Re: [HCP-Users] A minor question regarding HCP 7T movie data
Thanks Keith! I am currently working with the Movie Task fMRI 2mm/32k FIX-Denoised (Compact) dataset, and I noticed the issues below: 1) Two subjects (126931 and 74) do not have MSMAll-registered time-series data. 2) Five subjects (181636, 473952, 536647, 552241, and 973770) have two runs (MOVIE1 and MOVIE2). 3) One subject (585256) has three runs (MOVIE1, MOVIE3, and MOVIE4). Best, Reza On Mon, Jun 3, 2019 at 8:33 PM Keith Jamison wrote: > Hi Reza, > > Your interpretation of the timing is correct. The validation segment in > each movie scan was shifted by 40-200ms for the "v2" version. This was done > in order to make that final 83 second clip begin precisely at the start of > the next TR for all 4 movie sessions. > > Given HRF variability, ignoring this change will probably not adversely > impact most analyses. > > -Keith > > > On Fri, May 31, 2019 at 9:05 PM Reza Rajimehr wrote: > >> Hi, >> >> The HCP S1200 Reference Manual says that there are two versions of 4 >> movie files. Some subjects have been scanned with one version, and the >> remaining subjects have been scanned with another version. Version 2 >> includes these changes: >> >> 7T_MOVIE1_CC1_v2 remains unchanged. >> >> 7T_ MOVIE2_HO1_v2 removed 1 frame of rest before the validation clip. >> >> 7T_MOVIE3_CC2_v2 removed 5 frames of rest before the validation clip. >> >> 7T_MOVIE4_HO2_v2 added 4 frames of rest before the validation clip. >> >> Here *frame* is a frame of the movie, right? >> >> Assuming that the movies are ~25 frames per second, the deviations are >> between 0 and ~200 ms in each movie file. Considering the TR of one second >> and the slow hemodynamic BOLD responses, these deviations are negligible, >> and we can possibly ignore them when concatenating time-series data across >> all subjects. Would you agree? >> >> Thanks, >> Reza >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] A minor question regarding HCP 7T movie data
Hi, The HCP S1200 Reference Manual says that there are two versions of 4 movie files. Some subjects have been scanned with one version, and the remaining subjects have been scanned with another version. Version 2 includes these changes: 7T_MOVIE1_CC1_v2 remains unchanged. 7T_ MOVIE2_HO1_v2 removed 1 frame of rest before the validation clip. 7T_MOVIE3_CC2_v2 removed 5 frames of rest before the validation clip. 7T_MOVIE4_HO2_v2 added 4 frames of rest before the validation clip. Here *frame* is a frame of the movie, right? Assuming that the movies are ~25 frames per second, the deviations are between 0 and ~200 ms in each movie file. Considering the TR of one second and the slow hemodynamic BOLD responses, these deviations are negligible, and we can possibly ignore them when concatenating time-series data across all subjects. Would you agree? Thanks, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Group-averaging of task fMRI data
Thanks Michael for your detailed and helpful answers. Best, Reza On Thu, May 30, 2019 at 6:10 PM Harms, Michael wrote: > > > Hi Reza, > > > > 1) We’ve already generated Cohen’s d-style effect size maps for all > contrasts, using all subjects, as part of the “Group Average Dataset” > available at https://db.humanconnectome.org/data/projects/HCP_1200. If > you need it computed for a specific subset of subjects, then yes, you can > use the approach that you outlined. Note that the ensuing “effect size” > does not account for the family structure in the data (i.e., to the extent > that the estimate of the std across subjects is biased by the family > structure, then the estimate of the effect size is biased as well). > > > > 2) A .dtseries.nii file is still a “spatial map”. We just didn’t bother > to formally convert those particular outputs to a .dscalar.nii (e.g., via > -cifti-change-mapping). A dscalar version of all the copes (merged into a > single file) for a given task and subject are available in the root level > of the .feat directory containing the Level2 task analysis results for that > task and subject. In newer pipeline versions, we create separate merged > files for both the “zstat” and “cope” files of the individual contrasts. > However, at the time of the processing of the HCP-YA data, only a single > merged dscalar was created, and that was for the copes (and it does not > unfortunately have “cope” as part of its filename). > > > > 3) We recommend using PALM for group statistical analysis. You can find a > tutorial in the “tfMRI and PALM” practical available as part of the HCP > Course: > https://store.humanconnectome.org/courses/2018/exploring-the-human-connectome.php. > And no, you generally do **not** want to use the individual subject > “zstat1” maps as inputs to a statistical computation, which would be > “computing statistics of a statistic” (rather than the statistic of an > effect size). > > > > 4) The outputs produced are simply the same as those produced by FSL’s > FLAMEO, albeit in CIFTI rather than NIFTI format. So see FSL’s FLAMEO > documentation. > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > --- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave > <https://www.google.com/maps/search/660+South+Euclid+Ave?entry=gmail=g>. > Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: * on behalf of Reza > Rajimehr > *Date: *Wednesday, May 29, 2019 at 7:36 PM > *To: *hcp-users > *Subject: *[HCP-Users] Group-averaging of task fMRI data > > > > Hi, > > > > For a group of subjects (e.g. 100 subjects in HCP S1200), we want to > generate a group-average Cohen’s d map for a particular contrast in the > working memory task. For this, we take level2 “cope1.dtseries.nii” file in > cope20.feat folder of all those subjects, merge them using -cifti-merge, > then -cifti-reduce mean, -cifti-reduce stdev, and -cifti-math mean/stdev. > > > > Questions: > > > > 1) Is the above procedure correct? Or you recommend other commands? > > > > 2) Why the file name is cope1.dtseries.nii when it is not a time-series > data? Why not naming it cope1.dscalar.nii, as it is a spatial map? > > > > 3) If we want to generate a group-average zstat map, what should we do? I > guess it should involve using the “zstat1.dtseries.nii” files, but don’t > know how. > > > > 4) Is there any documentation somewhere describing all the files within > the cope folder? E.g. these files: > > > > mean_random_effects_var1.dtseries.nii > > pe1.dtseries.nii > > res4d.dtseries.nii > > tdof_t1.dtseries.nii > > tstat1.dtseries.nii > > varcope1.dtseries.nii > > weights1.dtseries.nii > > > > Thanks, > > Reza > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Group-averaging of task fMRI data
Hi, For a group of subjects (e.g. 100 subjects in HCP S1200), we want to generate a group-average Cohen’s d map for a particular contrast in the working memory task. For this, we take level2 “cope1.dtseries.nii” file in cope20.feat folder of all those subjects, merge them using -cifti-merge, then -cifti-reduce mean, -cifti-reduce stdev, and -cifti-math mean/stdev. Questions: 1) Is the above procedure correct? Or you recommend other commands? 2) Why the file name is cope1.dtseries.nii when it is not a time-series data? Why not naming it cope1.dscalar.nii, as it is a spatial map? 3) If we want to generate a group-average zstat map, what should we do? I guess it should involve using the “zstat1.dtseries.nii” files, but don’t know how. 4) Is there any documentation somewhere describing all the files within the cope folder? E.g. these files: mean_random_effects_var1.dtseries.nii pe1.dtseries.nii res4d.dtseries.nii tdof_t1.dtseries.nii tstat1.dtseries.nii varcope1.dtseries.nii weights1.dtseries.nii Thanks, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Local Gyrification Index
Hi, Does HCP database have Freesurfer-derived LGI for all 1200 subjects? Best, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] wb_command -metric-tfce
