Freesurfer March 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
161 discussions

thalamic segmentation analysis
by Parisi Veronica 28 Mar '20

28 Mar '20

External Email - Use Caution Hi there, I have been trying to learn and set-up Freesurfer for a research project I am working on, but I am having trouble with the set-up/installation process. Once Freesurfer is set-up, I will be using it to measure thalami and define their sub nuclei. I have followed the instructions online to the best of my ability but can't seem to figure this out. Any assistance would be very much appreciated. Thank you. Best, VP Rispetta l'ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.

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Re: [Freesurfer] hippocampal-subfields-T1 error
by Iglesias Gonzalez, Juan E. 28 Mar '20

28 Mar '20

Dear Aleks, Please try: chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/* Cheers, /Eugenio 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 "Duvnjak, Aleksandar" <aleksandar.duvnjak16(a)imperial.ac.uk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, March 27, 2020 at 14:39 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal-subfields-T1 error External Email - Use Caution Dear FreeSurfer Experts, FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platform: Secure Shell port of a high performance computer (HPC) accessed via Ubuntu 18.04 WSL Having processed a cohort of 1mm^3 MRI images via the recon-all command, we have had issues processing the hippocampal subfield command as described: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields Although we eventually want to run the command in array, we are currently attempting it on individual subjects to ensure a good output. Upon running the command we receive a "permission denied" error. The HPC is a shared cluster, and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot edit, and thus couldn't download the Matlab runtime to. We initially thought this may be the issue, and so tried multiple workarounds, including copying the entirety of the FreeSurfer installation package from the shared directory to our own directory, within which we have editing permissions. This didn't help, even when setting our personal directory as the FREESURFER_HOME. As you can see from the end of the recon-all.log file, we tried numerous attempts with various workarounds and all have the same outcome. I appreciate this may still be more of an issue with running FreeSurfer via a secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, but I'm sure you have many research labs asking questions regarding using HPC systems to run FreeSurfer, so any recommendations or thoughts would be welcome. Kind Regards, Aleks Duvnjak

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Re: [Freesurfer] Registration file types confusion
by Xiaojiang Yang 27 Mar '20

27 Mar '20

External Email - Use Caution Hi Douglas, The link you gave to me ( <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) has some information about .dat file, but no information about .lta file at all. I cannot see a clear relationship between .lta and .dat files. I have a script that's using the matrix from .dat file. I need to use the .lta to get that matrix. Could you please tell me how do I get the transformation matrix (as found in .dat file, line 5-7) given only the .lta file? Thank you! Xiaojiang

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hippocampal-subfields-T1 error
by Duvnjak, Aleksandar 27 Mar '20

27 Mar '20

External Email - Use Caution Dear FreeSurfer Experts, FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platform: Secure Shell port of a high performance computer (HPC) accessed via Ubuntu 18.04 WSL Having processed a cohort of 1mm^3 MRI images via the recon-all command, we have had issues processing the hippocampal subfield command as described: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields Although we eventually want to run the command in array, we are currently attempting it on individual subjects to ensure a good output. Upon running the command we receive a "permission denied" error. The HPC is a shared cluster, and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot edit, and thus couldn't download the Matlab runtime to. We initially thought this may be the issue, and so tried multiple workarounds, including copying the entirety of the FreeSurfer installation package from the shared directory to our own directory, within which we have editing permissions. This didn't help, even when setting our personal directory as the FREESURFER_HOME. As you can see from the end of the recon-all.log file, we tried numerous attempts with various workarounds and all have the same outcome. I appreciate this may still be more of an issue with running FreeSurfer via a secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, but I'm sure you have many research labs asking questions regarding using HPC systems to run FreeSurfer, so any recommendations or thoughts would be welcome. Kind Regards, Aleks Duvnjak

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Volume-defined roi
by Erik Lindberg 27 Mar '20

27 Mar '20

External Email - Use Caution Hi I am reading your tutorial about how to extract Cortical Thickness of a volume-defined ROI Wonder if there is a script that would run these steps in a bach particularly the steps that needs to be done on each individual subjects: map subject thickness data to the fsaverage and run mri_segstats to extract mean thickness Best Olof

