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30132 discussions

mri_normalize: different results for different resolution
by Falk Lüsebrink 23 May '17

23 May '17

Dear all, I'm processing native 250 µm T1-weighted MPRAGE data with v6. I downsampled the data gradually from 250 µm to 1 mm and am processing it with the -hires flag, openmp and expert options affecting mris_inflate and mris_make_surfaces. After intensity normalization of autorecon1 the white matter intensity is not set around 110 as it should be, but varies across the brain. Please find attach a screenshot of nu.mgz prior to the normalization and of T1.mgz after normalization. This happened in case of 250 µm data only, please also find attached the recon-all.log Having pre-processed the data slightly differently I have encountered the same with the 330 µm, but not in case of 250 µm. However, downsampling the nu.mz and running mri_normalize on the downsampled nu.mgz resulted in a usual T1.mgz in all cases tested. I can upload the subject folder if you wish. Folder size is approximately 1.3 GB without rawavg.mgz and 001.mgz Best, Falk ---------------------------------------- Falk Lüsebrink, M. Sc. Otto-von-Guericke-University, Magdeburg, Germany Faculty of natural sciences Institute for experimental physics Biomedical Magnetic Resonance (BMMR) http://www.bmmr.ovgu.de/mm/en/

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lh.pial of fsaverage with topological defect
by Sabrina Brigadoi 23 May '17

23 May '17

Dear FreeSurfer experts, the lh.pial surface of the /subjects/fsaverage subject seems to have a topological error. When I load it (in Freeview or Matlab) I can see a small area with lower node density (and bigger face area; see attached). Is there any updated correct version of this surface available? Or is there a way to fix it? I have a related question: the cvs_avg35_inMNI152 does not have this defect in the lh.pial surface. Is this the MNI152 atlas? Or is it different? Thank you for your help, Sabrina Brigadoi [image: Immagine incorporata 2] -- Sabrina Brigadoi, Ph.D. Post-doc Fellow Department of Developmental Psychology University of Padova via Venezia 8 35131, Padova, Italy Cognition and Language Research Laboratory http://colab.psy.unipd.it

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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

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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

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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

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