Thanks Michael. We will use PALM. But what is the application of wb_command -metric-tfce then? On Sun, Apr 21, 2019 at 2:38 AM Harms, Michael wrote: > > > Hi, > > We suggest you use PALM, since you need to use permutation to determine > the distribution of the TFCE metric. > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > --- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave > <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: * on behalf of Reza > Rajimehr > *Date: *Saturday, April 20, 2019 at 7:18 PM > *To: *hcp-users > *Subject: *[HCP-Users] wb_command -metric-tfce > > > > Hi, > > > > We have curvature data from two groups of subjects in a common anatomical > space (MSMAll). We performed a univariate comparison between the two groups > using t-test. We now have a map, which shows vertex-wise curvature > difference between the two groups (the curvature difference is shown only > for vertices which have a significant difference). The next step is to do > cluster-wise correction using TFCE method. It looks like this command can > do what we want: > > > > https://www.humanconnectome.org/software/workbench-command/-metric-tfce > > > > However, we couldn’t find any example command, and its usage is a bit > unclear for us. For example, how should we specify the two groups? > > > > Any help would be appreciated. > > > > Note: Our analysis here is somewhat similar to the analysis in Figure 5B > in Van Essen et al. 2012 paper: > > > > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432236/pdf/bhr291.pdf > > > > Best, > > Reza > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] wb_command -metric-tfce
Hi, We have curvature data from two groups of subjects in a common anatomical space (MSMAll). We performed a univariate comparison between the two groups using t-test. We now have a map, which shows vertex-wise curvature difference between the two groups (the curvature difference is shown only for vertices which have a significant difference). The next step is to do cluster-wise correction using TFCE method. It looks like this command can do what we want: https://www.humanconnectome.org/software/workbench-command/-metric-tfce However, we couldn’t find any example command, and its usage is a bit unclear for us. For example, how should we specify the two groups? Any help would be appreciated. Note: Our analysis here is somewhat similar to the analysis in Figure 5B in Van Essen et al. 2012 paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432236/pdf/bhr291.pdf Best, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] S1200 MSMSulc files
Would this be accurate to obtain group-average MSMSulc curvature file? Vertex-wise arithmetic mean of xx.curvature.32k_fs_LR.dscalar.nii maps in Matlab On Thu, Mar 21, 2019 at 11:36 PM Glasser, Matthew wrote: > Are there not versions already? One simply merges and averages the files. > > Matt. > > From: Reza Rajimehr > Date: Thursday, March 21, 2019 at 6:34 PM > To: Matt Glasser > Cc: hcp-users > Subject: Re: [HCP-Users] S1200 MSMSulc files > > Thanks Matt! > > In the fsaverage_LR32k folder of one subject, we have two versions of > files. E.g.: > > 100206.curvature.32k_fs_LR.dscalar.nii > 100206.curvature_MSMAll.32k_fs_LR.dscalar.nii > > So the first file is MSMSulc? > > How about the group-average MSMSulc files? Is there a procedure/command to > generate those files from individual MSMSulc files? > > Thanks, > Reza > > > On Thu, Mar 21, 2019 at 11:09 PM Glasser, Matthew > wrote: > >> MSMSulc might not have a specific registration tag, did you check for >> such files? >> >> Matt. >> >> From: on behalf of Reza Rajimehr >> >> Date: Thursday, March 21, 2019 at 4:42 PM >> To: hcp-users >> Subject: [HCP-Users] S1200 MSMSulc files >> >> For a control analysis, we would like to have access to the following >> files: >> >> 32k MSMSulc files for curvature, thickness, and myelin (individual >> subjects and group average) >> >> The current S1200 release only has the MSMAll files. How can we have >> access to the MSMSulc files? >> >> Thanks, >> Reza >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] S1200 MSMSulc files
Thanks Matt! In the fsaverage_LR32k folder of one subject, we have two versions of files. E.g.: 100206.curvature.32k_fs_LR.dscalar.nii 100206.curvature_MSMAll.32k_fs_LR.dscalar.nii So the first file is MSMSulc? How about the group-average MSMSulc files? Is there a procedure/command to generate those files from individual MSMSulc files? Thanks, Reza On Thu, Mar 21, 2019 at 11:09 PM Glasser, Matthew wrote: > MSMSulc might not have a specific registration tag, did you check for such > files? > > Matt. > > From: on behalf of Reza Rajimehr < > rajim...@gmail.com> > Date: Thursday, March 21, 2019 at 4:42 PM > To: hcp-users > Subject: [HCP-Users] S1200 MSMSulc files > > For a control analysis, we would like to have access to the following > files: > > 32k MSMSulc files for curvature, thickness, and myelin (individual > subjects and group average) > > The current S1200 release only has the MSMAll files. How can we have > access to the MSMSulc files? > > Thanks, > Reza > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] S1200 MSMSulc files
For a control analysis, we would like to have access to the following files: 32k MSMSulc files for curvature, thickness, and myelin (individual subjects and group average) The current S1200 release only has the MSMAll files. How can we have access to the MSMSulc files? Thanks, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Confusion about Destrieux labels
Thanks Tim! One remaining issue: no vertices has the label code 42 (Lat_Fis-post). I guess this is inherited from Freesurfer? On Fri, Feb 22, 2019 at 11:59 PM Timothy Coalson wrote: > In that gifti file, the label table indicates that ??? is label 0, as is > recommended (it means things that haven't been labeled, such as the medial > wall). The matlab gifti library must be shifting these values, possibly > because they are taken as indices into another matlab array (matlab doesn't > accept 0 as an array index). > > However, the labels appear to go up to 75 (L_S_temporal_transverse) in the > gifti file. I would expect that the freesurfer outputs already contain 75 > labels. > > Tim > > > On Fri, Feb 22, 2019 at 12:08 PM Reza Rajimehr wrote: > >> Hi, >> >> We have loaded Destrieux parcellation of one of the HCP subjects >> (100206.L.aparc.a2009s.32k_fs_LR.label.gii) in Matlab. It includes 76 >> labels. Label 1 is ??? and label 2 is G_and_S_frontomargin. However, >> Destrieux paper describes 74 labels and their label 1 >> is G_and_S_frontomargin. Could you please explain this discrepancy? >> >> Thanks, >> Reza >> > ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
Thanks Tim for clarifications! It was helpful to know that surface registration is by vertices, not by cifti indices. Best, Reza On Tue, Nov 20, 2018 at 11:48 PM Timothy Coalson wrote: > Surface registration (whether left/right or otherwise) is by vertices, not > by cifti indices, and is therefore a separate issue from the medial wall > masks (I would bet that the actual mismatches between the two medial walls > is more than 20 vertices - the Venn diagram of the sets of included > vertices is likely nonzero in all categories). You should think of cifti > indices as a "packed" representation of the data, and if you need to do > anything spatial with cifti data, you generally need to "unpack" it first, > do the operation, and then repack it. This is how wb_command operates > internally for spatial cifti operations. If you don't need to do a spatial > operation, then the simplest option is generally to put all the data into > cifti files using the same brainordinates, and then you can use them > indexwise. > > If we made our standard dscalar/dtseries use the whole surface, but dconn > exclude the medial wall, then we couldn't do indexwise math between those > cifti files (and doing correlation gradient on it would give us a dscalar > with the medial wall excluded again). Having more of our cifti files use > the same indices as each other still seems like the better option. > > If you prefer for your use, you can make a template cifti file that does > not exclude the medial wall, and use -cifti-create-dense-from-template to > expand any standard cifti file to full-surface. Doing something similar > for the subcortical voxels, however, would result in much larger files (and > -cifti-create-dense-from-template respects subcortical structure boundaries > when the input is cifti, so you would need a small script involving > -cifti-separate if you wanted a full in-order FOV representation of the > voxels). > > Tim > > > On Tue, Nov 20, 2018 at 6:30 AM Reza Rajimehr wrote: > >> Sorry ... I should have said 20 vertices difference. >> >> >> On Tue, Nov 20, 2018 at 3:52 PM Reza Rajimehr wrote: >> >>> ... 