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30098 discussions

Resting-state fcMRI analysis with GLM
by Eun Young Choi 06 May '16

06 May '16

Hi all, I'd like to run a resting-state fcMRI analysis within the GLM (mri_glmfit), but I'm not completely sure how to set this up in the FSGD file. I've seen the online tutorial of age vs cortical thickness, but I'm not sure how to specify a regressor with a timeseries. Does anyone have an example of an FSGD file for this? Thanks! Eun Young

2 5

does lGI needs correction for any global measure?
by maaike rive 06 May '16

06 May '16

Dear freesurfer experts,I have a question regarding correction of cortical measures or global measures (ICV, total surface area). As I understand from literature and the freesurfer wiki, a model for thickness should not be corrected for ICV (since thickness does not scale with total brain volume), but surface area should be corrected since is does scale with total brain volume. Three questions:1. should I use ICV or should I use total surface area (TSA) as covariate in the model to correct surface area (by the way, average ICV and TSA do not differ between the groups to compare )?2. does lGI also need correction? does it scale with volume? If so, do I need to correct for ICV or for TSA? Usually I see no correction but some do use ICV...3. even if the average of certain measures (like ICV/TSA, or gender, or age) does not differ between groups, should they be added to the model? If I do not correct for gender, for example, my results change and most papers do use age and gender as covariates if they compare groups despite a lack of differences between groups... Thanks,Maaike

3 4

patient case study at two time points
by Zeng, Qi 06 May '16

06 May '16

Hi All, I was running freesurfer for a patient case of two time points. Will you suggest to run it as a group, such as one time point as a template and followed by longitudinal study, discussing atrophy or run these two time points separately as two individual, running everything such recon-all, dt-recon twice and comparing the result, such as thickness, volume and FA? BTW, I post a question about FA display before: will anything lead to a rectangular FA display, with extra diffusion out of the brain skull (no errors during recon and dt …)? Best, Qi

2 1

Cortical Thickness of a Volume-defined ROI
by Mahtab Farahbakhsh 06 May '16

06 May '16

Dear FreeSurfer, I am trying to find the cortical thickness of my ROI which is the perisylvian region of the left hemisphere. What I did was to define a label based on the anatomical area of this region and tried to define a ROI based on this label and the command -mri_label2volume. Howevere, I am using freeview and the tutorial that I found about this issue was based on tkmedit. Would you please guide me how I should get this done? Best Regards, Mahtab Farahbakhsh.

1 0

Automatic parcellation of the postcentral gyrus
by pfannmoelj＠uni-greifswald.de 06 May '16

06 May '16

Dear Experts, in most of my subjects the cortical parcellation with the Desikan-Killiany atlas is all fine. I am especially interested in the postcentral gyrus. In several of my participants there is a typical problem with the automatic parcellation in this region. About half the postcentral gyrus is parcellated correctly (the lower half), but the upper half is shifted to a posterior part of the brain and the upper half of the postcentral gyrus is parcellated as the precentral gyrus. Attached you find a typical example, one hemisphere is parcellated correctly (left_hemisphere.jpg), the other one shows the problem (right_hemisphere.jpg). The postcentral gyrus is shown in red and the precentral gyrus in blue. The only difference that I can spot is in the anatomy of the superiorparietal and supramarginal regions. These regions are disconnected in the left hemisphere, but have a gyrus which connects them in the right hemisphere. May that cause the difference in the parcellations? Yours pfannmoe

2 1

glmfit --table (by tract TRACULA outputs)
by Pedro Rosa 05 May '16

05 May '16

Dear list, I am trying to use mri_glmfit to run statistics on TRACULA outputs (by tract), as suggested by the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics) I used the following command line: mri_glmfit --glmdir ilf.glmdir --table ilf.txt --fsgd sociodemo.fsgd --C 2G1V-1100.mtx It ends without errors. How should I proceed with correction for multiple comparisons, as I cannot use Monte Carlo? Best, Pedro.

1 0

no recon button
by Burke,Sarah E 05 May '16

05 May '16

Hello, I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do? Thank you

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Beyond thickness and local gyration indexes
by Caverzasi, Eduardo 04 May '16

04 May '16

Hi, I am processing data with freesurfer to look at thickness and local gyration index. I noticed that the aparcstats2table allows obtaining other values about curvature index, folding index and mean curvature. We are interested in understanding the folding pattern in children. I am not sure what the latter indexes are referring to precisely and if there is any other metrics we should consider. Best regards, Eduardo

1 0

error in fast_selxavg3 (line 1248)
by S.V.Shepherd [work] 04 May '16

04 May '16

I've modified an analysis to include a vector of noise time courses estimated using ICA. Since IC effects should be consistent across runs, I'm using taskregs instead of nuisregs. I can define the analysis and set up contrasts fine; however, when I run the analysis (selxavg3-sess), I get the following error: [...] Saving h.dat to /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat Error using zeros Size inputs must be integers. Error in fast_selxavg3 (line 1248) hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % Add zero for cond 0 >> ------------------------------------------ ERROR: fast_selxavg3() failed\n a_401_Av_s_task_fmov_bgrnd_icadenoise failed [...] ============================ Looking at h.dat, I notice "Nh" is set 3.625000e+00 rather than "1" as usual. Any tips on how to debug further? *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

2 8

External ROI for fcseed
by Martin Juneja 04 May '16

04 May '16

Hi all, I am trying to perform step-3 from the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… But I do not have segid because the LookUp table FreeSurfer creates after running recon-all doesn't have the area I am interested in. So I defined the ROI externally, converted it into surface using vol2surf and further into .label file using cor2label. I was wondering how can I use this externally created ROI (either in vol format, or surface format or label format) in this command: fcseed-config. I made sure that the external ROI is perfectly aligned where it was supposed to be. Thanks. MJ

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