Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

mri_binarize command help
by Yagmur Ozdemir 19 10 Aug '17

10 Aug '17

Dear FreeSurfer experts, I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line; mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf * (I have the native oriented version of this volume template as well, and I attached a photo of the template as well) I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help Idil

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Hippocampus subfield segmentation Aborted
by Dev vasu 10 Aug '17

10 Aug '17

Dear all, I am encountering following error when i run Hippocampus subfield segmentation "run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266 Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args ". I am annexing the log file for your notice please kindly review it and let me know why its getting intermittently aborted . Thanks Vasudev

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Re: [Freesurfer] GLM error - cannot read fsgd file for reading
by Nick Corriveau-Lecavalier 10 Aug '17

10 Aug '17

Hi Freesurfer team, First, sorry making a new post, I'm having trouble with my email and I'm not able to reply directly on my yesterday's post. Here's my issue: I'm trying to make a group analysis with 3 groups using the mri_glmfit command. This it what the terminal says: Loading y from /Applications/freesurfer/subjects/fsgd/y.mgh mghRead(/Applications/freesurfer/subjects/fsgd/y.mgh, -1): could not open file ERROR: loading y /Applications/freesurfer/subjects/fsgd/y.mgh The terminal says that it cannot load the y.mgh file, which seems logic to me, since there is no such file in my folder. What is that file supposed to be? It isn't mentionned in the tutorial I've been following (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) I also attached the log file. Thank you! FYI, here is my previous discussion with Douglas about this issue: Douglas N Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 09 Aug 2017 14:17:05 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> make sure you pass the full path to the fsgd, otherwise it looks in the current folder. Also make sure it is readable by you > Hi Freesurfer team, > > > I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) > with 0 covariables at the moment, but I would like to add two > eventually. I've been following the tutorial on this link: > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write > the command it says ''cannot open g3v0.fsgd for reading''. > > > In my /subjects/fsgd file, there is my fsgd file, and my contrast > file. Am I missing an additionnal file or something? Is the format of > my files correct? > > > If it can help, here's what my fsgd file looks likes: > > > GroupDescriptorFile 1 > Title OSGM > Class Control > Class SCD > Class MCI > Variables > Input 3431566 CTL > Input 3514091 CTL > Input 4051959 CTL > Input 4344061 CTL > Input 4557550 CTL > Input 7060373 CTL > Input 7274924 CTL ETC Nick Corriveau-Lecavalier, B.Sc. (Hons) Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

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Linear Mixed Effects model
by Kasper Jessen 10 Aug '17

10 Aug '17

Dear FreeSurfer, I have a longitudinal study (patients and controls) with two time points (i.e., baseline and six-weeks follow-up). I would like to use the LME model as it can handle unequal timing and different number of time points across subjects due to missing data. I would like to test if there is an effect of (a) time (b) group and (c) group x time interaction. However, i am trouble with my design matrix X: (1) How would i write X? Thanks in advance Best regards Kasper

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Reporting age differences between groups
by Martin Juneja 10 Aug '17

10 Aug '17

Hi, I need a general advice from the experts out there. I am comparing cortical measures (thickness and volume) between controls and patients using FreeSurfer. I used 'age' and 'gender' as covariates (in fsgd file) while calculating group differences. I was wondering even if I removed the effects of 'age' and 'gender' for this comparison, should I perform and report t-test/one way ANOVA results if there are significant differences in 'age' between the two groups or there is no need to report 'age' difference results in manuscript, regardless of being significant or non-significant. Thanks.

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Hippocampus subfield
by Lin, Yizhi 10 Aug '17

10 Aug '17

Dear experts in Freesurfer, I am doing analysis on hippocampus subfield and I'm wondering if I could obtain cortical thickness data from each segmentation? Thanks so much! Best, Ariel

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convert mgh to nii problems - cannot get output file to reshape properly
by Suzanne Witt 09 Aug '17

09 Aug '17

Hi. I am having a problem similar to that previously described on the freesurfer message boards from May 2011 (Subject: mgh conversion). Unfortunately, that thread ends with Doug asking the person to send him the files in question, so there does not appear to be any sort of publicly published solution. I was sent two .mgh files with the resulting activation maps from an fMRI analysis (both left and right hemispheres) and told that the maps were in fsaverage space. I was not sent any other accompanying files. I am trying to convert them to nii format. I have tried both: 1. mri_convert filename.mgh filename.nii.gz and mri_surf2surf (as was suggested in the previous thread) 2. mri_surf2surf —sval filename.mgh —tval filename.nii —reshape —reshape-factor 6 —s fsaverage —hemi lh (I realize that the command options should be preceded by double dashes, but my email program is quite insistent about automatically formatting these to long dashes.) In both cases the when checking the output file using mri_info, the dimensions are still: 163842 x 1 x 1. Are there any suggestions as to how best to proceed? Thanks in advance, Suzanne Witt

2 1

ROI labeling?
by Sadie Marvel 09 Aug '17

09 Aug '17

Hi again Freesurfers, I am doing a surface based ROI analysis where for each subject, isomorphic ROIs of 300 vertices (centered around peak functional activations) were found on the fsaverage surface space. I was wondering if I should register these masks that I have created back to each subject's individual surface before creating labels for these ROIs, and if so, what would the registration file be to register the fsaverage space back to each subject's space? The goal of this is to be able to run mri_glmfit on just the spaces within these labels. Is there a better method? Also, each subject will have a different number of labels considering that not every ROI was present on every subject. will this be a problem when running glmfit? ?Thanks

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Optseq2 timing outputs
by Ruthie Shaffer 09 Aug '17

09 Aug '17

Hi all, I sent a message previously and just wanted to check in one more time about this question (apologies for the repeat message!). I’m using Optseq2 to generate stimulus / jitter schedules and, depending on the TR I use, in the output files I see onset times like 124.4001 (instead of 124.4) or 124.7999 (instead of 124.8). This is the command I’m using: optseq2 --ntp 75 --tr 3.2 --psdwin 0 22.4 3.2 --ev wordPair 3.2 45 --nkeep 6 --o CRtiming.2017 --nsearch 100000 --tnullmin 0 --tnullmax 6.4 Should I be concerned about the outputs (does it mean that I’ve specified something incorrectly in the above command), or is it correct to assume that something like 124.4001 just means 124.4? Anyway, thank you so much for your help on this! Best wishes, Ruth Shaffer

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VBM
by Shane S 09 Aug '17

09 Aug '17

Hello Experts, Can we do VBM in MNI template using the outputs from recon all? Which file should I be using? And how do I smooth the volumes? Thank you for the tips! -- Shane S

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