Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

longitudinal base problem - bad surfaces
by Koolschijn, Cédric 02 Sep '14

02 Sep '14

Dear experts, I'm performing a longitudinal analysis, and have done so before, but I encounter an error after running -base for one subject which I haven't seen before. The cross surfaces of both timepoints look OK, but the base surface is seems to be shrunken for unknown reasons. I reran all steps, but with the same results. The log file also doesn't provide any useful information, no errors were reported. Below, please find screenshots of the surfaces for each tp. tp1: https://www.dropbox.com/s/5cwksrzqyw9jxxo/n4t1.tif?dl=0 tp2: https://www.dropbox.com/s/858062gh1uwigo2/n4t2.tif?dl=0 base: https://www.dropbox.com/s/hutaarl7jvthwcy/n4base.tif?dl=0 Do you have any idea what caused the mess-up in -base, and how to fix this? It will be a lot of editing should this be done manually, so I'm hoping for a better option. Many thanks! Best, Cédric

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Questions about mri_make_bem_surfaces function
by gamaliel huerta urrea 01 Sep '14

01 Sep '14

Hi experts I need use the mri_make_bem_surfaces function to generate the three surfaces from brain MRIs patient exam. I have installed Freesurfer and I have my series of MRIs in 001.mgz file. would be helpful if you could provide some material to use this function. regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso*

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questions about qdec, group and age interaction
by yaya ya 01 Sep '14

01 Sep '14

Dear all, I encountered several questions when using freesurfer. Although I searched carefully in this mailing list, I am still not very clear about some issues. My issues are described below: Based on a bunch of information, I know that before describing my results, I need to check whether there is an interaction effects between group and age. In order to do it, I demean my age variable and add it as a continuous covariate in Qdec. My discrete variable is group. Then I run the analysis on cortical thickness, producing several results. But I am not very sure about which of them described the group*age interaction effects in my data so that I could check the interaction results. That is why I need your help with confirming it. The name of several results are listed here: 1. does the average thickness differ from zero? (I don't think this is interacton effect) 2. does the correlation between thickness and demean-age, accounting for group, differ from zero? (this is not the interaction either. this should be the relation between thickness and age across 2 groups.) 3. does the average thickness differe between the two groups? (this should be the group main effect) 4, does the thickness-age correlation differ between 2 groups (*I think this should be what I need*). If so, I further checked whether the fourth one could survive the corrected threshold using monte carlo stimulation (threshold 1.3, p<0.05). two clusters survived. But one interesting thing is that the results from above 3 and 4 produced the same results except one thing. 3 gave the hightened thickness of several regions in patients groups compared with controls. In contrast, 4 found the same region but the opposite pattern (decresed thickness in patients compared with controls). When I add my age as a nuisance covariate, I get the same results 3. I don't know which one should report. Do my results make sense? My last question is that I could not find the data file which includes the thickness values from each subject resulting from above analysis because I want to do some correlation analysis with other clinical variables. I hope that it is clear to you all. Thank you for your help in advance. Best, Lickey

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Change in the location/path and the name of subject
by Reza Rajimehr 01 Sep '14

01 Sep '14

Hi, I have got anatomicals of a subject from someone else. The anatomicals have been processed, and the surfaces have been reconstructed. The path to these files in my machine is obviously different from the path where data have been analyzed. I also want to change the name of the subject and give a name based on a convention that I have for my other subjects. Would the change in the location and name of the subject be problematic later on when I want to work with the anatomical data or use them during the functional data analysis? (re-processing of the anatomicals is not an option, since these are monkey data with heavy amounts of manual editings) Thanks, Reza

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Freesurfer September 2014