2 Red=0.502 Green=0.502 Blue=0.502 Alpha=1![CDATA[u2_Ventral_frontal_temporal]]/Label Label Key=3 Red=1 Green=0 Blue=0 Alpha=1![CDATA[a3_Default_mode]]/Label Label Key=4 Red=0 Green=1 Blue=1 Alpha=1![CDATA[a4_Hand_somatosensory-motor]]/Label Label Key=5 Red=0 Green=0 Blue=1 Alpha=1![CDATA[a5_Visual]]/Label Label Key=6 Red=0.961 Green=0.961 Blue=0.059 Alpha=1![CDATA[a6_Fronto-parietal_task_control]]/Label Label Key=7 Red=0 Green=0.502 Blue=0.502 Alpha=1![CDATA[a7_Ventral_attention]]/Label Label Key=8 Red=0 Green=0.275 Blue=0.157 Alpha=1![CDATA[a8_Caudate_putamen]]/Label Label Key=9 Red=1 Green=0.722 Blue=0.831 Alpha=1![CDATA[a9_Superior_temporal_gyrus]]/Label Label Key=10 Red=0.675 Green=0.675 Blue=0.675 Alpha=1![CDATA[u10_Inferior_temporal_pole]]/Label You can also export the label table as ASCII text. But each vertex is associated with one of these keys in the label.gii file. Donna On Aug 28, 2014, at 2:27 PM, Tang, Yan yan.t...@ttu.edu wrote: I still have problem. How can I know which brain region is every vertex belonged to? From: Tang, Yan Sent: Friday, August 15, 2014 12:27 PM To: Caret, SureFit, and SuMS software users Subject: RE: [caret-users] projecting functional MRI to gii surfaces Thank all of you. Thank you very much. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Wednesday, August 13, 2014 2:27 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, I'm not sure about wb_import, but I know it won't downsample for you. This will, I hope: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/FSLR/downsample164_to_32k.zip login pub password download There is a script in there you will need to tweak to put in your pathnames and subject list. I tried it on some freesurfer_to_fs_LR output I had lying around, and it worked. The zip file also contains the spheres you need: ExtractDir=/home/donna/downsample164_to_32k SubjectDir=/mnt/myelin/donna/SUBJ/fs_LR_output_directory ResamplingMethod=BARYCENTRIC for Subject in $SubjList do for Hemisphere in L R do CoordInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.coord.gii TopoInput=$SubjectDir/$Subject/$Subject.$Hemisphere.164k_fs_LR.topo.gii SurfaceInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.surf.gii caret_command -file-convert -sc -is CARET $CoordInput $TopoInput -os GS $SurfaceInput CurrentSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.164k_fs_LR.surf.gii NewSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.32k_fs_LR.surf.gii SurfaceOutput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.32k_fs_LR.surf.gii wb_command -surface-resample \ $SurfaceInput \ $CurrentSphere \ $NewSphere \ $ResamplingMethod \ $SurfaceOutput done done Donna On Aug 13, 2014, at 10:42 AM, Tang, Yan yan.t...@ttu.edu wrote: You means I can finish this work by using the Connectome Workbench. So, the first thing I need to do is to convert all files to Workbench format by using wb_import. Is it true? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Tuesday, August 12, 2014 7:16 PM To: Caret, SureFit, and SuMS software users; Donna Dierker Subject: Re: [caret-users] projecting functional MRI to gii
Re: [caret-users] projecting functional MRI to gii surfaces
There are these deform_map files in the output of freesurfer_to_fs_LR: ./SAIS_216_MR1/164k_fs_164k_fs_LR_to_initial_mesh.R.deform_map ./SAIS_216_MR1/initial_mesh_to_164k_fs_LR.R.deform_map ./SAIS_216_MR1/164k_fs_164k_fs_LR_to_initial_mesh.L.deform_map ./SAIS_216_MR1/initial_mesh_to_164k_fs_LR.L.deform_map But I don't think they will work for this downsampling. I think Tim's surface-resample approach is better for this context. I will come up with what works on one of my existing freesurfer_to_fs_LR output directories and post it here when I have it working. On Aug 12, 2014, at 7:16 PM, Timothy Coalson tsc...@mst.edu wrote: -spec-file-change-resolution will not get you to the fs_LR 32k atlas from fs_LR 164k (but it may get you deceptively close, making it even more treacherous). Those messages aren't errors, and the reasons behind them are better left alone, as this isn't the command you want. What you need to do is to use the fs_LR atlas files for resampling the surface. In caret5, this requires deformation map files, which we have probably already made for going between fs_LR 32k and 164k (Donna, do you know if these are available?), with the -deformation-map-apply command. However, we now do this in Connectome Workbench using atlas spheres directly with the -surface-resample command (the fs_LR 32k and 164k spheres are aligned by definition, but going to or from other atlases will need a cross-atlas registered sphere). Tim On Tue, Aug 12, 2014 at 4:33 PM, Tang, Yan yan.t...@ttu.edu wrote: Sorry, I meet another problem. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. I think the vertex too much. So I want to down-sampled to a 32,492 vertex surface. I used the caret_command -spec-file-change-resolution. But, the error was followed: Nonstandard resolution specified... Using closest divided icosahedron, with 32492 nodes. Can you explain it? if I change the number, I find only a few files be created such as def_sphere.coord, def_sphere.deform_map,study1.R.2k_fs_LR.topo.gii and study1.R.mini+orig.2k_fs_LR.spc. Many files such as curvature.shape.gii, inflated.coord.gii, midthickness.coord.gii, pial.coord.gii, thickness.shape.gii and white.coord.gii all aren't changed. So, I do some wrong steps. How should I do it? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Monday, August 11, 2014 3:54 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan yan.t...@ttu.edu wrote: Yes，I have a lot of volumes which need be projected to surface. I only know how to use the 'map volume to surface '. I don't know how to use the command. Could you give me an example? Can the file of *.coord.gii be thought as the coordinate-file-name file? But I only found .coord file can be used in the menu of caret command executor . How about topo? .coord.gii should work, if it doesn't rename or copy the file to end in just .coord . The topo is the same file you need to load to be able to view the surface. another thing is how to set the input-metric-or-paint-file-name? From the pasted help: If the input metric or paint file name is not an empty string (), the newly create metric or paint columns will be appended to the file and then written with the output file name. In other words, if you don't want to append the columns to an existing metric file, use (a pair of double quotes) for the argument. Since you asked something related on the hcp_users list (wb_command volume to surface mapping), I will recommend that you try using wb_command for this, as caret5 is no longer under active development. The main hurdle in moving to Workbench is converting the separate coord/topo files into the combined .surf.gii format (with caret_command -file-convert with the -sc option). From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 9:14 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces I'm not clear on what you mean by I want get fMRI time course for surface vertices of every subject. If you just mean how do you scale up -- map that many volumes to all your subjects -- then I recommend scripting it and using caret_command. (Note that Workbench, the software that is superseding Caret 5.*, has more robust mapping features than caret_command, but I am going to provide the caret_command usage, since this is the caret-users list. There is also a hcp-users list that covers workbench.) Here is the usage for the command that maps volumes onto
