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 <glass...@wustl.edu>
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, "hcp-users-boun...@humanconnectome.org on behalf of
> Donna Dierker" <hcp-users-boun...@humanconnectome.org on behalf of
> do...@brainvis.wustl.edu> 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 <jarek.roki...@gmail.com>
> >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
> >> HCP-Users@humanconnectome.org
> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >>
> >
> >
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