Undefined function or variable 'spm_normalise'.

[Sebastian Miguel Toescu]

Hello AFQ experts,

I am trying to run the AFQ pipeline on an iMac (Mojave 10.14.6) in Matlab R2017b, SPM12_v6906. When I try to run 'AFQ_example.m', I get the following error (attached screenshot, text copied below):

Undefined function or variable 'spm_normalise'.

Error in mrAnatComputeSpmSpatialNorm (line 83)

sn = spm_normalise(Vtemplate, Vin, '', '', Vsw, params);

Error in AFQ_SegmentFiberGroups (line 176)

[sn, Vtemplate, invDef] = mrAnatComputeSpmSpatialNorm(alignIm, dt.xformToAcpc,

template, params);

Error in AFQ_example (line 41)

fg_classified = AFQ_SegmentFiberGroups(dt, wholebrainFG);

 

I have just recompiled SPM and added the latest updates (v7771) per their instructions here (https://www.fil.ion.ucl.ac.uk/spm/software/spm12/).

I am able to run AFQ satisfactorily on a Macbook Pro (Mojave 10.14.6, Matlab R2017b, SPM12_v7487).

Could it be that AFQ only currently works with SPM12_v7487? Or is there any other workaround to get it functioning on my iMac with SPM12_v7771.

Cheers

S

[Sebastian Miguel Toescu]

Should have said - the error persists on the iMac after recompilation of SPM with update v7771.

Hope you can help!

Cheers

S

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Sebastian M Toescu

Visiting Scholar, Stanford University / Lucille Packard Children's Hospital

GOSH Charity / RCS Surgeon Scientist PhD Fellow, UCL Institute of Child Health

Neurosurgery Registrar, Great Ormond Street Hospital

Treasurer, British Neurosurgical Trainees Association

M 0772 589 3370

E s.m.t...@gmail.com / sebastia...@ucl.ac.uk / s.to...@nhs.net

[Sebastian Miguel Toescu]

I emailed the SPM developers who replied: "this is due to spm_normalise being an old function that has now been moved into a toolbox. This can be fixed by adding the relevant path manually:

addpath(fullfile(spm('dir'),'toolbox','OldNorm')), or calling spm_jobman initcfg before using AFQ."

Both of these worked, although the addpath command is preferable as it only needs to be run once to save the path for future AFQ use.

Thought I'd post the solution in case any one else needs it at some point.

S

On Thursday, June 18, 2020 at 4:37:34 PM UTC+1, Sebastian Miguel Toescu wrote:

Should have said - the error persists on the iMac after recompilation of SPM with update v7771.

Hope you can help!

Cheers

S

On Thu, 18 Jun 2020 at 16:05, Sebastian Miguel Toescu <s.m.t...@gmail.com> wrote:

Hello AFQ experts,

I am trying to run the AFQ pipeline on an iMac (Mojave 10.14.6) in Matlab R2017b, SPM12_v6906. When I try to run 'AFQ_example.m', I get the following error (attached screenshot, text copied below):

Undefined function or variable 'spm_normalise'.

Error in mrAnatComputeSpmSpatialNorm (line 83)

sn = spm_normalise(Vtemplate, Vin, '', '', Vsw, params);

Error in AFQ_SegmentFiberGroups (line 176)

[sn, Vtemplate, invDef] = mrAnatComputeSpmSpatialNorm(alignIm, dt.xformToAcpc,

template, params);

Error in AFQ_example (line 41)

fg_classified = AFQ_SegmentFiberGroups(dt, wholebrainFG);

 

I have just recompiled SPM and added the latest updates (v7771) per their instructions here (https://www.fil.ion.ucl.ac.uk/spm/software/spm12/).

I am able to run AFQ satisfactorily on a Macbook Pro (Mojave 10.14.6, Matlab R2017b, SPM12_v7487).

Could it be that AFQ only currently works with SPM12_v7487? Or is there any other workaround to get it functioning on my iMac with SPM12_v7771.

Cheers

S

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