Ben Chernoff
Ph.D. Student, Concepts, Actions, and Objects Lab
Rochester Center for Brain Imaging, Room 2B231
University of Rochester

On Oct 8, 2018, at 9:58 AM, Niels Bergsland <[log in to unmask]> wrote:

Hi Ben,
I am unable to recreate the issue on my Mac with going from Excel to TextEdit. However, I was able to "repair" the design.txt that you attached in the second email in this way:

tr "\015" '\n' < design.txt > design_fixed.txt

"\015" is the escape sequence of the Control-M character. The tr command substitutes Control-M with a newline character in this case. At this point, you should be able to run Text2Vest.

Hopefully this takes care of it for you!

Niels

On Mon, Oct 8, 2018 at 3:48 PM Chernoff, Ben <[log in to unmask]> wrote:

Hi Niels,

I had been using excel and then copy pasting into TextEdit. However, before I paste into text edit I change the format to plain text in the same way you said. The original email had the wrong ones, that was a different program I tried when I couldn’t get anything else to work. I sent a second email when I replied to Matthew, but I’m not sure if you saw it. I tried to get rid of the control characters by using this command in terminal, but it didn’t help

awk 'sub("$", "\r")' unixfile.txt > winfile.txt

-Ben

Ben Chernoff
Ph.D. Student, Concepts, Actions, and Objects Lab
Rochester Center for Brain Imaging, Room 2B231
University of Rochester

On Oct 8, 2018, at 4:54 AM, Niels Bergsland <[log in to unmask]> wrote:

Hi Ben,
How are you creating your text file? Your design.txt and the design.mat in your original email have ^M control characters. You should use just a straight plain text editor to create your design. If you are using TextEdit on your mac, you can go to the "Format" menu and select "Make plain text", which should then result in a usable file.

-Niels

On Sat, Oct 6, 2018 at 10:38 PM Chernoff, Ben <[log in to unmask]> wrote:

Sorry, that was one of several versions I tried. See attached for a different version, same error. Only difference is how i try to “convert it” to windows format before Text2Vest. I’m also attaching the .txt file

-Ben

Ben Chernoff
Ph.D. Student, Concepts, Actions, and Objects Lab
Rochester Center for Brain Imaging, Room 2B231
University of Rochester

On Oct 6, 2018, at 4:32 PM, Glasser, Matthew <[log in to unmask]> wrote:

The mat file comes across for me with a blank line in-between every line.

Matt.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of "Chernoff, Ben" <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Saturday, October 6, 2018 at 3:27 PM
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] Randomise design matrix error

Hello experts,

I'm trying to use randomise for a basic 2 sample unpaired t-test via TBSS which I ran on 78 subjects. I made my design.mat and design.con files manually and then used text2vest. But when I run randomise, I keep receiving the error

An exception has been thrown

number of rows in design matrix doesn't match number of "time points" in input data!

I looked everywhere and can't figure out why. Iâ€™m worried about my original design.txt file being mac format instead of windows and thus there are 79 rows (one blank at the end) when I convert the .mat file back to .txt with Vest2Text. But I tried several different ways to convert it to windows format such as with awk or with perl. No matter what, I get the same result. I'm attaching the mat and con files. Here is the exact command I ran from inside the stats folder, where all files (including .con and .mat) are located:

randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2

Here is the output of fslinfo for all_FA_skeletonised:

data_type FLOAT32

dim1 182

dim2 218

dim3 182

dim4 78

datatype 16

pixdim1 1.000000

pixdim2 1.000000

pixdim3 1.000000

pixdim4 1.000000

cal_max 0.0000

cal_min 0.0000

file_type NIFTI-1+

Thank you for the help!

-Ben

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--

Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]

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--

Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]

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