Re: [caret-users] negative values displayed positive
Hi Dona, thank you very much for looking into this. The Volume I sent contained values that were thresholded for significance. This is why some values were zero. The blob probably results from the cluster-permutation approach that I applied in order to compute the significance. I should also say that the data comes from MEG source reconstruction and that I interpolated the data onto the SPM template brain (T1.nii). Based on your response I assume that the problem does not come from Caret but from the data that contains positive values. The problem must thus occur while I am exporting the data to a volume file. Thanks for the quick help! I know where to search now. Fred -- FR - Original Message - From: "Donna Dierker" To: "SureFit Caret, and SuMS software users" Sent: Monday, June 22, 2015 4:36:09 PM Subject: Re: [caret-users] negative values displayed positive Hi FR, This is rather an odd file. I did 3dhistog on it and got this output: http://brainmap.wustl.edu/pub/donna/SPAIN/BCBL/your_file.3dhistog.txt login pub password download Mostly zeroes, but 14184 voxels set to 32766 (and no voxels set to any values in between 0 and 32766). And when I map this to the PALS atlas, I get nothing on most vertices, but solid yellow over a perisylvian blob. And when I click in the yellow, sure enough the ID window confirms the vertex is set to 32766 intensity. Working as expected, but data a bit off the beaten path. Donna On Jun 21, 2015, at 4:55 PM, Frédéric Roux wrote: > Hi Dona, > > thanks for getting back on this. > I am using NIFTI, so nothing rare from that side. > > Just uploaded the file via the link you sent me. > > Thanks for looking into this. > > -- > FR > > - Original Message - > From: "Donna Dierker" > To: "SureFit Caret, and SuMS software users" > Sent: Sunday, June 21, 2015 6:37:50 PM > Subject: Re: [caret-users] negative values displayed positive > > I'm not sure what would do this. What format is your volume? NIFTI? Older > .hdr/.img pairs sometimes got x-flipped upon opening under some > circumstances, but nothing I know of (except explicit *(-1) using volume > math) does this. > > You can use something AFNI 3dinfo or 3dhistog to double-check your volume's > values, or you can upload your volume here and I can do so tomorrow: > > http://brainvis.wustl.edu/cgi-bin/upload.cgi > > You can also have a look at the palette format, and just make sure it's not > the palette that is making your values appear to be flipped: > > http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile > > Caret has some built-in palettes (see D/C: Metric Settings menu). > > > On Jun 21, 2015, at 3:55 AM, Frédéric Roux wrote: > >> Dear all, >> >> I'm trying to map a functional volume to the PLAS-B12 >> surface but the sign of the values gets flipped so that >> negative values appear as positive ones. >> >> Does anyone know what could be wrong? >> >> Many thanks. >> >> Fred >> >> -- >> FR >> >> - Original Message - >> From: "Matt Glasser" >> To: "SureFit Caret, and SuMS software users" >> Sent: Saturday, June 20, 2015 11:37:53 PM >> Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of >> nodes! >> >> Yes please use the HCP pipelines for myelin mapping. >> >> Peace, >> >> Matt. >> >> On 6/19/15, 4:17 AM, "Donna Dierker" wrote: >> >>> Hi Xara, >>> >>> Because you are in the enviable position of having high res T1 AND T2, >>> you may be able to use the Human Connectome Project pipelines on your >>> data, rather than this (older generation) caret-based myelin mapping >>> script: >>> >>> http://www.humanconnectome.org/documentation/HCP-pipelines/ >>> >>> This also has the advantage of writing output files in workbench formats, >>> rather than older caret formats. I have a hunch that Matt Glasser will >>> point you in that direction (he is probably at OHBM conference or on his >>> way home). >>> >>> I confess I am not as familiar with this script as Matt is, but from what >>> I read at the link you sent, it appears the maps are on the native mesh, >>> rather than 164k. And I don't see myelin represented in the list of >>> freesurfer_to_fs_LR output files here: >>> >>> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs >>> _LR/Output >>> >>> (These were independent effor
Re: [caret-users] negative values displayed positive
