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 $PATH
>> >>>> >>
>> >>>> >>
>> >>>>
>> /Applications/caret/bin_macosx:/sw/bin:/Library/Frameworks/Python.framework/
>> >>>>
>> Versions/2.7/bin:/Users/angelafavaro/miniconda/bin:/sw/bin:/sw/sbin:/usr/loc
>> >>>>
>> al/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X1
>> >>>> 1R6/bin:/usr/local/bic/bin:/Users/angelafavaro/abin
>> >>>> >> bash-3.2$
>> >>>> >>
>> >>>> >> 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-packages
>> >>>>>> >> >>
>> >>>>>> >> >> 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_functions.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 isnĀ¹t 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>
>
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