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Hi Dave,
Thank you very much for your help.
I have unpacked the tar files. When I did: cd ~/fsl_course_data/
followed by ls, I got: fdt, intro, reg, seg_struc, fmri, meldic, scripting, tbss listed.
Is this correct?
I found the "Select 4D data" control under the Data tab. I do not know why it is set to /home/fslcourse by default even it should be "/<your-home-dir>/fsl_course_data"..."
Where in the practical sheet does it mention about the "Select 4D data" control? I don't seem to find it.
After changing the path, FSL seems to be generating something after I pressed the Go button. The status is "STILL RUNNING".
Thank you once again.
Date: Sat, 26 Oct 2013 08:25:30 +0000
From: [log in to unmask]
Subject: Re: [FSL] Questions from Registration and Unwarping Practical
To: [log in to unmask]
The home directory should be your home directory, not necessarily "/home/..." Use the "~" shorthand to refer to it in the shell. Unpack the tar files in ~/fsl_course_data.
You say you still get the same error! Have you found the "Select 4D data" control? This is where the input is selected. If it still says "/home/fslcourse/fsl-course-data/..." and the data isn't actually there then it won't work. Change it so it refers to your copy of the data: "/<your-home-dir>/fsl_course_data/..."
Dave--Dave FlitneyIT Manager, FMRIB CentreHi Dave,
Thanks for the suggestions. I am very sorry but I still cannot make it. I did follow the instructions step by step. Could you please reconfirm the following? I am using a Mac.
1. Install FSL in /usr/local. After I typed: cd /usr/local, I see the fsl directory.
2. When you say "The tutorial assumes each user makes a personal copy of the fsl_course_data in their home directory", home directory means "~/" or "/Users/<username>" on the Mac rather than "/home" Am I right? To answer the issue that "Problem with FEAT input file (1): currently set to "/home/fslcourse/fsl_course_data/reg/feat_example/func_data", you mentioned "This clearly indicates that the data is expected in /home/fslcourse but you state you've copied it into /usr/local/fsl". I cannot write on the "/home" directory. Does FSL expect that the data be in /home/fslcourse?
How can I change this to ~/fsl_course_data which is what you recommended?
3. "mv /usr/local/fsl/fsl_course_data/ ~/fsl_course_data and repeated the steps."
I issued this command and repeated the instructions from the beginning. However, I still get the same error.
4. In http://fsl.fmrib.ox.ac.uk/fslcourse/ ,under "Data files", it states that "
Once you have downloaded the files they need to be uncompressed before you can begin the course. To do this, open a terminal, change into the folder where you downloaded the course files to and run the following commands:
tar zxf fsl_course_data1.tar.gz; tar zxf fsl_course_data2.tar.gz tar zxf fsl_course_data3.tar.gz; tar zxf fsl_course_data4.tar.gz tar zxf fsl_course_data5.tar.gz "
I don't think this will solve the problem but let's remove all the files in ~/fsl_course_data and
start from the beginning again. Where shall I put these files before issuing the tar command?
From your previous email, it seems that I am supposed to create a folder called "fsl_course_data" in "~/".
Then, store all these downloaded files in in this fsl_course_data folder. Then, issue the tar command.
Thank you.
Date: Wed, 23 Oct 2013 07:27:17 +0000
From: [log in to unmask]
Subject: Re: [FSL] Questions from Registration and Unwarping Practical
To: [log in to unmask]
A few suggestions...
--Dave FlitneyIT Manager, FMRIB CentreHello,
I have tried over 10 times but I still get the error when trying to follow the steps in "Using the FEAT GUI".
I moved the folder: /usr/local/fsl/Course/fsl_course_data/reg/feat_example
to: /usr/local/fsl/fsl_course_data/reg/feat_example
The tutorial assumes each user makes a personal copy of the fsl_course_data in their home directory. This way the instructions in the tutorials can be executed as is in the shell. If you choose to put the data elsewhere the you will need to adjust the instructions accordingly, i.e., where you see ~/fsl_course_data in the instructions you'd have to change it. Better to follow the tutorial exactly...
mv /usr/local/fsl/fsl_course_data/ ~/fsl_course_data
and repeated the steps.
Given the trouble you're having you should repeat the steps again, exactly, don't skip anything, the tutorial often requires that the instructions in prior sections have been completed successfully.
I keep getting the error after hitting the "Go" button. The error is:
"Error: you haven't filled in all the relevant selections with valid filenames:
Problem with FEAT input file (1): currently set to "/home/fslcourse/fsl_course_data/reg/feat_example/func_data"
This clearly indicates that the data is expected in /home/fslcourse but you state you've copied it into /usr/local/fsl. The button "Select 4D data" is where the data input files are specified.
