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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