29716 indices in RH and 29696 indices in LH of cifti file. >>> >>> >>> On Tue, Nov 20, 2018 at 3:43 PM Reza Rajimehr >>> wrote: >>> >>>> But there are 10 more vertices in right hemisphere than left hemisphere >>>> ... >>>> >>>> >>>> On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew >>>> wrote: >>>> >>>>> Left and right are registered. >>>>> >>>>> Matt. >>>>> >>>>> From: Reza Rajimehr >>>>> Date: Tuesday, November 20, 2018 at 2:04 AM >>>>> To: Matt Glasser >>>>> Cc: Timothy Coalson , hcp-users < >>>>> hcp-users@humanconnectome.org> >>>>> >>>>> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and >>>>> gifti files >>>>> >>>>> Thanks Matt! Yes, having symmetric medial wall and having registered >>>>> left and right hemispheres would be helpful and important. >>>>> >>>>> >>>>> On Tue, Nov 20, 2018 at 5:54 AM Glasser, Matthew >>>>> wrote: >>>>> >>>>>> We don’t want the non-greymatter medial wall in CIFTI; however, the >>>>>> medial wall may undergo revision in the future and making it symmetric >>>>>> might be more convenient, though this would might require rerunning the >>>>>> left/right registration, which remains in all HCP Pipelines derived >>>>>> standard mesh CIFTI and GIFTI files from the original landmark-based >>>>>> registration published in Van Essen et al 2012 Cerebral Cortex. >>>>>> >>>>>> Matt. >>>>>> >>>>>> From: on behalf of Timothy >>>>>> Coalson >>>>>> Date: Monday, November 19, 2018 at 2:57 PM >>>>>> To: Reza Rajimehr >>>>>> Cc: hcp-users >>>>>> >>>>>> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and >>>>>> gifti files >>>>>> >>>>>> External interoperation with GIFTI and NIFTI data is the purpose of >>>>>> the -cifti-separate command, it is much simpler than using >>>>>> -cifti-export-dense-mapping. >>>>>> >>>>>> A central goal of CIFTI was the exclusi
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
Sorry ... I should have said 20 vertices difference. On Tue, Nov 20, 2018 at 3:52 PM Reza Rajimehr wrote: > ... 29716 indices in RH and 29696 indices in LH of cifti file. > > > On Tue, Nov 20, 2018 at 3:43 PM Reza Rajimehr wrote: > >> But there are 10 more vertices in right hemisphere than left hemisphere >> ... >> >> >> On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew >> wrote: >> >>> Left and right are registered. >>> >>> Matt. >>> >>> From: Reza Rajimehr >>> Date: Tuesday, November 20, 2018 at 2:04 AM >>> To: Matt Glasser >>> Cc: Timothy Coalson , hcp-users < >>> hcp-users@humanconnectome.org> >>> >>> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti >>> files >>> >>> Thanks Matt! Yes, having symmetric medial wall and having registered >>> left and right hemispheres would be helpful and important. >>> >>> >>> On Tue, Nov 20, 2018 at 5:54 AM Glasser, Matthew >>> wrote: >>> >>>> We don’t want the non-greymatter medial wall in CIFTI; however, the >>>> medial wall may undergo revision in the future and making it symmetric >>>> might be more convenient, though this would might require rerunning the >>>> left/right registration, which remains in all HCP Pipelines derived >>>> standard mesh CIFTI and GIFTI files from the original landmark-based >>>> registration published in Van Essen et al 2012 Cerebral Cortex. >>>> >>>> Matt. >>>> >>>> From: on behalf of Timothy >>>> Coalson >>>> Date: Monday, November 19, 2018 at 2:57 PM >>>> To: Reza Rajimehr >>>> Cc: hcp-users >>>> >>>> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and >>>> gifti files >>>> >>>> External interoperation with GIFTI and NIFTI data is the purpose of the >>>> -cifti-separate command, it is much simpler than using >>>> -cifti-export-dense-mapping. >>>> >>>> A central goal of CIFTI was the exclusion of non-interesting locations >>>> from the file (this becomes more important with dense connectivity files, >>>> and is a far larger effect for voxel structures (avoiding filling out the >>>> entire FOV)). We do not expect people to use the >>>> -cifti-export-dense-mapping command just for file format interoperability >>>> (but only for special circumstances, basically if spatial relationship >>>> information must be obtained in software without full cifti support, >>>> without leaving the cifti format). >>>> >>>> Tim >>>> >>>> >>>> On Mon, Nov 19, 2018 at 2:43 PM Reza Rajimehr >>>> wrote: >>>> >>>>> Thanks! The file that we looked into was an MSMSulc file. I guess that >>>>> the difference of 10 indices/vertices between left and right hemis exists >>>>> for an MSMAll file as well, but I haven’t checked it yet. >>>>> >>>>> One comment: The medial wall has been left out in CIFTI files >>>>> because the medial wall is not cortical grey matter. This is legitimate, >>>>> however, it introduces confusions when communicating between CIFTI and >>>>> GIFTI files. It would be nice if HCP developers, in future, consider a >>>>> version of CIFTI with medial wall included. >>>>> >>>>> >>>>> On Mon, Nov 19, 2018 at 11:53 PM Timothy Coalson >>>>> wrote: >>>>> >>>>>> The left and right hemisphere are intended to be in register, though >>>>>> I don't recall what effort was put into this in MSMAll (maybe only the >>>>>> dedrifting to sulc). I believe the left and right hemisphere medial wall >>>>>> masks were generated separately without trying to synchronize across >>>>>> hemispheres, and used early on, and for ongoing compatibility we stayed >>>>>> with the same masks. >>>>>> >>>>>> Tim >>>>>> >>>>>> >>>>>> On Mon, Nov 19, 2018 at 11:51 AM Reza Rajimehr >>>>>> wrote: >>>>>> >>>>>>> We successfully used -cifti-export-dense-mapping to get the mapping >>>>>>> from cifti indices to surface vertices (all indices are zero-based). >>>>>>> &
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
... 29716 indices in RH and 29696 indices in LH of cifti file. On Tue, Nov 20, 2018 at 3:43 PM Reza Rajimehr wrote: > But there are 10 more vertices in right hemisphere than left hemisphere ... > > > On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew > wrote: > >> Left and right are registered. >> >> Matt. >> >> From: Reza Rajimehr >> Date: Tuesday, November 20, 2018 at 2:04 AM >> To: Matt Glasser >> Cc: Timothy Coalson , hcp-users < >> hcp-users@humanconnectome.org> >> >> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti >> files >> >> Thanks Matt! Yes, having symmetric medial wall and having registered left >> and right hemispheres would be helpful and important. >> >> >> On Tue, Nov 20, 2018 at 5:54 AM Glasser, Matthew >> wrote: >> >>> We don’t want the non-greymatter medial wall in CIFTI; however, the >>> medial wall may undergo revision in the future and making it symmetric >>> might be more convenient, though this would might require rerunning the >>> left/right registration, which remains in all HCP Pipelines derived >>> standard mesh CIFTI and GIFTI files from the original landmark-based >>> registration published in Van Essen et al 2012 Cerebral Cortex. >>> >>> Matt. >>> >>> From: on behalf of Timothy >>> Coalson >>> Date: Monday, November 19, 2018 at 2:57 PM >>> To: Reza Rajimehr >>> Cc: hcp-users >>> >>> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti >>> files >>> >>> External interoperation with GIFTI and NIFTI data is the purpose of the >>> -cifti-separate command, it is much simpler than using >>> -cifti-export-dense-mapping. >>> >>> A central goal of CIFTI was the exclusion of non-interesting locations >>> from the file (this becomes more important with dense connectivity files, >>> and is a far larger effect for voxel structures (avoiding filling out the >>> entire FOV)). We do not expect people to use the >>> -cifti-export-dense-mapping command just for file format interoperability >>> (but only for special circumstances, basically if spatial relationship >>> information must be obtained in software without full cifti support, >>> without leaving the cifti format). >>> >>> Tim >>> >>> >>> On Mon, Nov 19, 2018 at 2:43 PM Reza Rajimehr >>> wrote: >>> >>>> Thanks! The file that we looked into was an MSMSulc file. I guess that >>>> the difference of 10 indices/vertices between left and right hemis exists >>>> for an MSMAll file as well, but I haven’t checked it yet. >>>> >>>> One comment: The medial wall has been left out in CIFTI files >>>> because the medial wall is not cortical grey matter. This is legitimate, >>>> however, it introduces confusions when communicating between CIFTI and >>>> GIFTI files. It would be nice if HCP developers, in future, consider a >>>> version of CIFTI with medial wall included. >>>> >>>> >>>> On Mon, Nov 19, 2018 at 11:53 PM Timothy Coalson >>>> wrote: >>>> >>>>> The left and right hemisphere are intended to be in register, though I >>>>> don't recall what effort was put into this in MSMAll (maybe only the >>>>> dedrifting to sulc). I believe the left and right hemisphere medial wall >>>>> masks were generated separately without trying to synchronize across >>>>> hemispheres, and used early on, and for ongoing compatibility we stayed >>>>> with the same masks. >>>>> >>>>> Tim >>>>> >>>>> >>>>> On Mon, Nov 19, 2018 at 11:51 AM Reza Rajimehr >>>>> wrote: >>>>> >>>>>> We successfully used -cifti-export-dense-mapping to get the mapping >>>>>> from cifti indices to surface vertices (all indices are zero-based). >>>>>> >>>>>> wb_command -cifti-export-dense-mapping >>>>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_LEFT >>>>>> leftcortex.txt >>>>>> >>>>>> wb_command -cifti-export-dense-mapping >>>>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_RIGHT >>>>>> rightcortex.txt >>>>>> >>>>>> In the text files, there are 2969
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
But there are 10 more vertices in right hemisphere than left hemisphere ... On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew wrote: > Left and right are registered. > > Matt. > > From: Reza Rajimehr > Date: Tuesday, November 20, 2018 at 2:04 AM > To: Matt Glasser > Cc: Timothy Coalson , hcp-users < > hcp-users@humanconnectome.org> > > Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti > files > > Thanks Matt! Yes, having symmetric medial wall and having registered left > and right hemispheres would be helpful and important. > > > On Tue, Nov 20, 2018 at 5:54 AM Glasser, Matthew > wrote: > >> We don’t want the non-greymatter medial wall in CIFTI; however, the >> medial wall may undergo revision in the future and making it symmetric >> might be more convenient, though this would might require rerunning the >> left/right registration, which remains in all HCP Pipelines derived >> standard mesh CIFTI and GIFTI files from the original landmark-based >> registration published in Van Essen et al 2012 Cerebral Cortex. >> >> Matt. >> >> From: on behalf of Timothy >> Coalson >> Date: Monday, November 19, 2018 at 2:57 PM >> To: Reza Rajimehr >> Cc: hcp-users >> >> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti >> files >> >> External interoperation with GIFTI and NIFTI data is the purpose of the >> -cifti-separate command, it is much simpler than using >> -cifti-export-dense-mapping. >> >> A central goal of CIFTI was the exclusion of non-interesting locations >> from the file (this becomes more important with dense connectivity files, >> and is a far larger effect for voxel structures (avoiding filling out the >> entire FOV)). We do not expect people to use the >> -cifti-export-dense-mapping command just for file format interoperability >> (but only for special circumstances, basically if spatial relationship >> information must be obtained in software without full cifti support, >> without leaving the cifti format). >> >> Tim >> >> >> On Mon, Nov 19, 2018 at 2:43 PM Reza Rajimehr wrote: >> >>> Thanks! The file that we looked into was an MSMSulc file. I guess that >>> the difference of 10 indices/vertices between left and right hemis exists >>> for an MSMAll file as well, but I haven’t checked it yet. >>> >>> One comment: The medial wall has been left out in CIFTI files >>> because the medial wall is not cortical grey matter. This is legitimate, >>> however, it introduces confusions when communicating between CIFTI and >>> GIFTI files. It would be nice if HCP developers, in future, consider a >>> version of CIFTI with medial wall included. >>> >>> >>> On Mon, Nov 19, 2018 at 11:53 PM Timothy Coalson wrote: >>> >>>> The left and right hemisphere are intended to be in register, though I >>>> don't recall what effort was put into this in MSMAll (maybe only the >>>> dedrifting to sulc). I believe the left and right hemisphere medial wall >>>> masks were generated separately without trying to synchronize across >>>> hemispheres, and used early on, and for ongoing compatibility we stayed >>>> with the same masks. >>>> >>>> Tim >>>> >>>> >>>> On Mon, Nov 19, 2018 at 11:51 AM Reza Rajimehr >>>> wrote: >>>> >>>>> We successfully used -cifti-export-dense-mapping to get the mapping >>>>> from cifti indices to surface vertices (all indices are zero-based). >>>>> >>>>> wb_command -cifti-export-dense-mapping >>>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_LEFT >>>>> leftcortex.txt >>>>> >>>>> wb_command -cifti-export-dense-mapping >>>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_RIGHT >>>>> rightcortex.txt >>>>> >>>>> In the text files, there are 29696 left hemisphere indices and 29716 >>>>> right hemisphere indices. I always thought that left and right hemispheres >>>>> are in register in the standard space/mesh, and I was expecting to see the >>>>> same number of indices/vertices (exactly 29706) for both hemispheres. But >>>>> apparently this is not the case! Any reason for this? >>>>> >>>>> >>>>> On Fri, Nov 16, 2018 at 11:58 PM Timothy Coalson >>>>> wrote: >>>>>
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
Medial wall could have been excluded from a connectivity CIFTI file, not in the file itself, but during an operation on the file using an option like -exclude-medial-wall in the command. But I totally understand the rationale for removing it in the first place. On Tue, Nov 20, 2018 at 12:28 AM Timothy Coalson wrote: > External interoperation with GIFTI and NIFTI data is the purpose of the > -cifti-separate command, it is much simpler than using > -cifti-export-dense-mapping. > > A central goal of CIFTI was the exclusion of non-interesting locations > from the file (this becomes more important with dense connectivity files, > and is a far larger effect for voxel structures (avoiding filling out the > entire FOV)). We do not expect people to use the > -cifti-export-dense-mapping command just for file format interoperability > (but only for special circumstances, basically if spatial relationship > information must be obtained in software without full cifti support, > without leaving the cifti format). > > Tim > > > On Mon, Nov 19, 2018 at 2:43 PM Reza Rajimehr wrote: > >> Thanks! The file that we looked into was an MSMSulc file. I guess that >> the difference of 10 indices/vertices between left and right hemis exists >> for an MSMAll file as well, but I haven’t checked it yet. >> >> One comment: The medial wall has been left out in CIFTI files because the >> medial wall is not cortical grey matter. This is legitimate, however, it >> introduces confusions when communicating between CIFTI and GIFTI files. It >> would be nice if HCP