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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

 

 

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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.


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