Re: [caret-users] projecting functional MRI to gii surfaces
Hi Yan, I'm not sure about wb_import, but I know it won't downsample for you. This will, I hope: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/FSLR/downsample164_to_32k.zip login pub password download There is a script in there you will need to tweak to put in your pathnames and subject list. I tried it on some freesurfer_to_fs_LR output I had lying around, and it worked. The zip file also contains the spheres you need: ExtractDir=/home/donna/downsample164_to_32k SubjectDir=/mnt/myelin/donna/SUBJ/fs_LR_output_directory ResamplingMethod=BARYCENTRIC for Subject in $SubjList do for Hemisphere in L R do CoordInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.coord.gii TopoInput=$SubjectDir/$Subject/$Subject.$Hemisphere.164k_fs_LR.topo.gii SurfaceInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.surf.gii caret_command -file-convert -sc -is CARET $CoordInput $TopoInput -os GS $SurfaceInput CurrentSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.164k_fs_LR.surf.gii NewSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.32k_fs_LR.surf.gii SurfaceOutput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.32k_fs_LR.surf.gii wb_command -surface-resample \ $SurfaceInput \ $CurrentSphere \ $NewSphere \ $ResamplingMethod \ $SurfaceOutput done done Donna On Aug 13, 2014, at 10:42 AM, Tang, Yan yan.t...@ttu.edu wrote: You means I can finish this work by using the Connectome Workbench. So, the first thing I need to do is to convert all files to Workbench format by using wb_import. Is it true? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Tuesday, August 12, 2014 7:16 PM To: Caret, SureFit, and SuMS software users; Donna Dierker Subject: Re: [caret-users] projecting functional MRI to gii surfaces -spec-file-change-resolution will not get you to the fs_LR 32k atlas from fs_LR 164k (but it may get you deceptively close, making it even more treacherous). Those messages aren't errors, and the reasons behind them are better left alone, as this isn't the command you want. What you need to do is to use the fs_LR atlas files for resampling the surface. In caret5, this requires deformation map files, which we have probably already made for going between fs_LR 32k and 164k (Donna, do you know if these are available?), with the -deformation-map-apply command. However, we now do this in Connectome Workbench using atlas spheres directly with the -surface-resample command (the fs_LR 32k and 164k spheres are aligned by definition, but going to or from other atlases will need a cross-atlas registered sphere). Tim On Tue, Aug 12, 2014 at 4:33 PM, Tang, Yan yan.t...@ttu.edu wrote: Sorry, I meet another problem. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. I think the vertex too much. So I want to down-sampled to a 32,492 vertex surface. I used the caret_command -spec-file-change-resolution. But, the error was followed: Nonstandard resolution specified... Using closest divided icosahedron, with 32492 nodes. Can you explain it? if I change the number, I find only a few files be created such as def_sphere.coord, def_sphere.deform_map,study1.R.2k_fs_LR.topo.gii and study1.R.mini+orig.2k_fs_LR.spc. Many files such as curvature.shape.gii, inflated.coord.gii, midthickness.coord.gii, pial.coord.gii, thickness.shape.gii and white.coord.gii all aren't changed. So, I do some wrong steps. How should I do it? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Monday, August 11, 2014 3:54 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan yan.t...@ttu.edu wrote: Yes，I have a lot of volumes which need be projected to surface. I only know how to use the 'map volume to surface '. I don't know how to use the command. Could you give me an example? Can the file of *.coord.gii be thought as the coordinate-file-name file? But I only found .coord file can be used in the menu of caret command executor . How about topo? .coord.gii should work, if it doesn't rename or copy the file to end in just .coord . The topo is the same file you need to load to be able to view the surface. another thing is how to set the input-metric-or-paint-file-name? From the pasted help: If the input metric or paint file name is not an empty string (), the newly create metric or paint columns will be appended to the file and then written with the output file name. In other words, if you don't want to append the columns to an existing metric file, use (a pair of double quotes) for the argument
Re: [caret-users] projecting functional MRI to gii surfaces
wb_import should convert many of the file types, though I'm not as sure about surface files - if not, caret_command -file-convert -sc ... will take care of surface files, which I think you have done before to get the surfaces into matlab. If you already have nifti volumes, those don't need conversion. Since your earlier posts indicate your end goal may be putting volume data onto an fs_LR 32k surface, and this is something we put some thought into in the HCP pipelines, you might want to look at the methods we use (citation below). The short version is that we use wb_command's ribbon method of volume to surface mapping, which allows you to include just voxels between the white and pial surfaces (caret5 methods mainly make point estimates at the vertex locations). We do the volume to surface mapping using high resolution surfaces, and then downsample that data, rather than doing volume to surface mapping with a downsampled surface, because a resampled surface file loses some precision (gyral crowns can move slightly inwards, etc). We do this data downsampling with the new ADAP_BARY_AREA method of wb_command -metric-resample, which prevents SNR loss without needing smoothing before resampling. The most recent paper covering the methods we use is this one: http://www.ncbi.nlm.nih.gov/pubmed/23668970 (search in the text for HCP pipelines: fMRISurface). I believe we are working on getting our pipelines ready for release, which might make this process easier for you. Tim On Wed, Aug 13, 2014 at 2:27 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Yan, I'm not sure about wb_import, but I know it won't downsample for you. This will, I hope: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/FSLR/downsample164_to_32k.zip login pub password download There is a script in there you will need to tweak to put in your pathnames and subject list. I tried it on some freesurfer_to_fs_LR output I had lying around, and it worked. The zip file also contains the spheres you need: ExtractDir=/home/donna/downsample164_to_32k SubjectDir=/mnt/myelin/donna/SUBJ/fs_LR_output_directory ResamplingMethod=BARYCENTRIC for Subject in $SubjList do for Hemisphere in L R do CoordInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.coord.gii TopoInput=$SubjectDir/$Subject/$Subject.$Hemisphere.164k_fs_LR.topo.gii SurfaceInput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.164k_fs_LR.surf.gii caret_command -file-convert -sc -is CARET $CoordInput $TopoInput -os GS $SurfaceInput CurrentSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.164k_fs_LR.surf.gii NewSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.32k_fs_LR.surf.gii SurfaceOutput=$SubjectDir/$Subject/$Subject.