spm_vol>spm_vol_hdr error, new user

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Harry Moore

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Mar 5, 2018, 11:24:15 AM3/5/18
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Hello everyone,

Thanks for allowing me to join the group, I have already benefited greatly from the topics.

I'm a new GLM flex fast user, and when trying to run the script I encounter the following error:

Analysing Sub-Model #1 of 1; 40 Observations, across 162651 Voxels. 
Spatial non-sphericity (over scans)     :                        ...done 
File "RPV.img" does not exist.

Error in spm_vol (line 61)
        v = spm_vol_hdr(deblank(P(i,:)));

Error in openIMG (line 45)
V = spm_vol(fn);

Error in GLM_Flex_Fast2 (line 704)
                [tmpM tmpH] = openIMG('RPV.img');

Error in GLM_Flex_setup_dat_and_I_edit (line 53)
GLM_Flex_Fast2(I);

When I set I.estSmooth = 0 the code works, but when it is set to 1 I get the error.
I've looked through the group's posts and still haven't been able to resolve the problem, any help would be mostly appreciated.

Many thanks,
Harry

Aaron Schultz

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Mar 5, 2018, 11:40:40 AM3/5/18
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Can you confirm that mask.nii is a valid, uncorrupted file that is not all 0's?

-Aaron


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Harry Moore

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Mar 5, 2018, 12:25:57 PM3/5/18
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Hi Aaron,

I have opened it in xjview and as a text file and it seems to not be empty, but I wouldn't know if it was corrupted or not. I've attached it to this message if you would like to confirm it too.

Cheers
Harry

On 5 March 2018 at 16:40, Aaron Schultz <ap.sc...@gmail.com> wrote:
Can you confirm that mask.nii is a valid, uncorrupted file that is not all 0's?

-Aaron


On Mon, Mar 5, 2018 at 11:24 AM Harry Moore <htam...@gmail.com> wrote:
Hello everyone,

Thanks for allowing me to join the group, I have already benefited greatly from the topics.

I'm a new GLM flex fast user, and when trying to run the script I encounter the following error:

Analysing Sub-Model #1 of 1; 40 Observations, across 162651 Voxels. 
Spatial non-sphericity (over scans)     :                        ...done 
File "RPV.img" does not exist.

Error in spm_vol (line 61)
        v = spm_vol_hdr(deblank(P(i,:)));

Error in openIMG (line 45)
V = spm_vol(fn);

Error in GLM_Flex_Fast2 (line 704)
                [tmpM tmpH] = openIMG('RPV.img');

Error in GLM_Flex_setup_dat_and_I_edit (line 53)
GLM_Flex_Fast2(I);

When I set I.estSmooth = 0 the code works, but when it is set to 1 I get the error.
I've looked through the group's posts and still haven't been able to resolve the problem, any help would be mostly appreciated.

Many thanks,
Harry

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mask.nii

Aaron Schultz

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Mar 5, 2018, 1:03:02 PM3/5/18
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The mask looks ok.  I'll have to do some more digging.  I seem to recall that something like this happened once before.

-Aaron

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htam...@gmail.com

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Mar 5, 2018, 1:05:46 PM3/5/18
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Hi Aaron,

Ok, thanks for helping!

Cheers
Harry

Harry Moore

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Mar 12, 2018, 6:27:11 AM3/12/18
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Hi again Aaron,

I've been trying to find a solution since we last spoke and I'm still unable to fix it - I don't suppose you've had any luck?

Cheers
Harry

Aaron Schultz

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Mar 12, 2018, 8:50:15 AM3/12/18
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I have not.  Something is going wrong with the SPM computation of the RPV image, but I don't know what or why.  What version of SPM are you using?

-Aaron

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Harry Moore

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Mar 12, 2018, 9:10:24 AM3/12/18
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Hi Aaron,

SPM 12

Harry

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Aaron Schultz

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Mar 12, 2018, 9:28:22 AM3/12/18
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Ok, last up is to send me the exact script/commands that you are using.  I can simulate some data, and see if I can reproduce the error.  If I can't then it's likely something that involves your files/images.

-Aaron

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Harry Moore

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Mar 12, 2018, 9:47:39 AM3/12/18
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Hi Aaron,

OK, I have attached the script to this message. It is a 2 (Age Group) x 2 (Block type) x 4 (Memory condition) design

Cheers
Harry

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GLM_Flex_setup_dat_and_I_edit.m

Aaron Schultz

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Mar 12, 2018, 10:07:16 AM3/12/18
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Is Block Type a within or between factor?

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Harry Moore

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Mar 12, 2018, 10:12:12 AM3/12/18
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Hi Aaron,

It's a within factor, as is memory condition

Cheers
Harry

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Aaron Schultz

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Mar 12, 2018, 10:36:31 AM3/12/18
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I think I know the issue.  Try the attached version of GLM_Flex_Fast (v4).  I don't think the smoothness estimation with repeated measures worked in ver. 2.