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Fwd: recon-all-lh error : cannot allocate memory
by Jong-eun Lee 27 Mar '20

27 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to test Fmriprep pipeline for HBN datasets. But I got an error: CORRECTING DEFECT 158 (vertices=200262, convex hull=34956, v0=308501) Excessive topologic defect encountered: could not allocate -993586868 edges for retessellation Cannot allocate memory Linux cnir14 2.6.32-754.23.1.el6.x86_64 #1 SMP Thu Sep 26 12:05:41 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-NDARAC853DTE exited with ERRORS at Mon Mar 23 18:37:34 KST 202 I attach recon-all-lh log file. ᐧ ᐧ

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selxavg3-sess not working
by Nasiriavanaki, Zahra 27 Mar '20

27 Mar '20

Hi Freesurferers I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly, the terminal output shows that it doesn't need updating for preprocessing and ends with this: "Started at Thu Mar 12 10:48:09 EDT 2020 Ended at Thu Mar 12 10:48:12 EDT 2020 preproc-sess done". It seems that it just checks the preprocessing, but does not initiate the selxavg analysis. There is no error neither selxavg log file. my command: selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh -force I appreciate any comments on this issue. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Permutation with Non-Ortohgonal Matrices
by Hua, Jessica 27 Mar '20

27 Mar '20

External Email - Use Caution Hi FreeSurfer Experts, I am trying to correct for multiple comparisons by running a permutation for a non-orthogonal design. Based on reading through the blog, I came up with the follow script: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --sim perm-resid 1000 3.0 --sim-sign abs --cwp 0.05 --2spaces I am getting the following error message: ERROR: Flag abs unrecognized. And when I tried to put the "abs" after "1000 3.0," I got the error message saying that I needed to specify the --sim-sign. Could you please let me know how I need to edit my script? I have already run mris_preproc and mri_glmfit. Thanks! --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Registration file types confusion
by Xiaojiang Yang 27 Mar '20

27 Mar '20

External Email - Use Caution Hi everyone, I am confused by the two types of registration files: .lta and .dat. .dat file is simpler and easier to understand. But for the .lta files, there seems to be no detailed explanation regarding it. Can anyone point out to me where can I find the detail explanation of the file? And, what's the relationship between .lta and .dat file? Also, .lta files seem to cause some compatibility issues. For example, if I use the tkregister2 utility to make some changes to the registration file of type .lta (generated by bbregister), like below tkregister2 --mov $someSeries --reg $SUBJECTS_DIR/$subjectid/mri/transforms/FLAIR.auto.lta --surf pial and save it from the GUI, then many errors occur in the console window, like below: ...... MatrixAsciiReadFrom: could not scanf parms ERROR: TransformLTA2RegDat(): type = 2011264000, must be 1 or 0 or 14 Segmentation fault (core dumped) Actually that is because the registration file has been saved in the format of .dat, although the file extension is still .lta, and the tkregister2 program finally cracks when reading the newly saved .lta file. Anyone can solve my confusion? Thank you!

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Using mri_glmfit to regress out wm and ventricle signal
by Mcnorgan, Christopher 27 Mar '20

27 Mar '20

External Email - Use Caution I’ve been using mri_glmfit to regress out motion correction parameters and linear trends and saving residuals in surface space by first generating a QA matrix for the volume: mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \ --glmdir ${source_dir}/${r}/{hemi}.detrend \ --qa \ --surf ${SURFTOUSE} lh Then merging the QA and MC matrices into a single matrix of nuisance regressors: paste ${source_dir}/${r}/lh.detrend/Xg.dat mcprextreg > nuisance And finally, regressing out the nuisance values and saving the residuals mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \ --glmdir ${source_dir}/${r}/${hemi}.detrend \ --X nuisance \ --no-contrasts-ok --save-yhat --eres-save \ --surf ${SURFTOUSE} ${hemi} Is there a straightforward way of obtaining mean white matter and csf signal in my nuisance regressor matrix? I was unable to find any preprocessing step or application of mri_glmfit that will provide these values or regress out these values automatically. (Also note: the —qa flag is not documented in the mri_glmfit help; I must’ve learned of it from a previous email to this list) Thanks /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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Freesurfer March 2020