$Hemisphere.midthickness_orig.32k_fs_LR.surf.gii wb_command -surface-resample \ $SurfaceInput \ $CurrentSphere \ $NewSphere \ $ResamplingMethod \ $SurfaceOutput done done Donna On Aug 13, 2014, at 10:42 AM, Tang, Yan yan.t...@ttu.edu wrote: You means I can finish this work by using the Connectome Workbench. So, the first thing I need to do is to convert all files to Workbench format by using wb_import. Is it true? From: caret-users-boun...@brainvis.wustl.edu [ caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [ tsc...@mst.edu] Sent: Tuesday, August 12, 2014 7:16 PM To: Caret, SureFit, and SuMS software users; Donna Dierker Subject: Re: [caret-users] projecting functional MRI to gii surfaces -spec-file-change-resolution will not get you to the fs_LR 32k atlas from fs_LR 164k (but it may get you deceptively close, making it even more treacherous). Those messages aren't errors, and the reasons behind them are better left alone, as this isn't the command you want. What you need to do is to use the fs_LR atlas files for resampling the surface. In caret5, this requires deformation map files, which we have probably already made for going between fs_LR 32k and 164k (Donna, do you know if these are available?), with the -deformation-map-apply command. However, we now do this in Connectome Workbench using atlas spheres directly with the -surface-resample command (the fs_LR 32k and 164k spheres are aligned by definition, but going to or from other atlases will need a cross-atlas registered sphere). Tim On Tue, Aug 12, 2014 at 4:33 PM, Tang, Yan yan.t...@ttu.edu wrote: Sorry, I meet another problem. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. I think the vertex too much. So I want to down-sampled to a 32,492 vertex surface. I used the caret_command -spec-file-change-resolution. But, the error was followed: Nonstandard resolution specified... Using closest divided icosahedron, with 32492 nodes. Can you explain it? if I change the number, I find only a few files be created such as def_sphere.coord
Re: [caret-users] projecting functional MRI to gii surfaces
Sorry, I meet another problem. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. I think the vertex too much. So I want to down-sampled to a 32,492 vertex surface. I used the caret_command -spec-file-change-resolution. But, the error was followed: Nonstandard resolution specified... Using closest divided icosahedron, with 32492 nodes. Can you explain it? if I change the number, I find only a few files be created such as def_sphere.coord, def_sphere.deform_map,study1.R.2k_fs_LR.topo.gii and study1.R.mini+orig.2k_fs_LR.spc. Many files such as curvature.shape.gii, inflated.coord.gii, midthickness.coord.gii, pial.coord.gii, thickness.shape.gii and white.coord.gii all aren't changed. So, I do some wrong steps. How should I do it? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Monday, August 11, 2014 3:54 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan yan.t...@ttu.edumailto:yan.t...@ttu.edu wrote: Yes，I have a lot of volumes which need be projected to surface. I only know how to use the 'map volume to surface '. I don't know how to use the command. Could you give me an example? Can the file of *.coord.gii be thought as the coordinate-file-name file? But I only found .coord file can be used in the menu of caret command executor . How about topo? .coord.gii should work, if it doesn't rename or copy the file to end in just .coord . The topo is the same file you need to load to be able to view the surface. another thing is how to set the input-metric-or-paint-file-name? From the pasted help: If the input metric or paint file name is not an empty string (), the newly create metric or paint columns will be appended to the file and then written with the output file name. In other words, if you don't want to append the columns to an existing metric file, use (a pair of double quotes) for the argument. Since you asked something related on the hcp_users list (wb_command volume to surface mapping), I will recommend that you try using wb_command for this, as caret5 is no longer under active development. The main hurdle in moving to Workbench is converting the separate coord/topo files into the combined .surf.gii format (with caret_command -file-convert with the -sc option). From: caret-users-boun...@brainvis.wustl.edumailto:caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edumailto:caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edumailto:do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 9:14 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces I'm not clear on what you mean by I want get fMRI time course for surface vertices of every subject. If you just mean how do you scale up -- map that many volumes to all your subjects -- then I recommend scripting it and using caret_command. (Note that Workbench, the software that is superseding Caret 5.*, has more robust mapping features than caret_command, but I am going to provide the caret_command usage, since this is the caret-users list. There is also a hcp-users list that covers workbench.) Here is the usage for the command that maps volumes onto surfaces: caret_command -volume-map-to-surface coordinate-file-name topology-file-name input-metric-or-paint-file-name output-metric-or-paint-file-name algorithm input-volume-file-names [-av average-voxel-neighbor-cube-size (mm)] [-bf brain-fish-max-distance brain-fish-splat factor] [-g gaussian-neighbor-cube-size (mm) sigma-norm sigma-tang norm below cutoff (mm) norm above cutoff (mm) tang-cutoff (mm)] [-mv maximum-voxel-neighbor-cube-size (mm)] [-sv strongest-voxel-neighbor-cube-size (mm)] Map volume(s) to a surface metric or paint file. For successful mapping, both the surface and the volume must be in the same stereotaxic space. algorithm is one of: METRIC_AVERAGE_NODES METRIC_AVERAGE_VOXEL METRIC_ENCLOSING_VOXEL METRIC_GAUSSIAN METRIC_INTERPOLATED_VOXEL METRIC_MAXIMUM_VOXEL METRIC_MCW_BRAIN_FISH METRIC_STRONGEST_VOXEL PAINT_ENCLOSING_VOXEL If the input metric or paint file name is not an empty string (), the newly create metric or paint columns will be appended to the file and then written with the output file name. On Aug 4, 2014, at 3:49 PM, Tang
Re: [caret-users] projecting functional MRI to gii surfaces
