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Hi Darren, It looks like your design matrix is correct, with 192 lines, but one or both of the gii files are being read as if having 190 maps, instead of 192. Could you run: *wb_command -file-information ./HCP_subjects/Y192_right.func.gii* to see if the right hemisphere has the correct number of maps? If it says 192 as well, then I'll ask to see the files... All the best, Anderson On Fri, 1 Mar 2019 at 14:27, Harms, Michael <[log in to unmask]> wrote: > > > In that case, Anderson will have to take a look. > > > > FYI: The PALM Wiki page probably includes a more complete list of the full > set of available options: > > https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide > > > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: [log in to unmask] > > > > *From: *Darren Campbell <[log in to unmask]> > *Date: *Friday, March 1, 2019 at 1:24 PM > *To: *"Harms, Michael" <[log in to unmask]> > *Cc: *FSL - FMRIB's Software Library <[log in to unmask]>, "Anderson M. > Winkler" <[log in to unmask]>, "[log in to unmask]" < > [log in to unmask]>, "[log in to unmask]" < > [log in to unmask]> > *Subject: *Re: Palm feedback: # rows does not match # obs in data, but it > does :( > > > > Hi Michael et al., > > Thanks for the quick response. I did not see the specific transpose data > command in the palm -help list, so I inserted transposedata immediately > after the -i information inputs. the transposedata did not work (see > feedback below). Thanks again. > > Other suggestions? > > Darren > > > > *Feedback With transposedata inserted (in case it is diagnostically > helpful)* > > Running PALM alpha112 using Octave 4.2.2 with the following options: > > -i ./HCP_subjects/Y_left.func.gii > > -i ./HCP_subjects/Y_right.func.gii > > -transposedata > > -d ./HCP_subjects/Progs/Design.mat > > -t ./HCP_subjects/Progs/DesignGrpContr.con > > -o dense_cortical_Results > > -n 1000 > > -corrcon > > -corrmod > > -logp > > -accel tail > > -nouncorrected > > -T > > -tfce2D > > -s ./HCP_subjects/L_midthickness.surf.gii > > -s ./HCP_subjects/R_midthickness.surf.gii > > Found FSL in /usr/local/fsl > > Found FreeSurfer in /usr/local/freesurfer > > Found HCP Workbench executable in > /home/brain/workbench/bin_linux64/wb_command > > Loading surface 1/2: ./HCP_subjects/L_midthickness.surf.gii > > warning: xml_findstr is not compiled for your platform. > > This will result in a slowdown of the XML parsing. > > Loading surface 2/2: ./HCP_subjects/R_midthickness.surf.gii > > Reading input 1/2: ./HCP_subjects/Y_left.func.gii > > Error using palm_takeargs (/home/brain/PALM-master/palm_takeargs.m:1694) > > Surface file does not match the input data: > > - Surface file 1 has 32492 vertices and 64980 faces > (./HCP_subjects/L_midthickness.surf.gii) > > - Input data file 1 has 190 points (./HCP_subjects/Y_left.func.gii) > > > > Error in palm_core (/home/brain/PALM-master/palm_core.m:33->palm_takeargs) > > Error in palm (/home/brain/PALM-master/palm.m:81->palm_core) > > > > Dr. Darren Campbell > > Associate Professor > > Department of Psychology > > Nipissing University > > Office: H236 > > Phone: 705-474-3450 Ext. 4524 > > Lab: A222F > > > > > > > > On Fri, Mar 1, 2019 at 2:10 PM Harms, Michael <[log in to unmask]> wrote: > > > Try using the -tranposedata flag. If that doesn’t solve the problem, > Anderson will need to comment. > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: [log in to unmask] > > > > *From: *Darren Campbell <[log in to unmask]> > *Date: *Friday, March 1, 2019 at 1:04 PM > *To: *FSL - FMRIB's Software Library <[log in to unmask]> > *Cc: *"Anderson M. Winkler" <[log in to unmask]>, " > [log in to unmask]" <[log in to unmask]>, "[log in to unmask]" > <[log in to unmask]>, "Harms, Michael" <[log in to unmask]>, > Darren Campbell <[log