Hi Jarek, After a nice exchange with Tim and Matt, I think we've sorted out the issue with dscalar files. If you update to version alpha92 it should work with your data (with the -transposedata option).
This means that the CIFTI support that was only for dtseries now has been extended to (at least) dscalar. It might work with other types, but these hasn't been tested yet. Hope this helps. All the best, Anderson On 22 April 2016 at 18:33, Anderson M. Winkler <[email protected]> wrote: > Hi Jarek, > > Thanks for sending the file. It's a dscalar, which sadly isn't currently > supported. You'd have to save the data from the pipeline as dtseries. In > fact, from what I can see in the file, although it has extension dscalar, > internally it can be interpreted as a 6D vector field. Saving as a dtseries > will make it an actual scalar field that evolves along 6 timepoints (which > in this case are the 6 subjects). I expect it to work then. > > About the other error below, related to TFCE, it's a different issue, > simpler to solve: to run spatial statistics, such as cluster extent, mass, > or TFCE on surfaces, it's necessary to supply the surface geometry. This is > done with the option -s. > > Hope this helps. > > All the best, > > Anderson > > > > On 21 April 2016 at 04:46, Jarek Rokicki <[email protected]> wrote: > >> Thank you for the suggestions. >> It was not the FathersID issue. >> I've tried -transposedata too and it led to a new error: >> >> Running PALM alpha83 using Octave with the following options: >> -i output_32k_myelin.dscalar.nii >> -d ../GLM/6people.mat >> -t ../GLM/6people.con >> -n 5000 >> -T >> -o ../randomise/out >> -save1-p >> -transposedata >> Reading input 1/1: output_32k_myelin.dscalar.nii >> Reading design matrix and contrasts. >> Elapsed time parsing inputs: ~ 0.565688 seconds. >> Number of possible permutations is 20. >> Generating 20 shufflings (permutations only). >> Building null distribution. >> 1.25% [Design 1/1, Contrast 1/4, Shuffling 1/20, Modality 1/1] >> Saving file: ../randomise/out_dat_tstat_c1 >> >> While running: >> wb_command -cifti-convert -from-gifti-ext >> ../randomise/out_dat_tstat_c1.gii ../randomise/out_dat_tstat_c1.dtseries.nii >> >> >> >> >> >> >> >> *ERROR: dimensions of input gifti array (1 rows, 59412 columns) do not >> match dimensions of the Cifti XML (59412 rows, 6 columns)error: palm_tfce: >> A(I): index out of bounds; value 1 out of bound 0error: called from >> palm_tfce at line 77 column 5 palm_core at line 1764 column 45 palm >> at line 81 column 1* >> >> >> >> >> >> 宜しくお願い致します。 >> >> Sincerely, >> Jarek Rokicki, Ph.D. >> >> Integrative Brain Imaging Center (IBIC) >> National Center of Neurology and Psychiatry (NCNP) >> >> *4-1-1 Ogawahigashi-chyo, Kodaira, Tokyo 187-8551 Japan* >> >> TEL: +81-80-6628-5709 >> >> 国立精神・神経医療研究センター >> 脳病態統合イメージングセンター(IBIC) >> 臨床脳画像研究部 画像情報解析研究室 >> *〒187-8551 東京都小平市小川東町4-1-1* >> >> >> >> >> >> On Thu, Apr 21, 2016 at 9:42 AM, Glasser, Matthew <[email protected]> >> wrote: >> >>> Perhaps Anderson can comment more specifically on this error. As I >>> recall >>> some I/O issues with CIFTI in PALM were resolved a while back >>> >>> Matt. >>> >>> On 4/20/16, 9:39 AM, "[email protected] on behalf of >>> Donna Dierker" <[email protected] on behalf of >>> [email protected]> wrote: >>> >>> >Hi Jarek, >>> > >>> >Using palm's -transposedata is worth trying, but I had to use wb_command >>> >-cifti-separate to peel off left and right hems (or subcortical nifti) >>> >before input to PALM. Maybe that is not needed anymore. >>> > >>> >Donna >>> > >>> > >>> >On Apr 20, 2016, at 4:37 AM, Jarek Rokicki <[email protected]> >>> >wrote: >>> > >>> >> Dear hcp-Experts, >>> >> >>> >> I tried to find if there are significant differences in the >>> myelination >>> >>in two groups of subjects using PALM. Therefore after processing files >>> >>I've merged them using wb_command -cifti-merge >>> >> >>> >> File looks like this: >>> >> wb_command -file-information output_32k_myelin.dscalar.nii >>> >> Name: output_32k_myelin.dscalar.nii >>> >> Type: Connectivity - Dense Scalar >>> >> Structure: CortexLeft CortexRight >>> >> Data Size: 1.43 Megabytes >>> >> Maps to Surface: true >>> >> Maps to Volume: false >>> >> Maps with LabelTable: false >>> >> Maps with Palette: true >>> >> All Map Palettes Equal: true >>> >> Map Interval Units: NIFTI_UNITS_UNKNOWN >>> >> Number of Maps: 6 >>> >> Number of Rows: 59412 >>> >> Number of Columns: 6 >>> >> Volume Dim[0]: 0 >>> >> Volume Dim[1]: 0 >>> >> Volume Dim[2]: 0 >>> >> Palette Type: Map (Unique for each map) >>> >> CIFTI Dim[0]: 6 >>> >> CIFTI Dim[1]: 59412 >>> >> ALONG_ROW map type: SCALARS >>> >> ALONG_COLUMN map type: BRAIN_MODELS >>> >> Has Volume Data: false >>> >> CortexLeft: 29696 out of 32492 vertices >>> >> CortexRight: 29716 out of 32492 vertices >>> >> >>> >> But when i run it with palm i get following error: >>> >> >>> >> Reading input 1/1: output_32k_myelin.dscalar.nii >>> >> Reading design matrix and contrasts. >>> >> error: The number of rows in the design matrix does >>> >> not match the number of observations in the data. >>> >> - Rows in the matrix: 6 >>> >> - Observations in the data: 59412 >>> >> >>> >> So my question is there a way to make palm see that subjects are in >>> >>CIFTI Dim[0] rather than 1. Alternatively is there any other way to >>> >>assess differences? >>> >> >>> >> wb_command. Version: 1.1.1 >>> >> palm. Version: alpha83 >>> >> >>> >> >>> >> >>> >> Thank you for your answers in advance. >>> >> >>> >> 宜しくお願い致します。 >>> >> >>> >> Sincerely, >>> >> Jarek Rokicki, Ph.D. >>> >> >>> >> Integrative Brain Imaging Center (IBIC) >>> >> National Center of Neurology and Psychiatry (NCNP) >>> >> 4-1-1 Ogawahigashi-chyo, Kodaira, >>> >> Tokyo 187-8551 Japan >>> >> >>> >> TEL: +81-80-6628-5709 >>> >> >>> >> 国立精神・神経医療研究センター >>> >> 脳病態統合イメージングセンター(IBIC) >>> >> 臨床脳画像研究部 画像情報解析研究室 >>> >> 〒187-8551 東京都小平市小川東町4-1-1 >>> >> >>> >> >>> >> >>> >> >>> >> _______________________________________________ >>> >> HCP-Users mailing list >>> >> [email protected] >>> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >>> > >>> > >>> >_______________________________________________ >>> >HCP-Users mailing list >>> >[email protected] >>> >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. 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