Yes，I have a lot of volumes which need be projected to surface. I only know how to use the 'map volume to surface '. I don't know how to use the command. Could you give me an example? Can the file of *.coord.gii be thought as the coordinate-file-name file? But I only found .coord file can be used in the menu of caret command executor . How about topo? another thing is how to set the input-metric-or-paint-file-name? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 9:14 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces I'm not clear on what you mean by I want get fMRI time course for surface vertices of every subject. If you just mean how do you scale up -- map that many volumes to all your subjects -- then I recommend scripting it and using caret_command. (Note that Workbench, the software that is superseding Caret 5.*, has more robust mapping features than caret_command, but I am going to provide the caret_command usage, since this is the caret-users list. There is also a hcp-users list that covers workbench.) Here is the usage for the command that maps volumes onto surfaces: caret_command -volume-map-to-surface coordinate-file-name topology-file-name input-metric-or-paint-file-name output-metric-or-paint-file-name algorithm input-volume-file-names [-av average-voxel-neighbor-cube-size (mm)] [-bf brain-fish-max-distance brain-fish-splat factor] [-g gaussian-neighbor-cube-size (mm) sigma-norm sigma-tang norm below cutoff (mm) norm above cutoff (mm) tang-cutoff (mm)] [-mv maximum-voxel-neighbor-cube-size (mm)] [-sv strongest-voxel-neighbor-cube-size (mm)] Map volume(s) to a surface metric or paint file. For successful mapping, both the surface and the volume must be in the same stereotaxic space. algorithm is one of: METRIC_AVERAGE_NODES METRIC_AVERAGE_VOXEL METRIC_ENCLOSING_VOXEL METRIC_GAUSSIAN METRIC_INTERPOLATED_VOXEL METRIC_MAXIMUM_VOXEL METRIC_MCW_BRAIN_FISH METRIC_STRONGEST_VOXEL PAINT_ENCLOSING_VOXEL If the input metric or paint file name is not an empty string (), the newly create metric or paint columns will be appended to the file and then written with the output file name. On Aug 4, 2014, at 3:49 PM, Tang, Yan yan.t...@ttu.edu wrote: Thank you for your help. Now, I meet another problem. I project all functional MRI to 164k fs_LR surface. Every subject have 135 volumes. I want get fMRI time course for surface vertices of every subject. How should I do? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 5:34 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Push Toolbar: D/C and make sure the primary overlay is Metric. Make sure the right column is selected. If that check out okay, then I would do: File: Open Data File: Volume Functional File Load the volume you just mapped Switch to volume view and select view All (as opposed to H (horizontal or axial). Select D/C and on the page selection drop-down menu, scroll all the way to the bottom something like volume surface outline Toggle on the fiducial surface used for the mapping, so that you can see how the surface aligns with the volume. Sometimes there are header issues, and the origin is not set correctly, resulting in faulty volume-surface alignment. On Aug 1, 2014, at 4:29 PM, Tang, Yan yan.t...@ttu.edu wrote: When I open the spec file and mapped the Metric, only the surface was displayed. The result is in the attachment. How should I do? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 4:02 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hmmm. Sounds like more than a header to me. When you open the spec file you selected when you mapped the data, and select the output file that is 446kb, what happens? You must make sure you select Metric on the D/C: Overlay/Underlay Surface menu (primary or secondary, typically). Else it won't display
Re: [caret-users] projecting functional MRI to gii surfaces
On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan yan.t...@ttu.edu wrote: Yes，I have a lot of volumes which need be projected to surface. I only know how to use the 'map volume to surface '. I don't know how to use the command. Could you give me an example? Can the file of *.coord.gii be thought as the coordinate-file-name file? But I only found .coord file can be used in the menu of caret command executor . How about topo? .coord.gii should work, if it doesn't rename or copy the file to end in just .coord . The topo is the same file you need to load to be able to view the surface. another thing is how to set the input-metric-or-paint-file-name? From the pasted help: If the input metric or paint file name is not an empty string (), the newly create metric or paint columns will be appended to the file and then written with the output file name. In other words, if you don't want to append the columns to an existing metric file, use (a pair of double quotes) for the argument. Since you asked something related on the hcp_users list (wb_command volume to surface mapping), I will recommend that you try using wb_command for this, as caret5 is no longer under active development. The main hurdle in moving to Workbench is converting the separate coord/topo files into the combined .surf.gii format (with caret_command -file-convert with the -sc option). From: caret-users-boun...@brainvis.wustl.edu [ caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [ do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 9:14 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces I'm not clear on what you mean by I want get fMRI time course for surface vertices of every subject. If you just mean how do you scale up -- map that many volumes to all your subjects -- then I recommend scripting it and using caret_command. (Note that Workbench, the software that is superseding Caret 5.*, has more robust mapping features than caret_command, but I am going to provide the caret_command usage, since this is the caret-users list. There is also a hcp-users list that covers workbench.) Here is the usage for the command that maps volumes onto surfaces: caret_command -volume-map-to-surface coordinate-file-name topology-file-name input-metric-or-paint-file-name output-metric-or-paint-file-name algorithm input-volume-file-names [-av average-voxel-neighbor-cube-size (mm)] [-bf brain-fish-max-distance brain-fish-splat factor] [-g gaussian-neighbor-cube-size (mm) sigma-norm sigma-tang norm below cutoff (mm) norm above cutoff (mm) tang-cutoff (mm)] [-mv maximum-voxel-neighbor-cube-size (mm)] [-sv strongest-voxel-neighbor-cube-size (mm)] Map volume(s) to a surface metric or paint file. For successful mapping, both the surface and the volume must be in the same stereotaxic space. algorithm is one of: METRIC_AVERAGE_NODES METRIC_AVERAGE_VOXEL METRIC_ENCLOSING_VOXEL METRIC_GAUSSIAN METRIC_INTERPOLATED_VOXEL METRIC_MAXIMUM_VOXEL METRIC_MCW_BRAIN_FISH METRIC_STRONGEST_VOXEL PAINT_ENCLOSING_VOXEL If the input metric or paint file name is not an empty string (), the newly create metric or paint columns will be appended to the file and then written with the output file name. On Aug 4, 2014, at 3:49 PM, Tang, Yan yan.t...@ttu.edu wrote: Thank you for your help. Now, I meet another problem. I project all functional MRI to 164k fs_LR surface. Every subject have 135 volumes. I want get fMRI time course for surface vertices of every subject. How should I do? From: caret-users-boun...@brainvis.wustl.edu [ caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [ donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 5:34 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Push Toolbar: D/C and make sure the primary overlay is Metric. Make sure the right column is selected. If that check out okay, then I would do: File: Open Data File: Volume Functional File Load the volume you just mapped Switch to volume view and select view All (as opposed to H (horizontal or axial). Select D/C and on the page selection drop-down menu, scroll all the way to the bottom something like volume surface outline Toggle on the fiducial surface used for the mapping, so that you can see how the surface aligns
Re: [caret-users] projecting functional MRI to gii surfaces