Hi Dona, thanks for getting back on this. I am using NIFTI, so nothing rare from that side. Just uploaded the file via the link you sent me. Thanks for looking into this. -- FR - Original Message - From: "Donna Dierker" To: "SureFit Caret, and SuMS software users" Sent: Sunday, June 21, 2015 6:37:50 PM Subject: Re: [caret-users] negative values displayed positive I'm not sure what would do this. What format is your volume? NIFTI? Older .hdr/.img pairs sometimes got x-flipped upon opening under some circumstances, but nothing I know of (except explicit *(-1) using volume math) does this. You can use something AFNI 3dinfo or 3dhistog to double-check your volume's values, or you can upload your volume here and I can do so tomorrow: http://brainvis.wustl.edu/cgi-bin/upload.cgi You can also have a look at the palette format, and just make sure it's not the palette that is making your values appear to be flipped: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile Caret has some built-in palettes (see D/C: Metric Settings menu). On Jun 21, 2015, at 3:55 AM, Frédéric Roux wrote: > Dear all, > > I'm trying to map a functional volume to the PLAS-B12 > surface but the sign of the values gets flipped so that > negative values appear as positive ones. > > Does anyone know what could be wrong? > > Many thanks. > > Fred > > -- > FR > > - Original Message - > From: "Matt Glasser" > To: "SureFit Caret, and SuMS software users" > Sent: Saturday, June 20, 2015 11:37:53 PM > Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of > nodes! > > Yes please use the HCP pipelines for myelin mapping. > > Peace, > > Matt. > > On 6/19/15, 4:17 AM, "Donna Dierker" wrote: > >> Hi Xara, >> >> Because you are in the enviable position of having high res T1 AND T2, >> you may be able to use the Human Connectome Project pipelines on your >> data, rather than this (older generation) caret-based myelin mapping >> script: >> >> http://www.humanconnectome.org/documentation/HCP-pipelines/ >> >> This also has the advantage of writing output files in workbench formats, >> rather than older caret formats. I have a hunch that Matt Glasser will >> point you in that direction (he is probably at OHBM conference or on his >> way home). >> >> I confess I am not as familiar with this script as Matt is, but from what >> I read at the link you sent, it appears the maps are on the native mesh, >> rather than 164k. And I don't see myelin represented in the list of >> freesurfer_to_fs_LR output files here: >> >> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs >> _LR/Output >> >> (These were independent efforts going on at roughly the same time.) >> >> You may already have considered the HCP pipeline route, but if not, it is >> worth a look -- you've got the T2's at the right res, which is often a >> hitch. I suspect myelin maps on 164k won't be your only benefit. >> >> Donna >> >> >> On Jun 19, 2015, at 8:58 AM, "Shams, Z." wrote: >> >>> Dear users, >>> >>> >>> >>> I just started working with Caret for creating myelin maps. I used HCP >>> imaging protocols for data acquisition, both T1 and T2 data have the >>> voxel size of 0.7mm isotropic. >>> >>> I followed the instructions in >>> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping. >>> >>> Actually I managed to display the four outputs, but some parts of the >>> maps are missing when overlaying on a surface(they¹re not complete maps: >>> either raw or corrected myelin maps). >>> >>> Another problem is that I used the freesurfer to fs LR script to >>> convert all my freesurfer files to the 164k_fs_LR mesh, >>> >>> but when I try to show the myelin maps on e.g. very-inflated 164k fs >>> LR, It fails with the error of containing a different number of nodes >>> thanŠ . >>> >>> >>> >>> I¹d appreciate any help and instructions. >>> >>> >>> >>> Thanks, >>> >>> >>> Xara >>> >>> ___ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _
[caret-users] negative values displayed positive
Dear all, I'm trying to map a functional volume to the PLAS-B12 surface but the sign of the values gets flipped so that negative values appear as positive ones. Does anyone know what could be wrong? Many thanks. Fred -- FR - Original Message - From: "Matt Glasser" To: "SureFit Caret, and SuMS software users" Sent: Saturday, June 20, 2015 11:37:53 PM Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of nodes! Yes please use the HCP pipelines for myelin mapping. Peace, Matt. On 6/19/15, 4:17 AM, "Donna Dierker" wrote: >Hi Xara, > >Because you are in the enviable position of having high res T1 AND T2, >you may be able to use the Human Connectome Project pipelines on your >data, rather than this (older generation) caret-based myelin mapping >script: > >http://www.humanconnectome.org/documentation/HCP-pipelines/ > >This also has the advantage of writing output files in workbench formats, >rather than older caret formats. I have a hunch that Matt Glasser will >point you in that direction (he is probably at OHBM conference or on his >way home). > >I confess I am not as familiar with this script as Matt