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Dear Angela,

There seem to be two issues.

1) The mask files supplied with AROMA cannot be found. These need to be kept stored within the same folder as the scripts. Please check whether this is still the case. Otherwise, are you sure that you didn't change the file names of the masks?
2) By looking at your FNIRT command it seems you entered the warped structural image (fnirted brain) into AROMA. However, the file required by AROMA is the actual warp-file with the field coefficients (i.e. the –cout from FNIRT, in your case warp_highres2mni.nii.gz).

Best,
Raimon



-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Angela Favaro
Sent: maandag 1 juni 2015 17:16
To: [log in to unmask]
Subject: Re: [FSL] ICA AROMA help

Hi all,
I am now able to run ICA AROMA without problems using standardized images, but when I try to run ICA AROMA in native space I have problems.
the error message is:

bash-3.2$ python ICA_AROMA.py -in rest_smg.nii.gz -out ICA_AROMA -affmat example_func2highres2.mat -warp highres2standard_warp.nii.gz -mc rest_mc.1D

------------------------------- RUNNING ICA-AROMA --------------------------
--------------- 'ICA-based Automatic Removal Of Motion Artifacts' ----------

Step 1) MELODIC
Step 2) Automatic classification of the components
  - registering the spatial maps to MNI
An error occured while reading file:
highres2standard_warp.nii.gz
  - extracting the CSF & Edge fraction features Traceback (most recent call last):
  File "ICA_AROMA.py", line 196, in <module>
    edgeFract, csfFract = aromafunc.feature_spatial(fslDir, outDir, scriptDir, melIC_MNI)
  File "ICA_AROMA_functions.py", line 339, in feature_spatial
    numICs = int(commands.getoutput('%sfslinfo %s | grep dim4 | head -n1 | awk \'{print $2}\'' % (fslDir, melIC) ))
ValueError: invalid literal for int() with base 10: 'ERROR: Could not open file'

Before running ICA AROMA I run FLIRT and FNIRT

flirt -ref anat_brain -in example_func -out example_func2highres2 -omat example_func2highres2.mat -cost corratio -dof 6 -searchrx -90 90 -searchry
-90 90 -searchrz -90 90 -interp trilinear

fnirt --ref=standard --in=anat --aff=highres2standard.mat --cout=warp_highres2mni --iout=highres2standard_warp --config=T1_2_MNI152_2mm.cnf --warpres=10,10,10

the file highres2standard_warp.nii.gz is present and seems good at fslview...

what am I doing wrong?
thank you!