developers, in future, consider a version of CIFTI >> with medial wall included. >> >> >> On Mon, Nov 19, 2018 at 11:53 PM Timothy Coalson wrote: >> >>> The left and right hemisphere are intended to be in register, though I >>> don't recall what effort was put into this in MSMAll (maybe only the >>> dedrifting to sulc). I believe the left and right hemisphere medial wall >>> masks were generated separately without trying to synchronize across >>> hemispheres, and used early on, and for ongoing compatibility we stayed >>> with the same masks. >>> >>> Tim >>> >>> >>> On Mon, Nov 19, 2018 at 11:51 AM Reza Rajimehr >>> wrote: >>> >>>> We successfully used -cifti-export-dense-mapping to get the mapping >>>> from cifti indices to surface vertices (all indices are zero-based). >>>> >>>> wb_command -cifti-export-dense-mapping >>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_LEFT >>>> leftcortex.txt >>>> >>>> wb_command -cifti-export-dense-mapping >>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_RIGHT >>>> rightcortex.txt >>>> >>>> In the text files, there are 29696 left hemisphere indices and 29716 >>>> right hemisphere indices. I always thought that left and right hemispheres >>>> are in register in the standard space/mesh, and I was expecting to see the >>>> same number of indices/vertices (exactly 29706) for both hemispheres. But >>>> apparently this is not the case! Any reason for this? >>>> >>>> >>>> On Fri, Nov 16, 2018 at 11:58 PM Timothy Coalson >>>> wrote: >>>> >>>>> The easiest to use (especially if your goal is to match other cifti >>>>> files) is generally -cifti-create-dense-from-template. It will even turn >>>>> a >>>>> 59k surface-only cifti into a standard 91282 cifti (or vice versa, if you >>>>> are so inclined). >>>>> >>>>> Yes, -cifti-export-dense-mapping will give you the cifti index to >>>>> gifti vertex mapping as a text file, if you want to do things the hard >>>>> way. >>>>> >>>>> Tim >>>>> >>>>> >>>>> On Fri, Nov 16, 2018 at 2:06 PM Harms, Michael >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> See the various -cifti-create-* commands. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Michael Harms, Ph.D. >>>>>> >>>>>> --- >>>>>> >>>>>> Associate Professor of Psychiatry >>>>>> >>>>>> Washington University Schoo
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
Thanks Matt! Yes, having symmetric medial wall and having registered left and right hemispheres would be helpful and important. On Tue, Nov 20, 2018 at 5:54 AM Glasser, Matthew wrote: > We don’t want the non-greymatter medial wall in CIFTI; however, the medial > wall may undergo revision in the future and making it symmetric might be > more convenient, though this would might require rerunning the left/right > registration, which remains in all HCP Pipelines derived standard mesh > CIFTI and GIFTI files from the original landmark-based registration > published in Van Essen et al 2012 Cerebral Cortex. > > Matt. > > From: on behalf of Timothy > Coalson > Date: Monday, November 19, 2018 at 2:57 PM > To: Reza Rajimehr > Cc: hcp-users > > Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti > files > > External interoperation with GIFTI and NIFTI data is the purpose of the > -cifti-separate command, it is much simpler than using > -cifti-export-dense-mapping. > > A central goal of CIFTI was the exclusion of non-interesting locations > from the file (this becomes more important with dense connectivity files, > and is a far larger effect for voxel structures (avoiding filling out the > entire FOV)). We do not expect people to use the > -cifti-export-dense-mapping command just for file format interoperability > (but only for special circumstances, basically if spatial relationship > information must be obtained in software without full cifti support, > without leaving the cifti format). > > Tim > > > On Mon, Nov 19, 2018 at 2:43 PM Reza Rajimehr wrote: > >> Thanks! The file that we looked into was an MSMSulc file. I guess that >> the difference of 10 indices/vertices between left and right hemis exists >> for an MSMAll file as well, but I haven’t checked it yet. >> >> One comment: The medial wall has been left out in CIFTI files because the >> medial wall is not cortical grey matter. This is legitimate, however, it >> introduces confusions when communicating between CIFTI and GIFTI files. It >> would be nice if HCP developers, in future, consider a version of CIFTI >> with medial wall included. >> >> >> On Mon, Nov 19, 2018 at 11:53 PM Timothy Coalson wrote: >> >>> The left and right hemisphere are intended to be in register, though I >>> don't recall what effort was put into this in MSMAll (maybe only the >>> dedrifting to sulc). I believe the left and right hemisphere medial wall >>> masks were generated separately without trying to synchronize across >>> hemispheres, and used early on, and for ongoing compatibility we stayed >>> with the same masks. >>> >>> Tim >>> >>> >>> On Mon, Nov 19, 2018 at 11:51 AM Reza Rajimehr >>> wrote: >>> >>>> We successfully used -cifti-export-dense-mapping to get the mapping >>>> from cifti indices to surface vertices (all indices are zero-based). >>>> >>>> wb_command -cifti-export-dense-mapping >>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_LEFT >>>> leftcortex.txt >>>> >>>> wb_command -cifti-export-dense-mapping >>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_RIGHT >>>> rightcortex.txt >>>> >>>> In the text files, there are 29696 left hemisphere indices and 29716 >>>> right hemisphere indices. I always thought that left and right hemispheres >>>> are in register in the standard space/mesh, and I was expecting to see the >>>> same number of indices/vertices (exactly 29706) for both hemispheres. But >>>> apparently this is not the case! Any reason for this? >>>> >>>> >>>> On Fri, Nov 16, 2018 at 11:58 PM Timothy Coalson >>>> wrote: >>>> >>>>> The easiest to use (especially if your goal is to match other cifti >>>>> files) is generally -cifti-create-dense-from-template. It will even turn >>>>> a >>>>> 59k surface-only cifti into a standard 91282 cifti (or vice versa, if you >>>>> are so inclined). >>>>> >>>>> Yes, -cifti-export-dense-mapping will give you the cifti index to >>>>> gifti vertex mapping as a text file, if you want to do things the hard >>>>> way. >>>>> >>>>> Tim >>>>> >>>>> >>>>> On Fri, Nov 16, 2018 at 2:06 PM Harms, Michael >>>>> wrote: >>>>> >>>>>> >>>>>> >
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
Thanks! The file that we looked into was an MSMSulc file. I guess that the difference of 10 indices/vertices between left and right hemis exists for an MSMAll file as well, but I haven’t checked it yet. One comment: The medial wall has been left out in CIFTI files because the medial wall is not cortical grey matter. This is legitimate, however, it introduces confusions when communicating between CIFTI and GIFTI files. It would be nice if HCP developers, in future, consider a version of CIFTI with medial wall included. On Mon, Nov 19, 2018 at 11:53 PM Timothy Coalson wrote: > The left and right hemisphere are intended to be in register, though I > don't recall what effort was put into this in MSMAll (maybe only the > dedrifting to sulc). I believe the left and right hemisphere medial wall > masks were generated separately without trying to synchronize across > hemispheres, and used early on, and for ongoing compatibility we stayed > with the same masks. > > Tim > > > On Mon, Nov 19, 2018 at 11:51 AM Reza Rajimehr wrote: > >> We successfully used -cifti-export-dense-mapping to get the mapping from >> cifti indices to surface vertices (all indices are zero-based). >> >> wb_command -cifti-export-dense-mapping >> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_LEFT >> leftcortex.txt >> >> wb_command -cifti-export-dense-mapping >> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_RIGHT >> rightcortex.txt >> >> In the text files, there are 29696 left hemisphere indices and 29716 >> right hemisphere