Freesurfer

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30132 discussions

mri_surf2vol
by Rockers, Elijah D. 10 Aug '17

10 Aug '17

I am attempting to create a volume from a surface. My ultimate goal is to obtain a mask that includes everything "inside" the white matter surfaces. wm.mgz is close, but it would nicer to just get a mask from lh.white and rh.white. I would like these masks to be in the subject's native space. However I try the following command and see the resulting error: mri_surf2vol --o coleMRI06162006/mri/lh.white.mask.mgz --mkmask --hemi lh --identity coleMRI06162006 --template coleMRI06162006/mri/orig/orig.mgz gdiagno = -1 Using identity matrix for registration mghRead(coleMRI06162006/mri/orig/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading coleMRI06162006/mri/orig/orig.mgz header I'm obviously doing something wrong here, but I'm not sure what needs to change. I used --identity because native space, and it wouldn't let me run the command without specifying --template, which I'm not sure I understand, because, again, target is native space. Please illuminate me, Thank you, - Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Talairach error
by Yagmur Ozdemir 19 10 Aug '17

10 Aug '17

Hello FreeSurfer experts, I have been running into a consistent problem of Talairach alignment error in my recon-all for some of my subjects, even though I was able to get a completed recon-all for other subjects by using the same procedure to obtain my nifti files. I have attached the recon-all logs of a successful and a Talairach failed subject respectively, and as I try to understand the difference, in the successful one this was tried the last: INFO: Trying MINC mritotal to perform Talairach align... then failed, then there is a "New invocation of recon-all " which succeeded. I do not think I made that invocation. Could someone help me figure out what I am missing, and how can I make recon-all continue as I somehow did previously? Thank you so much! Idil

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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

2 1

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

2 1

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.

2 1

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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