Angela




>>
>> > Hi,
>> > also 6mm FWHM is quite a bit of smoothing.
>> > I would look at less smoothed data.
>> > Cheers,
>> > Andreas
>> >
>> > Von:  Maarten Mennes <[log in to unmask]> Antworten an:  FSL 
>> > - FMRIB's Software Library <[log in to unmask]>
>> > Datum:  Dienstag, 19. Mai 2015 13:39
>> > An:  <[log in to unmask]>
>> > Betreff:  Re: [FSL] ICA AROMA help
>> >
>> > Dear Angela,
>> >
>> > for that one subject with 3 components I would run Melodic before 
>> > registering to the standard image, then inspect the report to see 
>> > what
>> the
>> > components look like. In addition I would take a good look at the 
>> > raw
>> data
>> > to see if there was anything unusual going on... I agree that 3-8 
>> > components would not be typical...
>> >
>> > Maarten
>> >
>> > On Mon, May 18, 2015 at 11:14 PM, Angela Favaro
>> <[log in to unmask]>
>> > wrote:
>> >> Thank you for this. This solved my problem.
>> >>
>> >> I have another general question on ICA AROMa (but also generally 
>> >> on ICA).
>> >> I am analyzing a dataset of RS fMRI and comparing different 
>> >> methods
>> of
>> >> motion denoising. However, I noticed that for some subjects ICA 
>> >> processed only a limited number of components (7 or 8 instead of 
>> >> more than
>> 30-40
>> >> that I usually observe). In one subject the components were 3 and 
>> >> all
>> 3
>> >> were motion components (mean FD was 0.05mm).
>> >> How must I interpret this? Is it an artifact? or did I make 
>> >> something wrong in the preprocessing? my preprocessing consisted 
>> >> in: dropping first
>> >> 5 volumes, deobliquing (3drefit), motion correction to average of 
>> >> timeseries, skull stripping, registering to standard image 
>> >> (flirt), smoothing (FWHM=6).
>> >>
>> >> THank you for any help or advice
>> >>
>> >> Angela
>> >>
>> >>> > Hi Angela,
>> >>> >
>> >>> > You need to change your $PATH variable so that the Anaconda
>> version
>> >>> of
>> >>> > Python comes before the Framework version of Python. You can do
>> this
>> >>> by
>> >>> > opening the file '/Users/angelafavaro/.bash_profile' in a text
>> >>> editor, and
>> >>> > pasting this line at the bottom of that file:
>> >>> >
>> >>> > export PATH=/Users/angelafavaro/minconda/bin:$PATH
>> >>> >
>> >>> > Alternately, in that file there is probably a line near the 
>> >>> > bottom
>> >>> which
>> >>> > adds the Framework python installation to the PATH -
>> >>> removing/commenting
>> >>> > out this line will have the same effect.
>> >>> >
>> >>> > Cheers,
>> >>> >
>> >>> > Paul
>> >>> >
>> >>> > On 15 May 2015 at 15:39, Angela Favaro <[log in to unmask]>
>> >>> wrote:
>> >>> >
>> >>>> >> Hi Paul,
>> >>>> >> thank you for your help! I ma not very expert in using python...
>> >>>> >> this is the output of what you requested:
>> >>>> >>
>> >>>> >> bash-3.2$ which python
>> >>>> >> /Library/Frameworks/Python.framework/Versions/2.7/bin/python
>> >>>> >> bash-3.2$ which pip
>> >>>> >> /Users/angelafavaro/miniconda/bin/pip
>> >>>> >> bash-3.2$ which conda
>> >>>> >> /Users/angelafavaro/miniconda/bin/conda
>> >>>> >> bash-3.2$ echo $PATH
>> >>>> >>
>> >>>> >>
>> >>>>
>> /Applications/caret/bin_macosx:/sw/bin:/Library/Frameworks/Python.fra
>> mework/
>> >>>>
>> Versions/2.7/bin:/Users/angelafavaro/miniconda/bin:/sw/bin:/sw/sbin:/
>> usr/loc
>> >>>>
>> al/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:
>> /usr/X1
>> >>>> 1R6/bin:/usr/local/bic/bin:/Users/angelafavaro/abin
>> >>>> >> bash-3.2$
>> >>>> >>
>> >>>> >> thank you for any help
>> >>>> >> BW
>> >>>> >> Angela
>> >>>> >>
>> >>>> >>
>> >>>> >>
>> >>>> >>
>> >>>>> >> > Hi Angela,
>> >>>>> >> >
>> >>>>> >> > It is likely that you have python installed on your 
>> >>>>> >> > computer
>> >>>>> multiple
>> >>>>> >> > times, and the version which has numpy installed is not 
>> >>>>> >> > the
>> >>>>> version
>> >>>> >> that
>> >>>>> >> > is
>> >>>>> >> > being used by AROMA.
>> >>>>> >> >
>> >>>>> >> > Could you please provide us with the output of the 
>> >>>>> >> > following
>> >>>>> commands:
>> >>>>> >> >
>> >>>>> >> > which python
>> >>>>> >> > which pip
>> >>>>> >> > which conda
>> >>>>> >> > echo $PATH
>> >>>>> >> >
>> >>>>> >> > Thanks,
>> >>>>> >> >
>> >>>>> >> > Paul
>> >>>>> >> >
>> >>>>> >> > On 14 May 2015 at 21:13, Angela Favaro
>> <[log in to unmask]>
>> >>>>> wrote:
>> >>>>> >> >
>> >>>>>> >> >> Hi Christian,
>> >>>>>> >> >> numpy was already installed using the command (conda
>> install
>> >>>>>> numpy)
>> >>>>>> >> >>
>> >>>>>> >> >> bash-3.2$ pip install numpy Requirement already 
>> >>>>>> >> >> satisfied (use --upgrade to upgrade):
>> >>>>>> numpy in
>> >>>>>> >> >> /Users/angelafavaro/miniconda/lib/python2.7/site-package
>> >>>>>> >> >> s
>> >>>>>> >> >>
>> >>>>>> >> >> however, again ...
>> >>>>>> >> >>
>> >>>>>> >> >> --------------- 'ICA-based Automatic Removal Of Motion
>> >>>>>> Artifacts'
>> >>>>>> >> >> ---------------
>> >>>>>> >> >>
>> >>>>>> >> >> Step 1) MELODIC
>> >>>>>> >> >> Step 2) Automatic classification of the components
>> >>>>>> >> >>   - registering the spatial maps to MNI
>> >>>>>> >> >>   - extracting the CSF & Edge fraction features 
>> >>>>>> >> >> Traceback (most recent call last):
>> >>>>>> >> >>   File "ICA_AROMA.py", line 196, in <module>
>> >>>>>> >> >>     edgeFract, csfFract = 
>> >>>>>> >> >> aromafunc.feature_spatial(fslDir,
>> >>>>>> outDir,
>> >>>>>> >> >> scriptDir, melIC_MNI)
>> >>>>>> >> >>   File
>> >>>>>> >> >>
>> >>>>>> >> >>
>> >>>> >>
>> >>>>
>> >
>> "/Users/angelafavaro/Desktop/risonanze/network/aroma/ICA_AROMA_functi
>> ons.py",
>> >>>>>> >> >> line 334, in feature_spatial
>> >>>>>> >> >>     import numpy as np
>> >>>>>> >> >> ImportError: No module named numpy
>> >>>>>> >> >>
>> >>>>>> >> >>
>> >>>>>> >> >> What can be the problem?
>> >>>>>> >> >> thank you
>> >>>>>> >> >> Angela
>> >>>>>> >> >>
>> >>>>>> >> >>
>> >>>>>> >> >>
>> >>>>>>> >> >> > Hi
>> >>>>>>> >> >> >
>> >>>>>>> >> >> > Looks like numpy isn¹t installed on your system
>> >>>>>>> >> >> >
>> >>>>>>> >> >> > pip install numpy
>> >>>>>>> >> >> >
>> >>>>>>> >> >> > hth
>> >>>>>>> >> >> > Christian
>> >>>>>>> >> >> >
>> >>>>>>> >> >> >
>> >>>>>>>> >> >> >> On 13 May 2015, at 17:27, Angela Favaro
>> >>>>>>>> <[log in to unmask]>
>> >>>>>> >> >> wrote:
>> >>>>>>>> >> >> >>
>> >>>>>>>> >> >> >> Hi Maarten,
>> >>>>>>>> >> >> >> python 2.7
>> >>>>>>>> >> >> >>
>> >>>>>>>> >> >> >> thank you
>> >>>>>>>> >> >> >> Angela
>> >>>>>>>> >> >> >>
>> >>>>>>>> >> >> >>
>> >>>>>>>>> >> >> >>> Dear Angela,
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>> can you check whether you are using the correct
>> python
>> > version
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>> run
>> >>>>>>>>> >> >> >>> which python
