Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

freesurfer container - freeview error
by Arnaud Boré 24 Jan '20

24 Jan '20

External Email - Use Caution Dear Freesurfer' experts, I've created a singularity container from the official docker hub freesurfer repository (https://hub.docker.com/r/freesurfer/freesurfer) When running: singularity exec freesurfer.sif freeview I get this error: freeview_bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No suche file or directory. I would like to know if this is something related to the containers or the host computer and some tips to fix this. I tested the singularity on different computers/laptops and ended up with the same error so I think there is an issue with the singularity/docker container. Thank you in advance Arnaud

2 3

FreeSurfer analyses in MatLab
by Graduate Imaging 24 Jan '20

24 Jan '20

External Email - Use Caution Hello, I recently ran a vertex wise analysis on two different projects the first had three groups with three co-variates that looked at if group membership was associated with brain volume. The second project had two groups with three co-variates looking at psychiatric x BMI interaction effect on brain volume. I'm interested in running ROI analyses in matlab to ensure the same matrices were used. To run the ROI analyses I'm going to important the design matrix from the vertex wise analysis and use the fast_glmfit and fast_fratio commands as shown below: X = load('Xg.dat'); C = load('C.dat'); y = load('ROI.dat'); text file containing participant ROI values from the DKT atlas. [beta rvar] = fast_glmfit(y,X); [F pvalues] = fast_fratio(beta,X,rvar,C My first question is the beta values that are calculated from fast_glmfit are unstandardized is there anyway way to have it compute standardized values? My second question is when I ran the ROI analyses looking at the diagnosis x BMI interaction effect it outputs an array of beta values for each regressor. In addition to each groups beta value (for BMI) I'm interested in the beta value of the interaction (ie diagnosis x BMI). I was wondering how do i go about obtaining this? Would I have to create a new matrix with the interaction term included in it? If so would the analysis essentially be one group with the diagnosis x BMI interaction term plus the three co-variates?

2 6

Troubleshooting FLAIR Images
by Swanson,Clayton 24 Jan '20

24 Jan '20

External Email - Use Caution Hi FreeSurfer Developers, After looking through the archives my question still remains. I am wondering if the same rules apply for editing/correcting FLAIR images as it does for T1 images. For example, can I add control points to the WM.mgz then re-run recon-all using the command recon-all - s <subject> -autorecon2-cp -autorecon3. For visualization I have attached a screenshot of what I am attempting to correct. Thank you for your help, Clayton [cid:9B76FB99-0BA6-4427-99CE-74076577DE40@hsd1.co.comcast.net.]

2 1

help: fs-fast group level analysis per run
by Rami Hamati 24 Jan '20

24 Jan '20

External Email - Use Caution Hello freesurfers, I'm attempting to run second-level analysis on separate runs of a brain scan, that were generated by selxavg3-sess -run-wise (pr001, pr002, pr003, pr004) as described in selxavg3-sess --help. But, when attempting to concatenate the data using isxconcat-sess, (as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLev… ) there is no similar -run-wise function. I've searched the list and no similar errors have been reported.. I am wondering if there is a command or workaround for this. Thank you very much! -- Rami Hamati, MSc. Royal's Institute of Mental Health Research Molecular Imaging Laboratory (MIL) 1145 Carling Ave, Ottawa, ON K1Z 7K4 Rami.Hamati(a)theroyal.ca rhama036(a)uottawa.ca

2 1

Mean thickness values from sig.mgh
by Amrita Bedi 24 Jan '20

24 Jan '20

External Email - Use Caution Hello Freesurfer developers, I wanted to extract mean thickness values of all participants from the uncorrected significance maps obtained from mri glmfit for structural data instead of extracting it from the corrected maps from glmfit sim. Is there a way to do this? Thank you. Amrita

2 1

global measures of volume bug
by Christian Krog Tamnes 24 Jan '20

24 Jan '20

External Email - Use Caution Dear FS experts, I came across this post about a bug related to global measures of volume from version 6.0: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed I have two questions that I hope someone can clarify: 1) This bug does not affect measures of cortical thickness or area, or specific subcortical volumes, correct? 2) For longitudinally processed data, is it sufficient to run the proposed solution (recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels) on the longitudinal data, or do we need to first do it on the cross-sectionally processed data? Best regards, Christian