indices. I always thought that left and right hemispheres >> are in register in the standard space/mesh, and I was expecting to see the >> same number of indices/vertices (exactly 29706) for both hemispheres. But >> apparently this is not the case! Any reason for this? >> >> >> On Fri, Nov 16, 2018 at 11:58 PM Timothy Coalson wrote: >> >>> The easiest to use (especially if your goal is to match other cifti >>> files) is generally -cifti-create-dense-from-template. It will even turn a >>> 59k surface-only cifti into a standard 91282 cifti (or vice versa, if you >>> are so inclined). >>> >>> Yes, -cifti-export-dense-mapping will give you the cifti index to gifti >>> vertex mapping as a text file, if you want to do things the hard way. >>> >>> Tim >>> >>> >>> On Fri, Nov 16, 2018 at 2:06 PM Harms, Michael wrote: >>> >>>> >>>> >>>> See the various -cifti-create-* commands. >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> >>>> Michael Harms, Ph.D. >>>> >>>> --- >>>> >>>> Associate Professor of Psychiatry >>>> >>>> Washington University School of Medicine >>>> >>>> Department of Psychiatry, Box 8134 >>>> >>>> 660 South Euclid Ave >>>> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. >>>> Tel: 314-747-6173 >>>> >>>> St. Louis, MO 63110 Email: mha...@wustl.edu >>>> >>>> >>>> >>>> *From: *Reza Rajimehr >>>> *Date: *Friday, November 16, 2018 at 1:50 PM >>>> *To: *"Harms, Michael" >>>> *Cc: *"Glasser, Matthew" , " >>>> hcp-users@humanconnectome.org" >>>> *Subject: *Re: [HCP-Users] Number of cortical vertices in cifti and >>>> gifti files >>>> >>>> >>>> >>>> Is there a command to convert LH (or RH) gifti file to hcp cifti file? >>>> >>>> >>>> >>>> >>>> >>>> On Fri, Nov 16, 2018 at 10:55 PM Harms, Michael >>>> wrote: >>>> >>>> >>>> >>>> No, it is more complicated than that. >>>> >>>> >>>> >>>> I believe what you need is -cifti-export-dense-mapping >>>> >>>> >>>> >>>> Cheers, >>>> >>>> -MH >>>> >>>> >>>> >>>> -- >>>> >>>> Michael Harms, Ph.D. >>>> >>>> --- >>>> >>>> Associate Professor of Psychiatry >>>> >>>> Washington University School of Medicine >>>> >>>> Department of
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
We successfully used -cifti-export-dense-mapping to get the mapping from cifti indices to surface vertices (all indices are zero-based). wb_command -cifti-export-dense-mapping 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_LEFT leftcortex.txt wb_command -cifti-export-dense-mapping 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_RIGHT rightcortex.txt In the text files, there are 29696 left hemisphere indices and 29716 right hemisphere indices. I always thought that left and right hemispheres are in register in the standard space/mesh, and I was expecting to see the same number of indices/vertices (exactly 29706) for both hemispheres. But apparently this is not the case! Any reason for this? On Fri, Nov 16, 2018 at 11:58 PM Timothy Coalson wrote: > The easiest to use (especially if your goal is to match other cifti files) > is generally -cifti-create-dense-from-template. It will even turn a 59k > surface-only cifti into a standard 91282 cifti (or vice versa, if you are > so inclined). > > Yes, -cifti-export-dense-mapping will give you the cifti index to gifti > vertex mapping as a text file, if you want to do things the hard way. > > Tim > > > On Fri, Nov 16, 2018 at 2:06 PM Harms, Michael wrote: > >> >> >> See the various -cifti-create-* commands. >> >> >> >> >> >> -- >> >> Michael Harms, Ph.D. >> >> --- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave >> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. >> Tel: 314-747-6173 >> >> St. Louis, MO 63110 Email: mha...@wustl.edu >> >> >> >> *From: *Reza Rajimehr >> *Date: *Friday, November 16, 2018 at 1:50 PM >> *To: *"Harms, Michael" >> *Cc: *"Glasser, Matthew" , " >> hcp-users@humanconnectome.org" >> *Subject: *Re: [HCP-Users] Number of cortical vertices in cifti and >> gifti files >> >> >> >> Is there a command to convert LH (or RH) gifti file to hcp cifti file? >> >> >> >> >> >> On Fri, Nov 16, 2018 at 10:55 PM Harms, Michael wrote: >> >> >> >> No, it is more complicated than that. >> >> >> >> I believe what you need is -cifti-export-dense-mapping >> >> >> >> Cheers, >> >> -MH >> >> >> >> -- >> >> Michael Harms, Ph.D. >> >> --- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave >> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. >> Tel: 314-747-6173 >> >> St. Louis, MO 63110 Email: mha...@wustl.edu >> >> >> >> *From: * on behalf of Reza >> Rajimehr >> *Date: *Friday, November 16, 2018 at 1:17 PM >> *To: *"Glasser, Matthew" >> *Cc: *"hcp-users@humanconnectome.org" >> *Subject: *Re: [HCP-Users] Number of cortical vertices in cifti and >> gifti files >> >> >> >> Thanks! Can I simply say that: >> >> >> >> For left hemisphere: >> >> vertex number in cifti = vertex number (up to 29706) in LH gifti >> >> >> >> For right hemisphere: >> >> vertex number in cifti = vertex number (up to 29706) in RH gifti + 29706 >> >> >> >> Or the mapping is more complicated than this? >> >> >> >> >> >> On Fri, Nov 16, 2018 at 9:56 PM Glasser, Matthew >> wrote: >> >> That is correct, the medial wall is kept out. Usually when I want to do >> that I split the CIFTI file into hemispheric GIFTI files, but perhaps there >> is a good way to load in a specific mapping based on something we can >> output from wb_command. >> >> >> >> Matt. >> >> >> >> *From: * on behalf of Reza >> Rajimehr >> *Date: *Friday, November 16, 2018 at 10:17 AM >> *To: *"hcp-users@humanconnectome.org" >> *Subject: *[HCP-Users] Number of cortical vertices in cifti and gifti >> files >> >> >> >> Hi, >> >> >> >> A cifti file has 91282 vertices/voxels, a combined LR cifti file has >> 59412 vertices, and an individual hemis
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
Is there a command to convert LH (or RH) gifti file to hcp cifti file? On Fri, Nov 16, 2018 at 10:55 PM Harms, Michael wrote: > > > No, it is more complicated than that. > > > > I believe what you need is -cifti-export-dense-mapping > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > --- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave > <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: * on behalf of Reza > Rajimehr > *Date: *Friday, November 16, 2018 at 1:17 PM > *To: *"Glasser, Matthew" > *Cc: *"hcp-users@humanconnectome.org" > *Subject: *Re: [HCP-Users] Number of cortical vertices in cifti and gifti > files > > > > Thanks! Can I simply say that: > > > > For left hemisphere: > > vertex number in cifti = vertex number (up to 29706) in LH gifti > > > > For right hemisphere: > > vertex number in cifti = vertex number (up to 29706) in RH gifti + 29706 > > > > Or the mapping is more complicated than this? > > > > > > On Fri, Nov 16, 2018 at 9:56 PM Glasser, Matthew > wrote: > > That is correct, the medial wall is kept out. Usually when I want to do > that I split the CIFTI file into hemispheric GIFTI files, but perhaps there > is a good way to load in a specific mapping based on something we can > output from wb_command. > > > > Matt. > > > > *From: * on behalf of Reza > Rajimehr > *Date: *Friday, November 16, 2018 at 10:17 AM > *To: *"hcp-users@humanconnectome.org" > *Subject: *[HCP-Users] Number of cortical vertices in cifti and gifti > files > > > > Hi, > > > > A cifti file has 91282 vertices/voxels, a combined LR cifti file has 59412 > vertices, and an individual hemisphere gifti file has 32492 vertices. So > the number of cortical vertices in cifti files is less than the number of > cortical vertices in gifti files (left hemi vertices + right hemi vertices > = 64984). Looks like this is related to not having medial wall vertices in > the cifti files, right? > > > > We have loaded these files in Matlab. Now we want to know which vertex in > right (or left) hemisphere gifti file corresponds to which vertex in the > cifti file. How can we achieve this? > > > > Best, > > Reza > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Number of cortical vertices in cifti and gifti files