>> >>>>>>>>> >> >> >>> at the command line
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>> I also have the anaconda distribution on OSX 
>> >>>>>>>>> >> >> >>> 10.10,
>> >>>>>>>>> works
>> > like a
>> >>>>>> >> >> charm
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>> Maarten
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>> On Wed, May 13, 2015 at 12:15 AM, Angela Favaro 
>> >>>>>>>>> >> >> >>> <[log in to unmask]>
>> >>>>>>>>> >> >> >>> wrote:
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>>> >> >> >>>> Hi all,
>> >>>>>>>>>> >> >> >>>> I am not very expert in using python. The 
>> >>>>>>>>>> >> >> >>>> script
>> of
>> > ICA-AROMA
>> >>>> >> give
>> >>>>>> >> >> me
>> >>>>>>>>>> >> >> >>>> this
>> >>>>>>>>>> >> >> >>>> error:
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>> --------------- 'ICA-based Automatic Removal Of
>> >>>>>>>>>> Motion
>> >>>> >> Artifacts'
>> >>>>>>>>>> >> >> >>>> ----------
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>> Step 1) MELODIC Step 2) Automatic 
>> >>>>>>>>>> >> >> >>>> classification of the components
>> >>>>>>>>>> >> >> >>>>  - registering the spatial maps to MNI
>> >>>>>>>>>> >> >> >>>>  - extracting the CSF & Edge fraction features 
>> >>>>>>>>>> >> >> >>>> Traceback (most recent call last):
>> >>>>>>>>>> >> >> >>>>  File "ICA_AROMA.py", line 196, in <module>
>> >>>>>>>>>> >> >> >>>>    edgeFract, csfFract =
>> >>>>>>>>>> aromafunc.feature_spatial(fslDir,
>> >>>> >> outDir,
>> >>>>>>>>>> >> >> >>>> scriptDir, melIC_MNI)  File 
>> >>>>>>>>>> >> >> >>>> "ICA_AROMA_functions.py", line 334, in
>> >>>>>>>>>> feature_spatial
>> >>>>>>>>>> >> >> >>>>    import numpy as np
>> >>>>>>>>>> >> >> >>>> ImportError: No module named numpy bash-3.2$
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>> I had installed the numpy module (by using conda
>> >>>>>>>>>> install
>> > numpy).
>> >>>>>>>>>> >> >> >>>> I am using a OSX 10.6.8
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>> Can you help me in understanding the problem?
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>> thank you
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>> Angela
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>>>> >> >> >>>>> Dear Angela,
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> >> >> >>>>> We recommend applying ICA-AROMA after spatial
>> >>>>>>>>>>> smoothing,
>> > this
>> >>>> >> is
>> >>>>>> >> >> in
>> >>>>>>>>>> >> >> >>>> order
>> >>>>>>>>>>> >> >> >>>>> to 'condition' the subsequent ICA run. It will
>> >>>>>>>>>>> prevent
>> > the
>> >>>>>> >> >> resulting
>> >>>>>>>>>>> >> >> >>>>> components from fragmenting too much. We have
>> >>>>>>>>>>> extensively
>> >>>> >> tested
>> >>>>>> >> >> the
>> >>>>>>>>>>> >> >> >>>>> suggested pipeline and the ability to detect the
>> >>>>>>>>>>> motion-related
>> >>>>>>>>>> >> >> >>>> artifacts
>> >>>>>>>>>>> >> >> >>>>> is hampered when leaving out the smoothing step.
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> >> >> >>>>> If you would like to continue using unsmooth
>> data
>> >>>>>>>>>>> for
>> > your
>> >>>>>> >> >> analyses,
>> >>>>>>>>>> >> >> >>>> we
>> >>>>>>>>>>> >> >> >>>>> suggest running ICA-AROMA on the smoothed data,
>> >>>>>>>>>>> then
>> > applying
>> >>>>>>>>>> >> >> >>>> fsl_regfilt
>> >>>>>>>>>>> >> >> >>>>> with the identified components on the unsmooth