Thank you very much! From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Wednesday, August 06, 2014 5:18 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Yes, the vertices array appears to be the vertex coordinates. You may need to do the -file-convert -format-convert XML_BASE64_GZIP (not ASCII) on the metric file (and maybe even rename it to end in .func.gii) to load it in matlab as a gifti file. The metric file does not contain voxel values, it contains a value at each surface vertex. The correspondence between voxels and surface vertices is purely spatial, and unless you used enclosing voxel mapping (which is not good for continuous data values like functional activation), each vertex contains an interpolated value derived from several voxels. Tim On Wed, Aug 6, 2014 at 4:40 PM, Tang, Yan yan.t...@ttu.edumailto:yan.t...@ttu.edu wrote: Thank you for your help. I use the command caret_command -file-conver -sc -is CARET to get surf.gii file. And I use the GIFTI to open this surf.gii file and get two important variables vertices and faces. vertices= -6.8856 -52.5189 23.7218 -22.1394 -41.5367 68.0599 -49.4149 -0.5296 47.7317 -3.4733 22.7785 64.3392 -25.9901 -104.46824.0191 -47.4914 -56.3775 48.6392 -26.3158 45.2893 14.0113 -0.94799.10271.0427 -23.8312 -56.4579 -7.5924 -51.4654 -34.09551.4522 I think the vertices include the coordinates. Is it right? But I still can't open the metric file in GIFTI. This metric file was obtain by mapping functional volumes to surfaces in volume selection page. When I used the caret_command -file-convert -format-convert ASCII my_fmri.metric, I found some information in the metric 0 -3.944756 1 0.00 2 0.00 3 0.00 4 -0.291482 5 0.995688 6 6.848554 7 3.783060 8 0.804804 9 -4.805716 10 -6.419259 11 -0.036545 12 -5.132483 13 -6.023278 14 -6.115900 15 -6.208522 16 -6.301144 17 -6.347455 18 -5.193967 19 -3.463736 20 -2.005528 These information maybe display the every voxel's value. But I still can't use the use the vertices in surf.gii as seed to analysis the resting state functional connectivity. Because I don't know the correspondence between the vertices in surf.gii and the voxel in fMRI. Please help me. Thank you. From: caret-users-boun...@brainvis.wustl.edumailto:caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edumailto:caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edumailto:tsc...@mst.edu] Sent: Wednesday, August 06, 2014 1:27 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Correction, there is a matlab GIFTI toolbox, not CIFTI. Metric files are usually already GIFTI files, but caret5 coord/topo files need to be converted: to convert non-GIFTI metric file to GIFTI: caret_command -file-convert -format-convert XML_BASE64_GZIP file to convert topo/coord to GIFTI surface: caret_command -file-conver -sc -is CARET coord topo -os GS something.surf.gii I believe the matlab GIFTI toolbox will read surface files, but you'll need to separate the two data arrays in it as to which describes the triangles, and which is the vertex coordinates. Tim On Wed, Aug 6, 2014 at 8:32 AM, Donna Dierker do...@brainvis.wustl.edumailto:do...@brainvis.wustl.edu wrote: First, I want to point out that there is a CIFTI matlab toolkit, I think, but I know very little about it (or matlab in general). What I do know: * The freesurfer_to_fs_LR pipeline probably doesn't generate CIFTI output. But the forthcoming Human Connectome Project (HCP) pipeline does. * Questions about the CIFTI matlab toolkit might better be posed to the CIFTI forum on nitrc.orghttp://nitrc.org (http://www.nitrc.org/forum/?group_id=454). Using the caret5/caret_command tools, it is possible to convert the metric/func.gii files to ASCII, e.g.: caret_command -file-convert -format-convert ASCII my_fmri.metric … or: caret_command -file-convert -format-convert ASCII my_fmri.func.gii As for the coordinates, since you have the individual midthickness surfaces on 164k mesh, you can those for the unprojection command. If you really want a grid, then it is a border file you will get out of caret: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#borderFile Here is the Alex Cohen paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705206/ This is not a trivial task. ;-) On Aug 5, 2014, at 3:13 PM, Tang, Yan yan.t...@ttu.edumailto:yan.t...@ttu.edu wrote: Maybe I do some wrong things. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Then, I want
Re: [caret-users] projecting functional MRI to gii surfaces
First, I want to point out that there is a CIFTI matlab toolkit, I think, but I know very little about it (or matlab in general). What I do know: * The freesurfer_to_fs_LR pipeline probably doesn't generate CIFTI output. But the forthcoming Human Connectome Project (HCP) pipeline does. * Questions about the CIFTI matlab toolkit might better be posed to the CIFTI forum on nitrc.org (http://www.nitrc.org/forum/?group_id=454). Using the caret5/caret_command tools, it is possible to convert the metric/func.gii files to ASCII, e.g.: caret_command -file-convert -format-convert ASCII my_fmri.metric … or: caret_command -file-convert -format-convert ASCII my_fmri.func.gii As for the coordinates, since you have the individual midthickness surfaces on 164k mesh, you can those for the unprojection command. If you really want a grid, then it is a border file you will get out of caret: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#borderFile Here is the Alex Cohen paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705206/ This is not a trivial task. ;-) On Aug 5, 2014, at 3:13 PM, Tang, Yan yan.t...@ttu.edu wrote: Maybe I do some wrong things. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Then, I want to get the points in 164k fs_LR surface and use these points as seed to analysis the resting state functional connectivity. So I do project functional MRI to surface. But after that, I don't know how to do it in next step. I get metric file, but these files cannot be read in Matlab. And I also don't get the coordinates of the points in 164k fs_LR surface. Just you mention the method of Alex Cohen. I am beginner of Caret. Could you tell me the method in detail? thank you From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 10:26 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces You can do that, but I am not used to seeing this done with the mean midthickness surface. Alex Cohen did something like this when he was using resting state functional connectivity to find gradients in a subject's cortical networks. He used the PALS flat or spherical map to get a common grid onto a standard mesh. Once there, he projected that grid onto the individual's midthickness surface on the standard mesh. (Like the grid is getting folded back up into the individual's anatomical pattern.) Then he unprojected the points to use as seeds for his analysis. Do you mind if I ask how the mean midthickness surface comes into play? Caret's Layers: Borders has options for making grids on the flat map. People make grids on the sphere in matlab. There are caret_command tools for unprojecting borders. caret_command -surface-border-unprojection Border files differ from border projection files in that they are points not tied to a particular mesh. The advantage is that you can open the same border point on, say, a native and 164k mesh, and it will align with both, if it aligns with one (and they are identical except for mesh). The advantage of borderproj files is that they open on multiple configurations - flat, midthickness, inflated, etc. - but the price is that you're tied to a mesh. On Aug 5, 2014, at 10:06 AM, Tang, Yan yan.t...