Here is the test script I used, which worked fine for me:

% This can be any Nifti file you have handy.  A lower res image will use up

% less RAM.

h = spm_vol(which('02_DefaultMode.nii'));

 

Group = nominal([zeros(80,1); ones(80,1)],{'G1' 'G2'});

Block = {}; Condition = {}; SS = {};

for ii = 1:20

    SS = [SS; repmat({['Subj' sprintf('%0.3i',ii)]},8,1)];

    Condition = [Condition; {'C1' 'C2' 'C3' 'C4'}'; {'C1' 'C2' 'C3' 'C4'}'];

    Block =  [Block; {'B1' 'B1' 'B1' 'B1' 'B2' 'B2' 'B2' 'B2'}'];

end

 

dat = table;

dat.Group = Group;

dat.Block = nominal(Block);

dat.Condition = nominal(Condition);

dat.SS = nominal(SS);

 

clear I;

I.Scans = [];

I.Model = 'Group*Block*Condition + random(SS|Block*Condition)';

I.Data = dat;

I.OutputDir = '/Users/schultz/Users/schultz/Downloads/testmodel/';

I.RemoveOutliers = 0;

I.DoOnlyAll = 1;

I.estSmooth = 1;

I.v = h;

 

% Make fake data.

M = randn(size(dat,1),prod(h.dim));

GLM_Flex_Fast4(I,M);


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GLM_Flex_Fast4.m

htam...@gmail.com

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Mar 15, 2018, 10:03:28 AM3/15/18
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Hi again Aaron,

I’ve tried to run the script again with the version of GLM_Flex_Fast4 that you gave me and I’m still getting the same error. Could there be a problem with the input files I am using?

Cheers
Harry

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<GLM_Flex_Fast4.m>

Aaron Schultz

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Mar 15, 2018, 10:24:25 AM3/15/18
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If you were able to get it to run with the simulated data, then yes, I think there is an issue with the input files.

-Aaron

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Harry Moore

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Mar 15, 2018, 1:29:42 PM3/15/18
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Hi Aaron,

No, it wouldn't run with the simulated data either, it gave the following error and I couldn't figure out the problem:

Undefined function or variable 'searchCellStr'.

Error in GLM_Flex_Fast4 (line 770)
                if I.writeT == 1 && df==1 && isempty(searchCellStr('[\*|\:]',{name})) &&
                ~strcmpi('FullModel',name);

Perhaps there is something fundamental I have misunderstood about the whole procedure...

Cheers
Harry

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Aaron Schultz

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Mar 16, 2018, 8:00:32 AM3/16/18
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Ah, that's just about a missing script.  searchCellStr used to be contains, but contains is now the name of built-in matlab function and was causing problems.  Here is the searchCellStr Script.

-Aaron



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searchCellStr.m

Harry Moore

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Mar 16, 2018, 12:04:06 PM3/16/18
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Hi Aaron,

Thanks for that, the script now works with the simulated data - so as you said before, the problem could be with the input files. They're con.nii files that are produced from making 1st level contrasts in spm12, if you like I could send you a sample of images from one participant?

Cheers
Harry

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Aaron Schultz

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Mar 16, 2018, 4:19:05 PM3/16/18
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Sure, and also double check that you have 8 input images per subject.

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Harry Moore

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May 8, 2018, 9:56:41 AM5/8/18
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Hello again Aaron,

I'm still stuck with the same problem - do you think it could be anything to do with the fact that when it the script starts creating the first RPV file it is trying to make an RPV.nii rather than RPV.img file?

Cheers
Harry

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Aaron Schultz

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May 10, 2018, 9:28:49 AM5/10/18
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I have not, given that things work with simulated data, it must be an interaction between your data and what the code is trying to do.  I won't be able to figure out what the issue is unless I have all of the input images as well.

You can also try doing a little debugging on your own.  With matlab you can insert the statement "keyboard" into a specific location in the code.  The script will then pause execution at that point and you will have command line access to the variable space the script is using.  You can then try executing things line by line and inspect the data at the point to figure out what's happening.

The smoothness estimation happens around line 699 "if I.estSmooth == 1 && ll == 1"

I would try putting in a keyboard command just before that to see what's going on. Does it write out the ResAll* file? Are the mask images produced correctly? Is the residual computation returning sensible data? etc...

Sorry I can't be of more direct help, these type of idiosyncratic issues are difficult to diagnose remotely.

-Aaron

htam...@gmail.com

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May 10, 2018, 10:53:43 AM5/10/18
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Hi Aaron,

No no that’s great advice, at least I know how to keep digging now!