Hint. Hovering the mouse pointer over the controls in the GUI should pop up explanatory text for the controls you're seeing in some depth.
First, I don't know which "relevant selections" has the problem. Second, I cannot find "func_data" in any of the tabs in FEAT_GUI. In the example, I was told to type: func_data_flirt.feat under Selection in the Output directory under the Data tab. As func_data and func_data_flirt are different, I don't think this is the run.
I believe this segment starts by getting you to "Load..." an fsf file? Much of the setup was in this file but it assumed you had the data in the expected place.
Could anybody please help me to sort this out? Thanks.
You need to follow the tutorial steps accurately. The software is, necessarily, complex and can't work if you don't specify the files carefully.
Good luck.
Date: Mon, 21 Oct 2013 06:59:44 +0000
From: [log in to unmask]
Subject: Re: [FSL] Questions from Registration and Unwarping Practical
To: [log in to unmask]
Hi,
On 12 Oct 2013, at 16:07, brain human <[log in to unmask]> wrote:
Hi Mark,
Thank you for your reply.
- For Item 3, where do I change the input file location?
Look in the GUI for where files are specified.
My path is:
/usr/local/fsl/Course/fsl_course_data/reg/feat_example
- For Item 5, "In some situations you will want to move things between different spaces." Why sometimes we want to move things between different spaces? Could you please let me know what "things" and "spaces" you are talking about and how?
- For Item 6, what is "functional series"?
These are very basic questions and beyond what we can help with on this email list. I recommend that you read some introductory textbooks on MRI and fMRI (e.g. Functional Magnetic Resonance Imaging, Second Edition, by Huettel, Song and McCarthy; or
Handbook of Functional MRI Data Analysis, by Poldrack, Mumford and Nichols; or
Functional Magnetic Resonance Imaging: An Introduction to Methods, by Jezzard, Matthews and Smith).
All the best,Mark
> Date: Fri, 11 Oct 2013 21:20:57 +0000
> From: [log in to unmask]
> Subject: Re: [FSL] Questions from Registration and Unwarping Practical
> To: [log in to unmask]
>
> Hi,
>
> > Hello Mark,
> >
> > I have a few questions about this practical. Could you please clarify?
> >
> > 1. Under "Processing the fieldmap phase difference image": "Here we need to take this raw scanner output, which is scaled in a strange way (0 to 360 degrees are mapped to 0 to 4096), and convert it into a radians per second image." Why do we have to do this?
>
> Because the tools need values with particular units.
>
> > 2. Just before "Using the FEAT GUI": "View the output with fslview and check that most of the brain has small values (less than 100) while in the..." What is the point here?
>
> To familiarise yourself with the data.
>
> > 3. Last paragraph of "Using the FEAT GUI". I followed the steps and tried six times. Whenever I pressed the "Go" button, I got the following error:
> >
> > ERROR: you haven't filled in all the relevant selections with valid filenames:
> > Problem with FEAT input file (1): currently set to "/home/fslcourse/fsl_course_data/reg/feat_example/func_data"
>
> If you have installed your data in a location that is different to /home/fslcourse/fsl_course_data, then you need to change this input file location.
>
> > 4. Under "Registration command (FNIRT)" - "Visual Check (images)": The image created using FNIRT seems to match the MNI152_T1_2mm better than that created using FLIRT because of non-linearity. Is this the point you are trying to make?
>
> Yes.
>
> > 5. Under "Applying and Inverting Transformations"' - "Visual Check": Again, the image created using FNIRT seems to match the MNI152_T1_1mm better than that created using FLIRT because of non-linearity. Is this the point you are trying to make?
>
> Yes.
>
> > What is the different between this and the previous comparison mentioned in Point 4? What is the point of using high-res?
>
> In some situations you will want to move things between different spaces.
>
> > 6. "Standard-space masking - a useful application". Could you please explain what "standard-space mask" and "individual functional image" are?
>
> "standard-space mask" is a mask image in the standard space.
> "individual functional image" is one image from a functional series.
>
> > 7. "Fine Adjustments using Initialisation" - "Visual Check". Compared with the previous translation-only result, it seems that there is NO improvement using fine adjustment because I see the images being cut into two pieces and joined together like a step. Is this the "tilted" arbitrary cutoff line you mentioned in next paragraph?
>
> Yes.
>
> > 8. The paragraph before "Getting to Know the Transformation Matrix (Optional): "Note that a small FOV image that is "tilted".." I don't quite understand what you are talking about here. Could you please clarify?
>
> I don't really know what you are asking here. The sentence about tilting was referring to the "cut" that you see in individual slices.
>
> All the best,
> Mark