@ttu.edu wrote: Thank you for your help. Another problem is how to use the Caret software to generate regularly spaced Cartesian grids on the flattened PALS-B12 average surface of the left and right hemispheres. Can I use this 3-dimensional (3D) stereotactic coordinates from the PALS-B12 average fiducial (midthickness) surface for each grid location to obtain the voxel coordinates (3 × 3 × 3 mm resolution) containing that point in fMRI? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 5:34 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Push Toolbar: D/C and make sure the primary overlay is Metric. Make sure the right column is selected. If that check out okay, then I would do: File: Open Data File: Volume Functional File Load the volume you just mapped Switch to volume view and select view All (as opposed to H (horizontal or axial). Select D/C and on the page selection drop-down menu, scroll all the way to the bottom something like volume surface outline Toggle on the fiducial surface used for the mapping, so that you can see how the surface aligns with the volume. Sometimes there are header issues
Re: [caret-users] projecting functional MRI to gii surfaces
Thank you for your help. I use the command caret_command -file-conver -sc -is CARET to get surf.gii file. And I use the GIFTI to open this surf.gii file and get two important variables vertices and faces. vertices= -6.8856 -52.5189 23.7218 -22.1394 -41.5367 68.0599 -49.4149 -0.5296 47.7317 -3.4733 22.7785 64.3392 -25.9901 -104.46824.0191 -47.4914 -56.3775 48.6392 -26.3158 45.2893 14.0113 -0.94799.10271.0427 -23.8312 -56.4579 -7.5924 -51.4654 -34.09551.4522 I think the vertices include the coordinates. Is it right? But I still can't open the metric file in GIFTI. This metric file was obtain by mapping functional volumes to surfaces in volume selection page. When I used the caret_command -file-convert -format-convert ASCII my_fmri.metric, I found some information in the metric 0 -3.944756 1 0.00 2 0.00 3 0.00 4 -0.291482 5 0.995688 6 6.848554 7 3.783060 8 0.804804 9 -4.805716 10 -6.419259 11 -0.036545 12 -5.132483 13 -6.023278 14 -6.115900 15 -6.208522 16 -6.301144 17 -6.347455 18 -5.193967 19 -3.463736 20 -2.005528 These information maybe display the every voxel's value. But I still can't use the use the vertices in surf.gii as seed to analysis the resting state functional connectivity. Because I don't know the correspondence between the vertices in surf.gii and the voxel in fMRI. Please help me. Thank you. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Wednesday, August 06, 2014 1:27 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Correction, there is a matlab GIFTI toolbox, not CIFTI. Metric files are usually already GIFTI files, but caret5 coord/topo files need to be converted: to convert non-GIFTI metric file to GIFTI: caret_command -file-convert -format-convert XML_BASE64_GZIP file to convert topo/coord to GIFTI surface: caret_command -file-conver -sc -is CARET coord topo -os GS something.surf.gii I believe the matlab GIFTI toolbox will read surface files, but you'll need to separate the two data arrays in it as to which describes the triangles, and which is the vertex coordinates. Tim On Wed, Aug 6, 2014 at 8:32 AM, Donna Dierker do...@brainvis.wustl.edumailto:do...@brainvis.wustl.edu wrote: First, I want to point out that there is a CIFTI matlab toolkit, I think, but I know very little about it (or matlab in general). What I do know: * The freesurfer_to_fs_LR pipeline probably doesn't generate CIFTI output. But the forthcoming Human Connectome Project (HCP) pipeline does. * Questions about the CIFTI matlab toolkit might better be posed to the CIFTI forum on nitrc.orghttp://nitrc.org (http://www.nitrc.org/forum/?group_id=454). Using the caret5/caret_command tools, it is possible to convert the metric/func.gii files to ASCII, e.g.: caret_command -file-convert -format-convert ASCII my_fmri.metric … or: caret_command -file-convert -format-convert ASCII my_fmri.func.gii As for the coordinates, since you have the individual midthickness surfaces on 164k mesh, you can those for the unprojection command. If you really want a grid, then it is a border file you will get out of caret: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#borderFile Here is the Alex Cohen paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705206/ This is not a trivial task. ;-) On Aug 5, 2014, at 3:13 PM, Tang, Yan yan.t...@ttu.edumailto:yan.t...@ttu.edu wrote: Maybe I do some wrong things. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Then, I want to get the points in 164k fs_LR surface and use these points as seed to analysis the resting state functional connectivity. So I do project functional MRI to surface. But after that, I don't know how to do it in next step. I get metric file, but these files cannot be read in Matlab. And I also don't get the coordinates of the points in 164k fs_LR surface. Just you mention the method of Alex Cohen. I am beginner of Caret. Could you tell me the method in detail? thank you From: caret-users-boun...@brainvis.wustl.edumailto:caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edumailto:caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edumailto:do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 10:26 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces You can do that, but I am not used to seeing this done with the mean midthickness surface. Alex Cohen did something like this when he was using resting state functional connectivity to find gradients
Re: [caret-users] projecting functional MRI to gii surfaces
Yes, the vertices array appears to be the vertex coordinates. You may need to do the -file-convert -format-convert XML_BASE64_GZIP (not ASCII) on the metric file (and maybe even rename it to end in .func.gii) to load it in matlab as a gifti file. The metric file does not contain voxel values, it contains a value at each surface vertex. The correspondence between voxels and surface vertices is purely spatial, and unless you used enclosing voxel mapping (which is not good for continuous data values like functional activation), each vertex contains an interpolated value derived from several voxels. Tim On Wed, Aug 6, 2014 at 4:40 PM, Tang, Yan yan.t...@ttu.edu wrote: Thank you for your help. I use the command caret_command -file-conver -sc -is CARET to get surf.gii file. And I use the GIFTI to open this surf.gii file and get two important variables vertices and faces. vertices= -6.8856 -52.5189 23.7218 -22.1394 -41.5367 68.0599 -49.4149 -0.5296 47.7317 -3.4733 22.7785 64.3392 -25.9901 -104.46824.0191 -47.4914 -56.3775 48.6392 -26.3158 45.2893 14.0113 -0.94799.10271.0427 -23.8312 -56.4579 -7.5924 -51.4654 -34.09551.4522 I think the vertices include the coordinates. Is it right? But I still can't open the metric file in GIFTI. This metric file was obtain by mapping functional volumes to surfaces in volume selection page. When I used the caret_command -file-convert -format-convert ASCII my_fmri.metric, I found some information in the metric 0 -3.944756 1 0.00 2 0.00 3 0.00 4 -0.291482 5 0.995688 6 6.848554 7 3.783060 8 0.804804 9 -4.805716 10 -6.419259 11 -0.036545 12 -5.132483 13 -6.023278 14 -6.115900 15 -6.208522 16 -6.301144 17 -6.347455 18 -5.193967 19 -3.463736 20 -2.005528 These information maybe display the every voxel's value. But I still can't use the use the vertices in surf.gii as seed to analysis the resting state functional connectivity. Because I don't know the correspondence between the vertices in surf.gii and the voxel in fMRI. Please help me. Thank you. -- *From:* caret-users-boun...