2 1

Qdec error
by vittal korann 24 Jan '20

24 Jan '20

External Email - Use Caution Dear FreeSurfer experts I ran QDEC and got the following error. Design matrix ------------------ 1.00000 1.04000 -1.38574 2.00000 29.00000 19.00000; 1.00000 1.04000 -0.55066 2.00000 35.00000 19.00000; 1.00000 1.03000 2.31721 2.00000 23.00000 14.00000; 1.00000 1.03000 -0.22919 2.00000 23.00000 16.00000; 1.00000 1.03000 -2.69688 -2.00000 28.00000 19.00000; 1.00000 1.01000 0.84981 -2.00000 22.00000 19.00000; 1.00000 1.01000 0.43845 2.00000 36.00000 21.00000; 1.00000 1.06000 1.32888 2.00000 28.00000 17.00000; 1.00000 1.02000 0.52292 2.00000 34.00000 22.00000; 1.00000 1.02000 0.18104 2.00000 32.00000 17.00000; 1.00000 1.03000 -0.33783 -2.00000 32.00000 22.00000; 1.00000 1.04000 0.65805 2.00000 30.00000 17.00000; 1.00000 1.03000 1.21888 2.00000 37.00000 10.00000; 1.00000 1.02000 2.11598 2.00000 29.00000 10.00000; 1.00000 1.02000 -0.02853 2.00000 27.00000 16.00000; 1.00000 1.04000 0.21777 2.00000 36.00000 16.00000; 1.00000 1.01000 0.30821 2.00000 29.00000 15.00000; 1.00000 1.03000 -0.69389 2.00000 30.00000 12.00000; 1.00000 1.04000 0.44792 2.00000 23.00000 15.00000; 1.00000 1.03000 0.15876 2.00000 28.00000 15.00000; 1.00000 1.02000 -1.05796 2.00000 36.00000 10.00000; 1.00000 1.05000 -1.51878 2.00000 32.00000 15.00000; 1.00000 1.03000 -0.91870 -2.00000 30.00000 15.00000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 68200 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label /usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5) The scale is much different between columns 1 and 5, you may want to normalize by subtracting the mean and dividing by the standard deviation. Any help would be appreciated! With regards Korann

2 3

Qdec and TkSurfer input boxes
by Marcos Martins da Silva 24 Jan '20

24 Jan '20

External Email - Use Caution Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click inside the box and even select the content but it seems read only: I can't change it. So it is impossible to see the scatter plot from a specific vertex inputing its number. Any clue about what happened and how to fix it? Thank you for your attention.

2 5

Re: [Freesurfer] Hippocampal subfield validation
by Iglesias Gonzalez, Juan E. 24 Jan '20

24 Jan '20

Dear Dawn, Thank you very much for your interest in the tool, but we do not have such a dataset, sorry! Having said that, I don’t think the alveus should make a big difference in Dice scores… Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Dawn C. Matthews" <dmatthews(a)admdx.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 23 January 2020 at 20:36 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal subfield validation External Email - Use Caution Dear Freesurfer Team, Thank you for your work on the segmentation and analysis tools that have been provided through Freesurfer and that have been used so widely. We are wondering if there is a T1 image data set available for which manual delineation of the boundaries of the hippocampal subfield summation has been performed, and whether the images and masks might be available for DICE comparison to the masks and volume produced by FS in users’ hands? We note that the subfield summation does not include the alveus and therefore direct comparison to masks generated using standard manual hippocampal segmentation protocols is not straightforward. With thanks and best regards, Dawn Matthews Dawn C. Matthews CEO, ADM Diagnostics, Inc. 555 Skokie Blvd., Suite 500 Northbrook, Illinois 60062 dmatthews(a)admdx.com<mailto:dmatthews@admdx.com>

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Re: [Freesurfer] Hippocampal subfield validation
by Dawn C. Matthews 23 Jan '20

23 Jan '20

External Email - Use Caution Dear Freesurfer Team, This is a follow on to the question regarding manual validation results for the FS 6.0 hippocampal subfield total mask. Could you please also comment on the similarities and differences between the hippocampal subfield summation (ORing of the subfields) and the HARP manual protocol definition, and whether FS 6.0 aseg hippocampus and the subfield summation have been directly compared to the HarP validation set (Boccardi et al, 2015) using a DICE approach on same subjects? These questions pertain to the hippocampal subfield segmentation atlas prior to the more recent inclusion of amygdala, but the same questions regarding manual validation images and masks would apply for the latter as well. Thanks again, Dawn Matthews

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