in to unmask]> > *Subject: *Palm feedback: # rows does not match # obs in data, but it > does :( > > > > Hi > > Following the TFCE palm analyses example (Exploring the H C 2018 > Practical 11: Task fMRI) on a subsample of the HCP data, I successfully ran > the subcortical analyses command (# rows = # obs). But, when I ran the > parallel command for the lateralized cortical analyses, I received an error > (# rows does not match # obs). The wb_command -file-information on two > cortical .gii files indicated that there were the correct # of obs (192). I > have pasted the error and other potentially relevant info below. Any > suggestions? Thanks. > > Darren > > P.S. I am email rather than posting due to posting difficulties. > > > > # Step 5 - lateralized cortical analyses > > > > palm -i ./HCP_subjects/Y_left.func.gii -i ./HCP_subjects/Y_right.func.gii > -d ./HCP_subjects/Progs/Design.mat -t > ./HCP_subjects/Progs/DesignGrpContr.con -o dense_cortical_Results -n 1000 > -corrcon -corrmod -logp -accel tail -nouncorrected -T -tfce2D -s > ./HCP_subjects/L_midthickness.surf.gii -s > ./HCP_subjects/R_midthickness.surf.gii > > > > Running PALM alpha112 using Octave 4.2.2 with the following options: > > -i ./HCP_subjects/Y_left.func.gii > > -i ./HCP_subjects/Y_right.func.gii > > -d ./HCP_subjects/Progs/Design.mat > > -t ./HCP_subjects/Progs/DesignGrpContr.con > > -o dense_cortical_Results > > -n 1000 > > -corrcon > > -corrmod > > -logp > > -accel tail > > -nouncorrected > > -T > > -tfce2D > > -s ./HCP_subjects/L_midthickness.surf.gii > > -s ./HCP_subjects/R_midthickness.surf.gii > > Found FSL in /usr/local/fsl > > Found FreeSurfer in /usr/local/freesurfer > > Found HCP Workbench executable in > /home/brain/workbench/bin_linux64/wb_command > > Loading surface 1/2: ./HCP_subjects/L_midthickness.surf.gii > > warning: xml_findstr is not compiled for your platform. > > This will result in a slowdown of the XML parsing. > > Loading surface 2/2: ./HCP_subjects/R_midthickness.surf.gii > > Reading input 1/2: ./HCP_subjects/Y_left.func.gii > > Reading input 2/2: ./HCP_subjects/Y_right.func.gii > > Reading design matrix and contrasts. > > Error using palm_takeargs (/home/brain/PALM-master/palm_takeargs.m:2053) > > The number of rows in the design matrix does > > not match the number of observations in the data. > > - Rows in the matrix: 192 > > - Observations in the data: 190 > > In file ./HCP_subjects/Progs/Design.mat > > > > Error in palm_core (/home/brain/PALM-master/palm_core.m:33->palm_takeargs) > > Error in palm (/home/brain/PALM-master/palm.m:81->palm_core) > > > > *DesignGrpContr.con* > > /NumWaves 3 > > /NumPoints 3 > > /Matrix > > 1 -1 0 > > 1 0 -1 > > 0 1 -1 > > > > *Design.mat* > > /NumWaves 3 > > /NumPoints 192 > > /Matrix > > 1 0 0 > > 1 0 0 > > . . . > > 1 0 0 > > 0 1 0 *(Line 68 - my notation for you not in file)* > > 0 1 0 > > . . . > > 0 1 0 > > 0 0 1 > > 0 0 1 *(Line 132)* > > . . . > > 0 0 1 > > 0 0 1 *(Line 195)* > > > > *One of the Data Files* (Y_left.func.gii) > > wb_command -file-information ./HCP_subjects/Y192_left.func.gii > > Name: ./HCP_subjects/Y192_left.func.gii > > Type: Metric > > Structure: CortexLeft > > Data Size: 24.95 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: 192 > > Number of Vertices: 32492 > > > > Map Minimum Maximum Mean Sample Dev % Positive % Negative > Inf/NaN Map Name > > 1 -245.956 369.890 4.569 54.864 49.649 41.746 > 0 #1 > > . . . > > 191 -277.772 335.542 -15.126 60.584 33.316 58.079 > 0 #191 > > 192 -219.324 351.132 4.193 46.065 46.571 44.823 > 0 #192 > > > > Dr. Darren Campbell > > Associate Professor > > Department of Psychology > > Nipissing University > > Office: H236 > > Phone: 705-474-3450 Ext. 4524 > > Lab: A222F > > > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. 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