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30134 discussions

Questions about outputs in Longitudinal Stream
by Tamara Tavares 29 Oct '16

29 Oct '16

Hello, I am interested in looking at ventricular changes over time and thus, have ran the longitudinal stream on my participants scans. As suggested online, I am checking the ventricular segmentation in the longitudinal outputs and am planning on making any edits to the longitudinal stream if the segmentation of the ventricles are incorrect. I have a few questions related to this: 1) To check the segmentations, should I overlay the aseg.mgz with the brainmask.mgz or the brainmask_SubjID-Temp.mgz? 2) If I find that the segmentation of the ventricle is incorrect, should I make edits to the aseg output in the longitudinal outputs? What command line would I use to re-do the longitudinal stream with the corrected segmentation? 3) After looking to see whether there are errors in the longitudinal recon-all script output, are there any other things I should check to ensure that the base and longitudinal stream ran correctly? Thank you in advance for your help! Tamara

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Question regarding Checking Longitudinal Runs: Repost
by Tamara Tavares 29 Oct '16

29 Oct '16

Hello, I have a question regarding the outputs to the longitudinal processing stream. I ran my two participant's scans through the Cross, then created a Base and two longitudinal runs. I am primarily interested in looking at ventricular change over time. Other than the aseg output overlaid on the brainmask for each longitudinal time point, should I look at any other outputs to ensure the longitudinal process ran correctly? For example, should I inspect the templates to make sure they are not blurry? Should I also overlay the two longitudinal runs to inspect potential alignment problems? Thank you in advance for your help, Tamara

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Two Stage Longitudinal Model
by Timothy Hendrickson 29 Oct '16

29 Oct '16

FreeSurfer Experts, Hello I am attempting to perform a two stage longitudinal analysis. My entire data set has two time points for each participant. I understand that the subject order in the FSGD file should correspond with the QDEC file run through long_mris_slopes. In my case the FSGD file has half as many inputs as the QDEC file. My question is would I take the covariates from TP1 and TP2 and take the average to input into the FSGD file? If that is the case is there anything wrong with performing the long_qdec_table --qdec "qdec.table.dat --cross --out "cross.qdec.table.dat" command and using that co-variate data to input into the FSGD file? Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Re: [Freesurfer] T2pial and [LONG]
by Antonin Skoch 29 Oct '16

29 Oct '16

Dear experts, I am potentially also interested in correct using of -T2pial feature with longitudinal stream. The first (standard cross-sectional) and third step (-long ) was already elaborated here, but I am, however, not sure how to process by T2pial in the second step ( -base), which creates the unbiased template and process it by (almost) standard cross-sectional stream. I did not find creation of unbiased template of T2 in the recon-all code. Therefore, in order to use -T2pial on -base run, I would probably need to create my T2 template by calling mri_robust_template on my T2's first, and then pass the created T2 template as input to recon-all -base run, like: recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all -T2pial -T2 path_to_T2_template I am correct? Regards, Antonin

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Question about mri_glmfit-sim
by neuroimage analyst 29 Oct '16

29 Oct '16

Hi FreeSurfer experts, I am currently performing some cortical thickness comparisons in my group of subjects and using mri_glmfit-sim --glmdir my_dir --cache 2.3010 --cwpalthresh 0.05 --2spaces found some clusters that have significantly different cortical thickness values, Given Eklund et al PNAS paper, do you suggest I should rather use mri_glmfit-sim --glmdir my_dir --sim perm 5000 1.3 perm.pos.13 --sim-sign pos in order to convince that the results are not due to false positive? Thanks Regards

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clinical pysch programs?
by Bruce Fischl 29 Oct '16

29 Oct '16

Hi All, just a note to say that if there are any faculty in clinical psychology programs looking for a grad student for next September, you would be extremely fortunate to convince our stellar RA, Allison Moreau, to come work for you. She has done outstanding research with us for a number of years, and is applying to graduate programs for the Fall. She knows how to analyze data, run a scanner, do histology, pack samples, keep track of expderiments, manage her time independently, problem solve on her own, research and implement solutions to difficult problems and is a lovely person to boot. I strongly advise recruiting her! thanks Bruce

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tmp directory not created
by Sneha Pandya 28 Oct '16

28 Oct '16

Hi all, I am running recon-all stream for ~200 subjects and after successful run of them I observed that for some of the patients recon-all ran successfully without error but it did not create "tmp" sub-folder. Can anyone please advice when recon-all stream does not create "tmp" folder and do I need to run these subjects again even after its successful completion? Thanks, Sneha

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How to get numerical r values from analysis
by Marissa Pifer 28 Oct '16

28 Oct '16

Hi freesurfer experts, I've run into a problem of not being able to generate the numerical results of the analysis I've run through qdec.After I ran the analysis in qdec I opened the overlay in tksurfer, applied a label, and found a significant negative correlation between cortical thickness and one of our variables. I cannot figure out how to get the numerical r value of this correlation. How can I get this value? Thanks in advance Marissa

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Multiple Comparison Question for surface-based analyses
by Ajay Kurani 28 Oct '16

28 Oct '16

Hello Freesurfer Experts, Recently there were two article published regarding clusterwise simulations for volumetric fmri analyses and potential errors for underestimating clusterwise extent thresholds. 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes 2) biorxiv.org/content/early/2016/07/26/065862 One issue pointed out from these articles seems software specific, however the second issue is determining the proper clustersize. The heavy-tail nature of spatial smoothness seems to be ignored and a gaussian shape is generally assumed, leading to an underestimation of the spatial smoothness which can affect cluster size calculations. The issues are highlighted in the second article above. I created my own monte carlo simulation in Freesurfer for a specific brain template and I wanted to find out if these concerns also apply to my surface based simulations? I am not sure if it does since the monte carlo tool is a GRF simulation as opposed to an analytic equation, however given that these articles were highlighted very recently, I wanted to ensure I am running things appropriately for surface based cortical thickness/dti analyses. Thanks, Ajay

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Group analysis Cortical Thickness
by Dev vasu 28 Oct '16

28 Oct '16

Dear Freesurfer Group, I would like to perform group analysis for 50 Subjects (25 healthy controls and 25 Subjects with BLVP ) and examine the changes in cortical thickness between 2 groups, could you please kindly inform me some methods that i should adapt to perform the analysis. Thanks Vasudev

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