Thanks! Can I simply say that: For left hemisphere: vertex number in cifti = vertex number (up to 29706) in LH gifti For right hemisphere: vertex number in cifti = vertex number (up to 29706) in RH gifti + 29706 Or the mapping is more complicated than this? On Fri, Nov 16, 2018 at 9:56 PM Glasser, Matthew wrote: > That is correct, the medial wall is kept out. Usually when I want to do > that I split the CIFTI file into hemispheric GIFTI files, but perhaps there > is a good way to load in a specific mapping based on something we can > output from wb_command. > > Matt. > > From: on behalf of Reza Rajimehr < > rajim...@gmail.com> > Date: Friday, November 16, 2018 at 10:17 AM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] Number of cortical vertices in cifti and gifti files > > Hi, > > A cifti file has 91282 vertices/voxels, a combined LR cifti file has 59412 > vertices, and an individual hemisphere gifti file has 32492 vertices. So > the number of cortical vertices in cifti files is less than the number of > cortical vertices in gifti files (left hemi vertices + right hemi vertices > = 64984). Looks like this is related to not having medial wall vertices in > the cifti files, right? > > We have loaded these files in Matlab. Now we want to know which vertex in > right (or left) hemisphere gifti file corresponds to which vertex in the > cifti file. How can we achieve this? > > Best, > Reza > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Number of cortical vertices in cifti and gifti files
Hi, A cifti file has 91282 vertices/voxels, a combined LR cifti file has 59412 vertices, and an individual hemisphere gifti file has 32492 vertices. So the number of cortical vertices in cifti files is less than the number of cortical vertices in gifti files (left hemi vertices + right hemi vertices = 64984). Looks like this is related to not having medial wall vertices in the cifti files, right? We have loaded these files in Matlab. Now we want to know which vertex in right (or left) hemisphere gifti file corresponds to which vertex in the cifti file. How can we achieve this? Best, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Questions about sulc, curvature, and thickness files
Thanks Matt! And: What the midthickness dscalar.nii files are? What does BC in MyelinMap_BC stand for? Reza On Mon, Nov 5, 2018 at 11:51 PM Glasser, Matthew wrote: > >1. They are the same >2. Mean curvature same as FreeSurfer >3. Thickness is same as FreeSurfer, CorrThickness has the curvature >regressed out. > > Peace, > > Matt. > > From: on behalf of Reza Rajimehr < > rajim...@gmail.com> > Date: Monday, November 5, 2018 at 2:48 PM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] Questions about sulc, curvature, and thickness files > > Hi, > > 1) The Sulc maps in HCP seem to be similar to the sulcal depth maps in > Freesurfer; both show major sulci. Is there any detailed information on how > these maps are obtained? > > 2) What is the type of curvature in the Curvature files of HCP? Mean > curvature or Gaussian curvature? > > 3) There are two Thickness files in HCP: Thickness and corrThickness. It > looks like that the corrThickness maps are slightly smoothed compared to > the Thickness maps. But what is the exact difference between them? > > Thanks, > Reza > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Questions about sulc, curvature, and thickness files
Hi, 1) The Sulc maps in HCP seem to be similar to the sulcal depth maps in Freesurfer; both show major sulci. Is there any detailed information on how these maps are obtained? 2) What is the type of curvature in the Curvature files of HCP? Mean curvature or Gaussian curvature? 3) There are two Thickness files in HCP: Thickness and corrThickness. It looks like that the corrThickness maps are slightly smoothed compared to the Thickness maps. But what is the exact difference between them? Thanks, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Question about dense functional connectome
Thanks Tim! I will consider your suggestions. Reza On Thu, Oct 25, 2018 at 11:51 PM Timothy Coalson wrote: > If you have their cifti indices then you can just make a new cifti dscalar > with only those grayordinates set to 1 (double check this in wb_view, > matlab uses 1-based indexing, and I don't remember which convention we use > for cifti indices). If you don't have the cifti indices, you can use > -cifti-export-dense-mapping output to make text files that translate > between them and vertex/voxel. I suggest loading some standard dscalar > file to use as the template for saving the data out (use > ciftiopen/ciftisavereset, the ft_read_cifti and related functions do some > unexpected things with the cifti matrix). > > Single points out of a dconn are likely to be noisy, you may also want to > consider -cifti-parcellate (if possible, -cifti-parcellate on the dtseries, > and then do the correlations on the parcellated timeseries, rather than > averaging correlations together). > > Tim > > > On Thu, Oct 25, 2018 at 10:20 AM, Reza Rajimehr > wrote: > >> Thanks Matt! Looks like -cifti-restrict-dense-map can do what I want if I >> run it twice (first run it along the COLUMN direction to get an output, >> then run it again on the output along the ROW direction). For this to work, >> I need to specify an roi file. In a .mat file, I have a list of >> grayordinate vertices/voxels (some in left hemi, some in right hemi, some >> in subcortex). How can I put all of them in one cifti roi file in Matlab? >> >> Reza >> >> >> On Thu, Oct 25, 2018 at 2:40 PM Glasser, Matthew >> wrote: >> >>> Yes that would be a better solution. I think the wb_command >>> -cifti-restrict-dense-map might work. >>> >>> Matt. >>> >>> From: Reza Rajimehr >>> Date: Thursday, October 25, 2018 at 3:16 AM >>> To: Matt Glasser >>> Cc: Timothy Coalson , "hcp-users@humanconnectome.org" < >>> hcp-users@humanconnectome.org> >>> >>> Subject: Re: [HCP-Users] Question about dense functional connectome >>> >>> We tried to open *.dconn.nii in Matlab using ft_read_cifti on an Ubuntu >>> system with 48 GB RAM. It used 48 GB RAM and 18 GB (out of 60 GB) swap, >>> then Matlab gave out of memory error! Will try to use a system with even >>> higher RAM. >>> >>> Tim: We have a list of 913 grayordinate voxels (we have their voxel >>> numbers/indices). These voxels are somewhat distributed in gray matter. We >>> are basically interested in the functional connectivity matrix just for >>> these 913 voxels (i.e. a 913 * 913 matrix). Is it possible to use >>> wb_command to select part of *.dconn.nii corresponding to the voxels of >>> interest? >>> >>> Best, >>> Reza >>> >>> >>> On Thu, Oct 25, 2018 at 3:49 AM Glasser, Matthew >>> wrote: >>> >>>> Use swap space. >>>> >>>> Matt. >>>> >>>> From: on behalf of Timothy >>>> Coalson >>>> Date: Wednesday, October 24, 2018 at 4:57 PM >>>> To: Reza Rajimehr >>>> Cc: "hcp-users@humanconnectome.org" >>>> Subject: Re: [HCP-Users] Question about dense functional connectome >>>> >>>> The cifti format doesn't support that, because it is designed to allow >>>> use without loading the entire file into memory - there is no obvious file >>>> organization that would allow efficient loading of a full row from a single >>>> triangular file, when seek times are nontrivial (rotating disks). I don't >>>> believe we have these files in any other format. I'm also not sure how >>>> easy it would be to work on such a matrix in matlab. If wb_command is >>>> capable of doing the operations you want, it is usually possible for it to >>>> do them without loading the entire cifti file into memory at once. wb_view >>>> will also display maps from it without loading the entire file into memory. >>>> >>>> DDR4 has 16GB modules available at reasonable prices, which should >>>> allow recent computers with even 4 slots for memory to expand to 64GB. You >>>> should also consider the "high-end desktop" platforms (threadripper, >>>> lga2066, lga2011), which typically offer 8 memory slots, and processors >>>> with more cores. >>>> >>>> Tim >>>> >>>> >>>> On Wed, Oct 24
