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: [email protected] [[email protected]] on behalf of Donna Dierker [[email protected]] 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" <[email protected]> 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: [email protected] > [[email protected]] on behalf of Donna Dierker > [[email protected]] > 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" <[email protected]> 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: [email protected] >> [[email protected]] on behalf of Donna Dierker >> [[email protected]] >> 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" <[email protected]> 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: [email protected] >>> [[email protected]] on behalf of Timothy Coalson >>> [[email protected]] >>> 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 <[email protected]> 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: [email protected] >>> [[email protected]] on behalf of Timothy Coalson >>> [[email protected]] >>> 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 <[email protected]> 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: [email protected] >>> [[email protected]] on behalf of Donna Dierker >>> [[email protected]] >>> 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" <[email protected]> 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: [email protected] >>>> [[email protected]] on behalf of Donna Dierker >>>> [[email protected]] >>>> 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" <[email protected]> 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: [email protected] >>>>> [[email protected]] on behalf of Donna Dierker >>>>> [[email protected]] >>>>> 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" <[email protected]> wrote: >>>>> >>>>>> I am sure that the file exist and the size of file is 446KB. Is It >>>>>> correct? >>>>>> ________________________________________ >>>>>> From: [email protected] >>>>>> [[email protected]] on behalf of Donna Dierker >>>>>> [[email protected]] >>>>>> 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" <[email protected]> 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 >>>>>>> [email protected] >>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> caret-users mailing list >>>>>> [email protected] >>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>> >>>>>> _______________________________________________ >>>>>> caret-users mailing list >>>>>> [email protected] >>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> >>>>> >>>>> _______________________________________________ >>>>> caret-users mailing list >>>>> [email protected] >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> <QQ截图20140801162715.png>_______________________________________________ >>>>> caret-users mailing list >>>>> [email protected] >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> [email protected] >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> [email protected] >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
