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FSL  September 2018

FSL September 2018

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Subject:

Re: First shape analysis (no data to decimate)

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 14 Sep 2018 09:10:53 +0000

Content-Type:

text/plain

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text/plain (67 lines)

Hi,

I think the problem with first3Dview is that it is only really designed to show significant results, so if there are no results it crashes.  All it could show in that case would just be the average structure in 3D.

As for the GLM, that looks fine.  It ignores the group column, so you don't have to worry about that.
If you don't want to run the F-test then just remove the -f option from the randomise call.  You already specify the t-contrasts via the -t option.

I hope this helps.
All the best,
	Mark


> On 11 Sep 2018, at 12:43, Therese Gilligan <[log in to unmask]> wrote:
> 
> Hello,
> 
> I'm trying to run shape analysis using First.
> 
> Using bias-corrected T1 files, I have applied the following steps:
> 
> for f in old_*_T1_biascorr.nii.gz; do run_first_all -i $f -o "$f"; done
> 
> cat*.logs/*.e*
> 
> I checked both the registrations and the segmentations on a subject by subject basis using overlays in fslview and looked at overview with slicesdir method. They both seem acceptable, for the segmentation my focus was on checking the larger structures of interest.
> 
> concat_bvars command with controls first and then patients
> 
> The GLM design is attached.
> 
> first_utils --usebvars --vertexAnalysis -i old_to_mci_L_Hipp.bvars -d old1_mci2.mat -o old1_mci2_L_Hipp_mni --useReconMNI  -v >& old1_mci2_L_Hipp_output.txt
> 
> randomise -i old1_mci2_L_Hipp - m old1_mci2_L_Hipp_mask -o old1_mci2_L_Hipp_rand -d old1_mci2.mat -t old1_mci2.con -f old1_mci2.fts -D -T n 500
> (At the moment, n=14 per group hence the smaller number of permutations.)
> 
> first3Dview old1_mci2_L_Hipp_mni_mask  old1_mci2_L_Hipp_rand_corrp_tstat1
> 
> When I open the 3D viewer in fslview, the following error is displayed in the terminal:
> 
> 80
> ERROR: In /build/vtk-BebTbT/vtk-5.8.0/Graphics/vtkDecimatePro.cxx, line 163
> vtkDecimatePro (0x46fd1be0): No data to decimate!
> 
> ERROR: In /build/vtk-BebTbT/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx, line 211
> vtkSmoothPolyDataFilter (0x43866130): No data to smooth!
> 
> In the 3Dviewer I can see the left hippocampus perfectly displayed in solid blue (i.e., no indication of any stats). I have separately run volumetric analysis and there is no significant volume difference between the groups. Perhaps this is why there are no colour changes in the shape? However, I don't understand the meaning of the error message and whether it relates to the shape analysis. Following a previous thread, I have tried to adjust the figure (intensity ?) shown beside the clipping tick box but it makes no difference and I cannot change the intensity values shown beside the co-ordinates. I'm using fslview version 4.01.
> 
> Additionally, I am unsure as to whether I set up the GLM correctly. I have attached a png of the design. The wiki states that First ignores the group column but I couldn't figure out how to set up contrasts without assigning group membership. (In fact, rather than the attached design, I'd like to do a one-sided t-test  testing only old>mci, but I was stumped.)
> 
> If you can help regarding the first3Dview error and the GLM query (they may be related?), I would greatly appreciate it.
> 
> Many thanks,
> 
> Therese
> 
> 
> ########################################################################
> 
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
> <old1_mci2.png>

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