Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

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>

1 0

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

1 0

Freeview froze when trying to open volume file
by Tarui, Tomo 23 Jan '20

23 Jan '20

External Email - Use Caution Dear Freesurfer community, I have been also experiencing problem that freeview froze when I tried to select and open a new volume file. This started after I upgraded mac OS X to Catalina. Until that I have been using freeview fine for five years. Error message said Last login: Thu Jan 23 13:43:03 on ttys000 [tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer [tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl [tup09900bj11:~] tomotarui% freeview 2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited prematurely - check for a reentrant call to endModalSession: I do have read permissions for those volume files when I checked with ls -l and mri_info. I have tried cleaned up and reinstall freesurfer, which did not solve the problem. It may be unique to my computer, but I would appreciate very much for any recommendation. Tomo The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, contact the sender and properly dispose of the e-mail. Please consider the environment and the security of the information contained within or attached to this e-mail before printing or saving to an insecure location.

3 3

Hippocampal subfield validation
by Dawn C. Matthews 23 Jan '20

23 Jan '20

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

1 0

different target image for registration
by Sam W 23 Jan '20

23 Jan '20

External Email - Use Caution Hello! I would like to register my dwidata to the anatomical image (rawavg.mgz). I have run bbregister, but how can I specify a different target image? bbregister uses the orig.mgz right? These are the commands I used: bbregister --s sub001 --mov nodif.nii.gz --reg nodif2orig.dat --dti --init-fsl mri_vol2vol --fstarg --reg nodif2orig.dat --mov dwidata.nii --o dwialigned.nii mri_label2vol --regheader dwialigned.nii.g --temp mri/rawavg.mgz --aparc+ageg --o labels.nii I'm not sure if the last command is valid, because I think bbregister and mri_vol2vol use the orig.mgz, whereas mri_label2vol uses rawavg. Best regards, Sam

1 0

mri_robust_template Internal Error: Rotation should not scale
by Biles, Mandy K 23 Jan '20

23 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run the longitudinal pipeline for recon-all outside of fmriprep. The first step, cross, ran fine and I received the expected outputs. I started the base step and for most of my subjects it appears to be working but for some of my subjects I get the following error when running the mri_robust_template command: Internal Error for tp 0 -> template Rotation should not scale ( 1.23014e-05 ) I've searched the list and no similar errors have been reported outside of fmriprep forums that I can find. Does anyone have any thoughts on how to troubleshoot this issue? Also, I’ve attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Red Hat Enterprise Linux Server, VERSION=7.7 (Maipo). This is being run on a HPC server. 3) uname -a: Linux c0072 3.10.0-1062.9.1.el7.x86_64 #1 SMP Mon Dec 2 08:31:54 EST 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you, Mandy Mandy K. Biles, MS | PhD Candidate Psychology/Behavioral Neuroscience Program UAB | The University of Alabama at Birmingham CIRC Suite 252A | 1719 6th Avenue South | Birmingham, AL 35294 P: 205.975.4060 | mkbiles(a)uab.edu uab.edu<http://uab.edu>

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Freesurfer January 2020