is, but from what >I read at the link you sent, it appears the maps are on the native mesh, >rather than 164k. And I don't see myelin represented in the list of >freesurfer_to_fs_LR output files here: > >http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs >_LR/Output > >(These were independent efforts going on at roughly the same time.) > >You may already have considered the HCP pipeline route, but if not, it is >worth a look -- you've got the T2's at the right res, which is often a >hitch. I suspect myelin maps on 164k won't be your only benefit. > >Donna > > >On Jun 19, 2015, at 8:58 AM, "Shams, Z." wrote: > >> Dear users, >> >> >> >> I just started working with Caret for creating myelin maps. I used HCP >>imaging protocols for data acquisition, both T1 and T2 data have the >>voxel size of 0.7mm isotropic. >> >> I followed the instructions in >>http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping. >> >> Actually I managed to display the four outputs, but some parts of the >>maps are missing when overlaying on a surface(they¹re not complete maps: >>either raw or corrected myelin maps). >> >> Another problem is that I used the freesurfer to fs LR script to >>convert all my freesurfer files to the 164k_fs_LR mesh, >> >> but when I try to show the myelin maps on e.g. very-inflated 164k fs >>LR, It fails with the error of containing a different number of nodes >>thanŠ . >> >> >> >> I¹d appreciate any help and instructions. >> >> >> >> Thanks, >> >> >> Xara >> >> ___ >> 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
[caret-users] problem with mapping volume to surface
Dear all, a while ago I managed to map my functional data with caret onto the PALS-B12 template. Unfortunately, I cannot reproduce this anymore so I am hoping that somebody may be able to guide me to figure out what goes wrong. The steps that I take are: 1) Attributes -> Map volume(s) to surface. Here I select a .nii file which contains a functional volume and the PALS-B12 spec-file from a tutorial data set that I downloaded. 2) I run the voxel-enclosing algorithm and after the mapping is completed I exit caret. 3) I load the PALS-B12 spec-file from the tutorial data set. Then I go to Display-Control and look under Volume Overlay/Underlay. In the past I was able to select metric under primary overlay and could then chose the .nii file containing the functional data, but this menu point does not appear anymore. Any help or suggestions on how to enable the metric option in the Overlay would be greatly appreciated. Best, Fred -- --- ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] blacking out subcortical regions
thanks Donna! Frédéric Roux - Original Message - From: "Donna Dierker" To: "SureFit Caret, and SuMS software users" Sent: Monday, November 10, 2014 4:52:53 PM Subject: Re: [caret-users] blacking out subcortical regions There is a paint file that comes with many of the PALS-B12 datasets (e.g., Sept 2006 tutorial) that has a medial wall column. Use that as the primary overlay with your metric or other overlay as the secondary overlay. This grays out the medial wall. On Nov 9, 2014, at 10:43 AM, Frédéric Roux wrote: > Hi there, > > I've finally managed to get to visualize my MEG source-reconstruction data > using caret !!! > So far I am very satisfied with the way everything looks. > > The only thing that's missing is a way to black out the sub-cortical areas? > I've seen > people do this regularly in their publications and I would like to do the > same as from > what I understand the PALS-B12 surface is only meant for cortical > representations? > > I could basically try to null all the values which lie below a certain > coordinate of > the Z-axis in my data, but I was wondering if there is a simple and easier > way to do > it in in Caret. > > Any help or suggestions would be highly appreciated. > > Thanks. > > Fred > --- > > > ___ > 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] blacking out subcortical regions
Hi there, I've finally managed to get to visualize my MEG source-reconstruction data using caret !!! So far I am very satisfied with the way everything looks. The only thing that's missing is a way to black out the sub-cortical areas? I've seen people do this regularly in their publications and I would like to do the same as from what I understand the PALS-B12 surface is only meant for cortical representations? I could basically try to null all the values which lie below a certain coordinate of the Z-axis in my data, but I was wondering if there is a simple and easier way to do it in in Caret. Any help or suggestions would be highly appreciated. Thanks. Fred --- ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