>> data
>> > (AROMA will
>> >>>>>>>>>>> >> >> >>>>> return
>> >>>>>>>>>> >> >> >>>> a
>> >>>>>>>>>>> >> >> >>>>> list of identified components).
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> >> >> >>>>> hope this helps,
>> >>>>>>>>>>> >> >> >>>>> Maarten
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> >> >> >>>>> On Mon, May 11, 2015 at 9:40 PM, Angela Favaro
>> >>>>>>>>>> >> >> >>>> <[log in to unmask]>
>> >>>>>>>>>>> >> >> >>>>> wrote:
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>>> >> >> >>>>>> Hi FSL expert,
>> >>>>>>>>>>>> >> >> >>>>>> I would like to test the effects of ICA AROMA
>> on
>> >>>>>>>>>>>> my
>> > dataset
>> >>>>>> >> >> (RSFC).
>> >>>>>>>>>>>> >> >> >>>>>> In the website it is suggested to use the
>> script
>> >>>>>>>>>>>> after
>> > spatial
>> >>>>>>>>>>>> >> >> >>>>>> smoothing.
>> >>>>>>>>>>>> >> >> >>>>>> Is smoothing a needed step to use ICA AROMA?
>> in
>> >>>>>>>>>>>> some
>> >>>> >> particular
>> >>>>>>>>>> >> >> >>>> cases,
>> >>>>>>>>>>>> >> >> >>>>>> smoothing can create spurious correlations and
>> I
>> >>>>>>>>>>>> want
>> > to know
>> >>>> >> if
>> >>>>>> >> >> the
>> >>>>>>>>>>>> >> >> >>>>>> ability of the method to denoise data is
>> impaired
>> >>>>>>>>>>>> by
>> > omitting
>> >>>>>>>>>>>> >> >> >>>>>> spatial
>> >>>>>>>>>>>> >> >> >>>>>> smoothing of data.
>> >>>>>>>>>>>> >> >> >>>>>>
>> >>>>>>>>>>>> >> >> >>>>>> thank you
>> >>>>>>>>>>>> >> >> >>>>>>
>> >>>>>>>>>>>> >> >> >>>>>> Angela
>> >>>>>>>>>>>> >> >> >>>>>>
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> >> >> >>>>> --
>> >>>>>>>>>>> >> >> >>>>> Maarten Mennes, Ph.D.
>> >>>>>>>>>>> >> >> >>>>> Senior Researcher
>> >>>>>>>>>>> >> >> >>>>> Donders Institute for Brain, Cognition and
>> >>>>>>>>>>> Behaviour
>> >>>>>>>>>>> >> >> >>>>> Radboud University Nijmegen
>> >>>>>>>>>>> >> >> >>>>> Nijmegen
>> >>>>>>>>>>> >> >> >>>>> The Netherlands
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> >> >> >>>>> Google Scholar Author Link
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>>> <http://scholar.google.com/citations?user=pLlSTVgAAAAJ&hl=en>
>> >>>>>>>>>>> >> >> >>>>>
>> >>>>>>>>>> >> >> >>>>
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>> --
>> >>>>>>>>> >> >> >>> Maarten Mennes, Ph.D.
>> >>>>>>>>> >> >> >>> Senior Researcher
>> >>>>>>>>> >> >> >>> Donders Institute for Brain, Cognition and Behaviour
>> >>>>>>>>> >> >> >>> Radboud University Nijmegen
>> >>>>>>>>> >> >> >>> Nijmegen
>> >>>>>>>>> >> >> >>> The Netherlands
>> >>>>>>>>> >> >> >>>
>> >>>>>>>>> >> >> >>> Google Scholar Author Link
>> >>>>>>>>> >> >> >>> <
>> http://scholar.google.com/citations?user=pLlSTVgAAAAJ&hl=en>
>> >>>>>>>>> >> >> >>>
>> >>>>>>> >> >> >
>> >>>>>>> >> >> >
>> >>>>>> >> >>
>> >>>>> >> >
>> >>>> >>
>> >>> >
>> >
>> >
>> >
>> > --
>> > Maarten Mennes, Ph.D.
>> > Senior Researcher
>> > Donders Institute for Brain, Cognition and Behaviour
>> > Radboud University Nijmegen
>> > Nijmegen
>> > The Netherlands
>> >
>> > Google Scholar Author Link
>> > <http://scholar.google.com/citations?user=pLlSTVgAAAAJ&hl=en>
>> >
>> >
>> >
>>
>
>
>
> --
> Maarten Mennes, Ph.D.
> Senior Researcher
> Donders Institute for Brain, Cognition and Behaviour
> Radboud University Nijmegen
> Nijmegen
> The Netherlands
>
> Google Scholar Author Link
> <http://scholar.google.com/citations?user=pLlSTVgAAAAJ&hl=en>
>