@brainvis.wustl.edu [ caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [ tsc...@mst.edu] *Sent:* Wednesday, August 06, 2014 1:27 PM *To:* Caret, SureFit, and SuMS software users *Cc:* Tang, Yiyuan *Subject:* Re: [caret-users] projecting functional MRI to gii surfaces Correction, there is a matlab GIFTI toolbox, not CIFTI. Metric files are usually already GIFTI files, but caret5 coord/topo files need to be converted: to convert non-GIFTI metric file to GIFTI: caret_command -file-convert -format-convert XML_BASE64_GZIP file to convert topo/coord to GIFTI surface: caret_command -file-conver -sc -is CARET coord topo -os GS something.surf.gii I believe the matlab GIFTI toolbox will read surface files, but you'll need to separate the two data arrays in it as to which describes the triangles, and which is the vertex coordinates. Tim On Wed, Aug 6, 2014 at 8:32 AM, Donna Dierker do...@brainvis.wustl.edu wrote: First, I want to point out that there is a CIFTI matlab toolkit, I think, but I know very little about it (or matlab in general). What I do know: * The freesurfer_to_fs_LR pipeline probably doesn't generate CIFTI output. But the forthcoming Human Connectome Project (HCP) pipeline does. * Questions about the CIFTI matlab toolkit might better be posed to the CIFTI forum on nitrc.org (http://www.nitrc.org/forum/?group_id=454). Using the caret5/caret_command tools, it is possible to convert the metric/func.gii files to ASCII, e.g.: caret_command -file-convert -format-convert ASCII my_fmri.metric … or: caret_command -file-convert -format-convert ASCII my_fmri.func.gii As for the coordinates, since you have the individual midthickness surfaces on 164k mesh, you can those for the unprojection command. If you really want a grid, then it is a border file you will get out of caret: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#borderFile Here is the Alex Cohen paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705206/ This is not a trivial task. ;-) On Aug 5, 2014, at 3:13 PM, Tang, Yan yan.t...@ttu.edu wrote: Maybe I do some wrong things. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Then, I want to get the points in 164k fs_LR surface and use these points as seed to analysis the resting state functional connectivity. So I do project functional MRI to surface. But after that, I don't know how to do it in next step. I get metric file, but these files cannot be read in Matlab. And I also don't get the coordinates of the points in 164k fs_LR surface. Just you mention the method of Alex Cohen. I am beginner of Caret. Could you tell me the method in detail
Re: [caret-users] projecting functional MRI to gii surfaces
I'm not clear on what you mean by I want get fMRI time course for surface vertices of every subject. If you just mean how do you scale up -- map that many volumes to all your subjects -- then I recommend scripting it and using caret_command. (Note that Workbench, the software that is superseding Caret 5.*, has more robust mapping features than caret_command, but I am going to provide the caret_command usage, since this is the caret-users list. There is also a hcp-users list that covers workbench.) Here is the usage for the command that maps volumes onto surfaces: caret_command -volume-map-to-surface coordinate-file-name topology-file-name input-metric-or-paint-file-name output-metric-or-paint-file-name algorithm input-volume-file-names [-av average-voxel-neighbor-cube-size (mm)] [-bf brain-fish-max-distance brain-fish-splat factor] [-g gaussian-neighbor-cube-size (mm) sigma-norm sigma-tang norm below cutoff (mm) norm above cutoff (mm) tang-cutoff (mm)] [-mv maximum-voxel-neighbor-cube-size (mm)] [-sv strongest-voxel-neighbor-cube-size (mm)] Map volume(s) to a surface metric or paint file. For successful mapping, both the surface and the volume must be in the same stereotaxic space. algorithm is one of: METRIC_AVERAGE_NODES METRIC_AVERAGE_VOXEL METRIC_ENCLOSING_VOXEL METRIC_GAUSSIAN METRIC_INTERPOLATED_VOXEL METRIC_MAXIMUM_VOXEL METRIC_MCW_BRAIN_FISH METRIC_STRONGEST_VOXEL PAINT_ENCLOSING_VOXEL If the input metric or paint file name is not an empty string (), the newly create metric or paint columns will be appended to the file and then written with the output file name. On Aug 4, 2014, at 3:49 PM, Tang, Yan yan.t...@ttu.edu wrote: Thank you for your help. Now, I meet another problem. I project all functional MRI to 164k fs_LR surface. Every subject have 135 volumes. I want get fMRI time course for surface vertices of every subject. How should I do? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 5:34 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Push Toolbar: D/C and make sure the primary overlay is Metric. Make sure the right column is selected. If that check out okay, then I would do: File: Open Data File: Volume Functional File Load the volume you just mapped Switch to volume view and select view All (as opposed to H (horizontal or axial). Select D/C and on the page selection drop-down menu, scroll all the way to the bottom something like volume surface outline Toggle on the fiducial surface used for the mapping, so that you can see how the surface aligns with the volume. Sometimes there are header issues, and the origin is not set correctly, resulting in faulty volume-surface alignment. On Aug 1, 2014, at 4:29 PM, Tang, Yan yan.t...@ttu.edu wrote: When I open the spec file and mapped the Metric, only the surface was displayed. The result is in the attachment. How should I do? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 4:02 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hmmm. Sounds like more than a header to me. When you open the spec file you selected when you mapped the data, and select the output file that is 446kb, what happens? You must make sure you select Metric on the D/C: Overlay/Underlay Surface menu (primary or secondary, typically). Else it won't display. On Aug 1, 2014, at 2:47 PM, Tang, Yan yan.t...@ttu.edu wrote: I am sure that the file exist and the size of file is 446KB. Is It correct? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 10:10 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, Could you use a terminal window or file manager to check whether the file exists, and if so, what its size is. We have seen cases before where the file was just a header -- no data. Inexplicably
Re: [caret-users] projecting functional MRI to gii surfaces
