Hi - actually - the following might be more useful in terms of a more recent (non-current) release:
> www.fmrib.ox.ac.uk/~steve/ftp/fslnets0.5.tar.gz
Cheers
On 3 Apr 2014, at 15:51, Stephen Smith <[log in to unmask]> wrote:
> Hi
>
> On 3 Apr 2014, at 15:39, Paul Beach <[log in to unmask]> wrote:
>
>> Stephen,
>>
>> My data were all pre and post processed in AFNI. Thus my ROIs and correlational time series files/maps are all .HEAD/.BRIK files. Do you have any suggestions as to how to get these into the 4D nifti format necessary to get the "group_maps" file created for FSLNets? This is assuming it could be done without running everything through FSL in the first place. :)
>
> you would need to convert BRIK to NIFTI - I would imaging that AFNI can do that.
>
>>
>> Alternatively, is there an archive available of prior versions of FSLNets? I'd like to re-run my hierarchical clustering but the current version requires the group_maps files.
>
> sure - though no longer supported - one old version:
> www.fmrib.ox.ac.uk/~steve/ftp/fslnets0.3.tar.gz
>
>
> Cheers
>
>
>
>>
>>
>> Thanks for your help.
>>
>>
>> On Sat, Mar 29, 2014 at 10:30 AM, Stephen Smith <[log in to unmask]> wrote:
>> Hi
>>
>>
>> On 29 Mar 2014, at 13:58, Paul Beach <[log in to unmask]> wrote:
>>> Any help on the issues below would be greatly helpful!
>>>
>>> Steve,
>>>
>>> Thanks for the prior replies about the new FSLnets version.
>>>
>>> I have a few more questions based on other issues I'm now having with the new FSLnets version. My processing stream takes resting time series data from a set of ROIs using AFNI commands and putting them into the FSLnets setup. I'm currently not using the dual-regression/ICA approach in FSL. Thusly, I do not have any "group maps" to include, making several of the steps currently not possible.
>>
>> If you have a 4D NIFTI file of the maps then it should be easy to create a [maps].sum folder using the slices_summary command (see nets_examples.m).
>>
>>> Is there a way to compile ROI files/networks using FSL commands in a way that will make the FSLNets scripts happy? Alternatively, is there a workaround so I can avoid using the "group maps" variable for all of the steps?
>>>
>>> Also, in the new version of the "nets_glm" function I'm not getting a color coded correlation matrix figure for each contrast when I try to look at all my ROIs at once. Instead the output looks more like a frequency figure.
>>
>> this happens when the nets_glm function thinks that you haven't given it a square matrix as input.... so no, in normal use it should look like the same as before.
>>
>> The nets_glm corrected p-values are FWE using randomise (see randomise on the FSL wiki) - not Bonferroni corrected.
>>
>> Cheers.
>>
>>
>>>
>>> My nets_glm command is as follows:
>>> [p_uncorrected,p_corrected]=nets_glm(netmats2,'GLM_painad3_AgeGenderCovar.mat','GLM_painad3_AgeGenderCovar.con',1);
>>>
>>> The error message I'm getting is:
>>> Cannot open //group_maps.sum/0017.png for reading
>>> ??? Error using ==> imread at 374
>>> File "/private/tmp/tpec358c26_bb1b_4c2a_9647_234f90dd9fab.png" does not
>>> exist.
>>>
>>> Error in ==> nets_edgepics at 40
>>> system(sprintf('slices_summary %s %s
>>> %s',group_maps,grott,num2str(ts.DD([xxx])-1))); picgood=imread(grott);
>>>
>>> Error in ==> FSLNets_AllNets_pbeach at 75
>>> nets_edgepics(ts,group_maps,Znet2,reshape(p_corrected(1,:),ts.Nnodes,ts.Nnodes),6);
>>>
>>> A screenshot of the output figure (figure 2) is below. Nothing shows up for Figure3.
>>> <image.png>
>>> Note that I don't have this figure problem with smaller numbers of ROIs. I get the correlation matrix as expected.
>>>
>>>
>>> Finally: I have a general question about the way the FWE is being calculated. Typically you just divide your p-value by the number of comparisons. However, it looks as though this isn't what's being done when I compare the "best p-values" that are output for the nets_glm function. Can you elaborate a bit on this?
>>>
>>>
>>> Thanks for your help
>>> Paul
>>>
>>>
>>>
>>> On Fri, Mar 21, 2014 at 12:00 AM, Stephen Smith <[log in to unmask]> wrote:
>>> Hi
>>>
>>> In general FSLNets will not allow different run lengths. This is primarily because at this point the software isn't setup to handle that, but more conceptually one should not in general be trying to do quantitative comparisons when you have such different run lengths anyway.
>>>
>>> However - if what you have is different numbers of runs for different subjects, that is easier to handle....just load in all the different runs as different files, and then you can deal with the varying numbers of runs in different subjects at the multi-subject stats stage - although if it was me I would probably avoid that complication and just dump that subject.
>>>
>>> Cheers, Steve.
>>>
>>>
>>>
>>> On 20 Mar 2014, at 18:47, Paul Beach <[log in to unmask]> wrote:
>>>
>>>> FSL folks,
>>>>
>>>> I'm trying to use the new version of FSLnets (released last week, I believe) and I'm getting an error that wasn't occurring previously.
>>>>
>>>> "Error: not all subjects have the same number of timepoints!
>>>> ??? index exceeds matrix dimensions
>>>>
>>>> Error in ==> nets_spectra at 32..."
>>>>
>>>> This is likely referring to the fact that one of my subjects only had one resting state scan whereas everyone else had two. How do I correct for this error without simply dumping a whole subject?
>>>>
>>>> Thanks
>>>> --
>>>> Paul Beach
>>>> DO/PhD candidate - Year VI
>>>> Michigan State University
>>>> - College of Osteopathic Medicine
>>>> - Neuroscience Program
>>>> - Bozoki Lab: Neurology/Radiology
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>> ---------------------------------------------------------------------------
>>>
>>> Stop the cultural destruction of Tibet
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Paul Beach
>>> DO/PhD candidate - Year VI
>>> Michigan State University
>>> - College of Osteopathic Medicine
>>> - Neuroscience Program
>>> - Bozoki Lab: Neurology/Radiology
>>>
>>>
>>>
>>> --
>>> Paul Beach
>>> DO/PhD candidate - Year VI
>>> Michigan State University
>>> - College of Osteopathic Medicine
>>> - Neuroscience Program
>>> - Bozoki Lab: Neurology/Radiology
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>>
>> Stop the cultural destruction of Tibet
>>
>>
>>
>>
>>
>>
>>
>> --
>> Paul Beach
>> DO/PhD candidate - Year VI
>> Michigan State University
>> - College of Osteopathic Medicine
>> - Neuroscience Program
>> - Bozoki Lab: Neurology/Radiology
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
Stop the cultural destruction of Tibet
|