Thanks again for your help,
Cheers
Harry

Harry Moore

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May 21, 2018, 12:32:30 PM5/21/18
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Hi Aaron, I thought I'd let you know that I came by a solution to the problem - I just changed the code so that I looks for RPV.nii instead of RPV.img:

The original GLM_Flex_Fast2.m code (start line: 704):

[tmpM tmpH] = openIMG('RPV.img');

                tmpH.fname = ['RPV' tm(end-2:end) '.nii'];

                spm_write_vol(tmpH,tmpM);

                delete('RPV.*')


Changed to:

[tmpM tmpH] = openIMG('RPV.nii’);

                tmpH.fname = ['RPV' tm(end-2:end) '.nii'];

                spm_write_vol(tmpH,tmpM);

                delete('RPV.*')


Hopefully this solution genuinely gives me valid output.

Cheers
Harry



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Aaron Schultz

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May 21, 2018, 4:55:29 PM5/21/18
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That should be absolutely fine.

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Harry Moore

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Jun 4, 2018, 6:16:11 AM6/4/18
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Thank you very much!

I also have one more question: I'm trying to locate the VOI.data structure in the matlab workspace to look at the beta values and I can't find it, could it be hidden within other structures or should it be directly visible in the workspace?

Cheers
Harry

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Aaron Schultz

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Jun 4, 2018, 8:24:12 AM6/4/18
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After you call the plot function from FIVE or should be directly visible in the workspace. Was there an error after calling one of the plot functions?

Aaron

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htam...@gmail.com

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Jun 4, 2018, 9:30:29 AM6/4/18
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Hi Aaron,

I just about managed to get surf plot to plot an .nii image and it didn’t give an error. Its the first time i’ve used the function but it looks coherent with when the image is viewed in FIVE.

Cheers
Harry

Aaron Schultz

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Jun 4, 2018, 11:52:20 AM6/4/18
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Ah.  Surface plot and paper plot option will not return a VOI structure.  VOI is for plotting options triggered by right clicking on the image and choosing one of the plot options, where you can extract and plot data for a voxel, sphere, or blob.

-Aaron

Harry Moore

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Jun 4, 2018, 12:14:21 PM6/4/18
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Hi Aaron, I've opened the images in FIVE as well and there is still no VOI structure. Also, I right-clicked on the image in FIVE to plot voxels and got the following error:
Reading in original input files
Reference to non-existent field 'PostHoc1'.

Error in GLM_Plot_Fast>ParseEffect (line 263)
            var = data.(step6{1});

Error in GLM_Plot_Fast (line 197)
    [con ind tr] = ParseEffect(effect,mod.X,mod.data);

Error in FIVE/plotVOI (line 3062)
                [yres xres part] = GLM_Plot_Fast(VOI.data,DM,effect);
 
Error while evaluating Menu Callback

I'm going through the GLM_Plot_Fast script but I can't fix it...

Cheers
Harry

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Aaron Schultz

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Jun 4, 2018, 1:17:42 PM6/4/18
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The plot voi function can’t deal with post hocs. I think it should still dump out a VOI though. Try it on one of the canonical contrasts to see if it’s an issue with the post-hocs.

Aaron

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Harry Moore

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Jun 4, 2018, 1:23:52 PM6/4/18
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Hi Aaron,
Yeah I just did it on a main effect contrast and it gives the VOI structure, but only when I plot voxels. Thank you very much for your help! Also, can I assume that the raw data plot is the beta values?

Thanks again!
Harry

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Aaron Schultz

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Jun 4, 2018, 7:58:32 PM6/4/18
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The raw data plot is whatever values are stored in the input images. The VOI will always have data from all images, so you can extract data from that for plotting specific post hocs.

Aaron

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htam...@gmail.com

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Jun 5, 2018, 4:13:33 AM6/5/18
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Hi Aaron, 

OK, and thanks again for the help.

Cheers
Harry

Harry Moore

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Jul 11, 2018, 12:05:55 PM7/11/18
to Aaron's fMRI matlab tools.
Hi again Aaron,

Following on from this point, although I know that FIVE can plot voxel values etc for post hoc contrasts, is there any way I can access the values to make my own plots? When I try to plot a post hoc contrast it doesn't create the VOI structure.

Thanks for your help
Harry

Aaron Schultz

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Jul 11, 2018, 12:36:33 PM7/11/18
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When you use FIVE to generate a plot it extracts measures from all of the input images and stores them in the VOI structure.  When dealing with a Post-hoc contrast, generating a plot from one of the standard contrasts will return all of the information that you need to generate your own plot.  If you want to plot data from a cluster, load both a standard contrast and the post-hoc contrast in the same FIVE viewer.  Find the cluster you want to plot in the post-hoc, and the right click and choose "Cache Cluster Index" then switch back to the the standard contrast and right click and choose "Plot Cached Cluster", that should return the VOI with data extracted from the post-hoc cluster.  Data will be ordered that same way it was in the input data, so you can then use your input table/structure to get the right rows and make whatever plot you would like.

-Aaron


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htam...@gmail.com

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Jul 12, 2018, 10:45:51 AM7/12/18
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Hi Aaron,

Thanks, that has helped a lot!

Regards
Harry
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