Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

lgi vertex coordinate problem
by Serian doma 23 May '17

23 May '17

Hi there, I am trying to use local gyrification index values for the purpose of adaptive smoothing. I use recon -all and calculate lgi values for vertices on the surface. To show related voxels on the MR volume I changed vertex coordinates to voxel coordinates with the help of freesurfer_surf2voxels command. Then I changed the colour of these voxels on the volume obtained by normalization which is under mri/norm.mgz. However there are several types of shifts both left - right and superior - inferior. Could you please help me to identify the problem here? -- Serian DOMA

2 2

results not displayed in Qdec
by francesca ponteduro 23 May '17

23 May '17

Dear Experts, I am having some trouble with the display of the area in Freesurfer/Qdec. In particular, after running the analysis, I can see some results in the terminal but in the display section of Qdec, no areas are shown. I have tried to wait or re-launch the analysis but the result was the same. What shall I do in order to have the result displayed properly? thank you again for your time, BW Francesca

1 0

Re: [Freesurfer] Two group two time longitudinal analysis
by Livia Liu 23 May '17

23 May '17

Dear Martin， Thank you for your reply. I used a paired analysis to do "two groups two times data of the longitudinal analysis". But unfortunately, I did not make the results, and I use “mri_glmfit-sim” to find 0 vertices in mask. My files are as follows. Fsgd 1: (pairs.fsgd) GroupDescriptorFile 1 Class Sub Class Con Input sub01_MR1 Sub Input sub01_MR2 Sub Input con01_MR1 Con Input con01_MR2 Con ... Fsgd 2: (paired-diff.fsgd) GroupDescriptorFile 1 Class Sub Class Con Input sub01pair Sub Input con01pair Con ... mean.mtx: 1 -1 Are they correct in my Paired analysis? And I am trying LME now. However, I see other people in the mailing list of the questions and replys, I realize that I may be wrong. My two groups of two time are the experimental group (bs) and the placebo group (placebo). I want to do “the crossover analysis” Just like:(postbs-prebs) - (postplacebo-preplacebo) Should not I use longitudinal analysis for these two groups? What kind of analysis do I need to do? Please tell me where I should look in the wiki. Looking forward to reply, and thanks very much. Kind regards, Livia

2 1

Differences for the longitudinal processing with FreeSurfer 6.0 versus 5.3 ?
by Lisa Delalande 23 May '17

23 May '17

Hello everyone, I would like to know if there are big differences between the new verson 6.0 versus the old one 5.3 regarding the recon-all and qcache processing ? Thanks, Best regards, Lisa

2 1

Longitudinal study concept question
by Gregory Book 23 May '17

23 May '17

In writing a paper of longitudinal changes in a large heterogeneous population with no group comparisons, what would be considered "more important" to include: absolute ROI volumes, or volumes corrected for ICV? Using ICV corrected volumes makes sense when comparing groups, but when just describing population changes over time, for example a cross section of a population over a lifespan, is it better to use absolute volumes, corrected volumes, or both?

2 1

LME : longitudinal correlations between imaging and cognition scores
by Matthieu Vanhoutte 23 May '17

23 May '17

Dear Freesurfer's experts, I have searched through the mailing list but haven't found any answer to my question. Is it possible with LME model to make correlations between for example cortical thickness surface data and cognition scores along time ? As it is possible to test for interaction of group X time, is this also in the same way feasible to test for coognition score X time on cortical thickness ? Many thanks for your advice ! Best regards, Matthieu

2 9

generating an annotation using Nibabel - how to create last column for ctab?
by Razvan Marinescu 22 May '17

22 May '17

Dear Freesurfer experts, I'm having trouble generating an annotation file for a large number of ROIs (3000) from Python using Nibabel. The function call that I used is: nib.freesurfer.io.write_annot(filepath, labels, ctab, names) where filepath = 'myFile.annot' labels = numpy 1D array of type int64, elements between 0-2999 inclusive ctab = 3000 x 5 array ctab[:, 0:3] = unique colors for each row ctab[:, 3] = 255 ctab[:, 4] = [1, 2, 3, etc ..] # this is where I think the problem is names = [ b'patch0', b'patch1', etc ... ] The annotation file is created without any warnings, but when I load it with freesurfer it only shows me only around 10 ROIs (screenshot here https://ibb.co/dZnkSa) and gives me the following warning: CTABisEntryValid: index -1 was OOB Resource temporarily unavailable I think the problem is with the IDs I generate on the last column of ctab. I thought those are some unique IDs, one for each ctab row, but they seem to be used to somehow map colors for each vertex. Does anyone know how they must be generated? When I did this before for only around 30 ROIs, I hacked around this problem by loading in Python the annotation file from fsaverage lh.aparc.annot, and using the ctab from there, only replacing the labels and names with my desired values. However, I cannot use this hack for more than 36 ROIs (the number of ctab entries in aparc.annot). Any help will be greatly appreciated! Many thanks, Razvan

1 0

Hyperintensities Volume ?
by Yi-Yu Chou 22 May '17

22 May '17

Dear FreeSurfer experts: Does the white matter volume shown in the aseg.stats include the hyperintensities volume ? Thanks Best Regards, Yiyu

2 1

Freesurfer white matter outer edge to volume
by Gamaliz 22 May '17

22 May '17

I need to create an image which overlaps the T1/mgz and the outer surface of the white matter. How do I convert the surface into a mgz volume? -- gAbE

4 19

estimated Total Intracranial Volume
by John Anderson 22 May '17

22 May '17

Dear experts, i want to know if the eTIV can be used to adjust non-morphometric measures like ,diffusion, PET, ASL ,, etc. Can these measures be adjusted to eTIV. if yes what is the correct command to be used? Thank you Jon

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Freesurfer May 2017