Re: [HCP-Users] Question about dense functional connectome
Thanks Michael! Your suggestion was quite useful. I successfully loaded the connectivity matrix into Matlab using ciftiopen and did the operation that I wanted (i.e. selecting part of the matrix). Reza On Thu, Oct 25, 2018 at 6:41 PM Harms, Michael wrote: > > > As an aside, if ‘ft_read_cifti’ is expanding all the data to type double > (64 bit), then you are looking at needing > 66 GB to load a 91282x91282 > dconn.nii in matlab. I assume that is what is happening based on your > experience. > > > > If you want to see how far you can get in Matlab, I would at least try > switching to using ‘ciftiopen.m’ to load it into matlab, which uses the > gifti toolbox, which preserves the underlying data type of the .dconn.nii > (type single; i.e., 32 bit) upon load into matlab. > > > > I tested that just now on a system with 64 GB of RAM (and 64 GB of swap), > and after what must have been at least 5 min, it loaded successfully into > matlab (R2015a) with a size in matlab of 32 GB (and a type of ‘single’). > Note however that as that process was ongoing, the memory usage of the > overall system hit 56 GB (not counting cached memory), which decreased to > 33 GB when the load was completed (presumably that is reflective of there > essentially being two copies in memory during the loading process). > > > > Working with a dconn in matlab is inevitably going to be cumbersome and > slow, but by using this approach you might actually be able to get it > loaded and see where you can get from that point. Obviously, you would > have to be extremely conscious of memory issues for whatever operations you > try to perform in matlab. > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > --- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave > <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: * on behalf of Reza > Rajimehr > *Date: *Thursday, October 25, 2018 at 3:17 AM > *To: *"Glasser, Matthew" > > > *Cc: *"hcp-users@humanconnectome.org" > *Subject: *Re: [HCP-Users] Question about dense functional connectome > > > > We tried to open *.dconn.nii in Matlab using ft_read_cifti on an Ubuntu > system with 48 GB RAM. It used 48 GB RAM and 18 GB (out of 60 GB) swap, > then Matlab gave out of memory error! Will try to use a system with even > higher RAM. > > > > Tim: We have a list of 913 grayordinate voxels (we have their voxel > numbers/indices). These voxels are somewhat distributed in gray matter. We > are basically interested in the functional connectivity matrix just for > these 913 voxels (i.e. a 913 * 913 matrix). Is it possible to use > wb_command to select part of *.dconn.nii corresponding to the voxels of > interest? > > > > Best, > > Reza > > > > > > On Thu, Oct 25, 2018 at 3:49 AM Glasser, Matthew > wrote: > > Use swap space. > > > > Matt. > > > > *From: * on behalf of Timothy > Coalson > *Date: *Wednesday, October 24, 2018 at 4:57 PM > *To: *Reza Rajimehr > *Cc: *"hcp-users@humanconnectome.org" > *Subject: *Re: [HCP-Users] Question about dense functional connectome > > > > The cifti format doesn't support that, because it is designed to allow use > without loading the entire file into memory - there is no obvious file > organization that would allow efficient loading of a full row from a single > triangular file, when seek times are nontrivial (rotating disks). I don't > believe we have these files in any other format. I'm also not sure how > easy it would be to work on such a matrix in matlab. If wb_command is > capable of doing the operations you want, it is usually possible for it to > do them without loading the entire cifti file into memory at once. wb_view > will also display maps from it without loading the entire file into memory. > > > > DDR4 has 16GB modules available at reasonable prices, which should allow > recent computers with even 4 slots for memory to expand to 64GB. You > should also consider the "high-end desktop" platforms (threadripper, > lga2066, lga2011), which typically offer 8 memory slots, and processors > with more cores. > > > > Tim > > > > > > On Wed, Oct 24, 2018 at 3:56 PM, Reza Rajimehr wrote: > > Hi, > > > > We are trying to unzip and load dense functional connectome > (HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500
Re: [HCP-Users] Question about dense functional connectome
We tried to open *.dconn.nii in Matlab using ft_read_cifti on an Ubuntu system with 48 GB RAM. It used 48 GB RAM and 18 GB (out of 60 GB) swap, then Matlab gave out of memory error! Will try to use a system with even higher RAM. Tim: We have a list of 913 grayordinate voxels (we have their voxel numbers/indices). These voxels are somewhat distributed in gray matter. We are basically interested in the functional connectivity matrix just for these 913 voxels (i.e. a 913 * 913 matrix). Is it possible to use wb_command to select part of *.dconn.nii corresponding to the voxels of interest? Best, Reza On Thu, Oct 25, 2018 at 3:49 AM Glasser, Matthew wrote: > Use swap space. > > Matt. > > From: on behalf of Timothy > Coalson > Date: Wednesday, October 24, 2018 at 4:57 PM > To: Reza Rajimehr > Cc: "hcp-users@humanconnectome.org" > Subject: Re: [HCP-Users] Question about dense functional connectome > > The cifti format doesn't support that, because it is designed to allow use > without loading the entire file into memory - there is no obvious file > organization that would allow efficient loading of a full row from a single > triangular file, when seek times are nontrivial (rotating disks). I don't > believe we have these files in any other format. I'm also not sure how > easy it would be to work on such a matrix in matlab. If wb_command is > capable of doing the operations you want, it is usually possible for it to > do them without loading the entire cifti file into memory at once. wb_view > will also display maps from it without loading the entire file into memory. > > DDR4 has 16GB modules available at reasonable prices, which should allow > recent computers with even 4 slots for memory to expand to 64GB. You > should also consider the "high-end desktop" platforms (threadripper, > lga2066, lga2011), which typically offer 8 memory slots, and processors > with more cores. > > Tim > > > On Wed, Oct 24, 2018 at 3:56 PM, Reza Rajimehr wrote: > >> Hi, >> >> We are trying to unzip and load dense functional connectome >> (HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.zip or >> HCP_S900_820_rfMRI_MSMSulc_groupPCA_d4500ROW_zcorr.zip from >> >> https://www.humanconnectome.org/study/hcp-young-adult/article/announcing-release-of-s900-ptn-and-other-group-average-data) >> in Matlab on a system that has 32 GB RAM. This is of course impossible due >> to the fact that the files are ~33 GB in size. Due to matrix symmetry, it >> would be sufficient to store only the upper or lower triangular part of a >> functional connectivity matrix, reducing memory occupancy by about 50% >> (Loewe et al., 2016). Does HCP provide such files that could be >> memory-friendly? >> >> Best, >> Reza >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Question about dense functional connectome
Hi, We are trying to unzip and load dense functional connectome (HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.zip or HCP_S900_820_rfMRI_MSMSulc_groupPCA_d4500ROW_zcorr.zip from https://www.humanconnectome.org/study/hcp-young-adult/article/announcing-release-of-s900-ptn-and-other-group-average-data) in Matlab on a system that has 32 GB RAM. This is of course impossible due to the fact that the files are ~33 GB in size. Due to matrix symmetry, it would be sufficient to store only the upper or lower triangular part of a functional connectivity matrix, reducing memory occupancy by about 50% (Loewe et al., 2016). Does HCP provide such files that could be memory-friendly? Best, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