Maybe I do some wrong things. I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Then, I want to get the points in 164k fs_LR surface and use these points as seed to analysis the resting state functional connectivity. So I do project functional MRI to surface. But after that, I don't know how to do it in next step. I get metric file, but these files cannot be read in Matlab. And I also don't get the coordinates of the points in 164k fs_LR surface. Just you mention the method of Alex Cohen. I am beginner of Caret. Could you tell me the method in detail? thank you From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 10:26 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces You can do that, but I am not used to seeing this done with the mean midthickness surface. Alex Cohen did something like this when he was using resting state functional connectivity to find gradients in a subject's cortical networks. He used the PALS flat or spherical map to get a common grid onto a standard mesh. Once there, he projected that grid onto the individual's midthickness surface on the standard mesh. (Like the grid is getting folded back up into the individual's anatomical pattern.) Then he unprojected the points to use as seeds for his analysis. Do you mind if I ask how the mean midthickness surface comes into play? Caret's Layers: Borders has options for making grids on the flat map. People make grids on the sphere in matlab. There are caret_command tools for unprojecting borders. caret_command -surface-border-unprojection Border files differ from border projection files in that they are points not tied to a particular mesh. The advantage is that you can open the same border point on, say, a native and 164k mesh, and it will align with both, if it aligns with one (and they are identical except for mesh). The advantage of borderproj files is that they open on multiple configurations - flat, midthickness, inflated, etc. - but the price is that you're tied to a mesh. On Aug 5, 2014, at 10:06 AM, Tang, Yan yan.t...@ttu.edu wrote: Thank you for your help. Another problem is how to use the Caret software to generate regularly spaced Cartesian grids on the flattened PALS-B12 average surface of the left and right hemispheres. Can I use this 3-dimensional (3D) stereotactic coordinates from the PALS-B12 average fiducial (midthickness) surface for each grid location to obtain the voxel coordinates (3 × 3 × 3 mm resolution) containing that point in fMRI? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 5:34 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Push Toolbar: D/C and make sure the primary overlay is Metric. Make sure the right column is selected. If that check out okay, then I would do: File: Open Data File: Volume Functional File Load the volume you just mapped Switch to volume view and select view All (as opposed to H (horizontal or axial). Select D/C and on the page selection drop-down menu, scroll all the way to the bottom something like volume surface outline Toggle on the fiducial surface used for the mapping, so that you can see how the surface aligns with the volume. Sometimes there are header issues, and the origin is not set correctly, resulting in faulty volume-surface alignment. On Aug 1, 2014, at 4:29 PM, Tang, Yan yan.t...@ttu.edu wrote: When I open the spec file and mapped the Metric, only the surface was displayed. The result is in the attachment. How should I do? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 4:02 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hmmm. Sounds like more than a header to me. When you open the spec file you selected when you mapped the data, and select the output file that is 446kb, what happens? You must make sure you select Metric on the D/C: Overlay/Underlay Surface menu (primary or secondary, typically). Else it won't display. On Aug 1, 2014, at 2:47 PM, Tang, Yan yan.t...@ttu.edu wrote: I am sure that the file exist and the size of file is 446KB. Is It correct? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu
Re: [caret-users] projecting functional MRI to gii surfaces
Hi Yan, Could you use a terminal window or file manager to check whether the file exists, and if so, what its size is. We have seen cases before where the file was just a header -- no data. Inexplicably, the presence of a non-english character set on the system used has caused this sort of trouble. If there is a system nearby that does not have a non-english character set installed, you might see if Caret works there. Or remove any non-english character sets on your system and see if it helps. Donna On Jul 31, 2014, at 3:52 PM, Tang, Yan yan.t...@ttu.edu wrote: Dear all, I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Now I want to map functional volumes to surfaces. In volume selection page, I choose my file 'ff001_010.nii'; In spec file and surface selection page, I choose the file 'study1.L.orig.164k_fs_LR'. I get a file 'map_data_0_31_Jul_2014_15_10_13.metric'. But I find I couldn't open this file. Which step is wrong? How can you do it? ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] projecting functional MRI to gii surfaces
I am sure that the file exist and the size of file is 446KB. Is It correct? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 10:10 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, Could you use a terminal window or file manager to check whether the file exists, and if so, what its size is. We have seen cases before where the file was just a header -- no data. Inexplicably, the presence of a non-english character set on the system used has caused this sort of trouble. If there is a system nearby that does not have a non-english character set installed, you might see if Caret works there. Or remove any non-english character sets on your system and see if it helps. Donna On Jul 31, 2014, at 3:52 PM, Tang, Yan yan.t...@ttu.edu wrote: Dear all, I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Now I want to map functional volumes to surfaces. In volume selection page, I choose my file 'ff001_010.nii'; In spec file and surface selection page, I choose the file 'study1.L.orig.164k_fs_LR'. I get a file 'map_data_0_31_Jul_2014_15_10_13.metric'. But I find I couldn't open this file. Which step is wrong? How can you do it? ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] projecting functional MRI to gii surfaces
Hmmm. Sounds like more than a header to me. When you open the spec file you selected when you mapped the data, and select the output file that is 446kb, what happens? You must make sure you select Metric on the D/C: Overlay/Underlay Surface menu (primary or secondary, typically). Else it won't display. On Aug 1, 2014, at 2:47 PM, Tang, Yan yan.t...@ttu.edu wrote: I am sure that the file exist and the size of file is 446KB. Is It correct? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 10:10 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, Could you use a terminal window or file manager to check whether the file exists, and if so, what its size is. We have seen cases before where the file was just a header -- no data. Inexplicably, the presence of a non-english character set on the system used has caused this sort of trouble. If there is a system nearby that does not have a non-english character set installed, you might see if Caret works there. Or remove any non-english character sets on your system and see if it helps. Donna On Jul 31, 2014, at 3:52 PM, Tang, Yan yan.t...@ttu.edu wrote: Dear all, I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Now I want to map functional volumes to surfaces. In volume selection page, I choose my file 'ff001_010.nii'; In spec file and surface selection page, I choose the file 'study1.L.orig.164k_fs_LR'. I get a file 'map_data_0_31_Jul_2014_15_10_13.metric'. But I find I couldn't open this file. Which step is wrong? How can you do it? ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
