Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

Not seeing effects of manual edits and re-running recon-all
by Kevin Miller 08 Oct '21

08 Oct '21

External Email - Use Caution Hi, I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice. Thanks

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Fmriprep transform matrix
by I. Kelleher-Unger 08 Oct '21

08 Oct '21

External Email - Use Caution Hi there, I have used fmriprep to preprocess my BOLD data. One of the outputs of this pipeline is a T1w-to-MNI transformation matrix in h5 format. I wanted to know if it is possible to apply this transformation with freesurfer tools? Thanks! Isaac

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glmfit sig file all zeros
by Pedersen, Walker Scott 08 Oct '21

08 Oct '21

Hi, I am running glmfit on some functional data (using ces.nii.gz surface files as input) using ROIs and the --mask argument, that I plan to later submit to glmfit-sim for small volume correction. I have some rois that are subcortical and some that are surfaces. For the glmfit run within the surface ROIs the output sig.nii.gz files all voxels have a value of zero. However, this is not the case for the F.nii.gz and z.nii.gz files output by the same glmfit command - they have non-zero voxels. This issue only occurs for the surface ROIs, when I run glmfit in subcortical ROIs the sig.nii.gz files look normal. The surface ROIs were created by using afnis 3dundump to create 10mm spheres from MNI coordinates. I then ran the MNI template through freesurfer, and used the regheader from this to run mri_vol2surf to put the spherical ROIs into fsaverage space. I am able to view the resulting surface ROIs projected onto the fsaverage surface in freeview, and have checked that my ces.nii.gz function files can also be overlayed onto the same fsaverage template in freeview. The output of one of the glmfit commands in question is below. thanks! WARNING: gdfReadV1: no variables on 'Variables' line found Reading source surface /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/surf/lh.white gdfRead(): reading /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles/ /fsgd.txt INFO: gd2mtx_method is dods Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.1.1 cwd /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast cmdline mri_glmfit --glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lC S+E_m_lCS-atCS+E/outputFiles/lIFG/ --y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recal l//recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz --surf fsaverage lh --fsgd /autofs/space/uriline_003/users/projects/OC D_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt --C /autofs/space/uriline_003/users/projects/OCD_NM/ walker_pedersen/data/image/main/recall/inputFiles//groupDiff.mtx --nii.gz --mask /autofs/cluster/neuromod/NIFTI/OCD_N M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz --eres-save sysname Linux hostname r440-28.nmr.mgh.harvard.edu machine x86_64 user wsp6 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E /ces.nii.gz logyflag 0 usedti 0 FSGD /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz maskinv 0 glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outp utFiles/lIFG/ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+ E_m_lCS-atCS+E/outputFiles/lIFG/ Loading y from /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_ lCS-atCS+E/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_ m_lCS-atCS+E/outputFiles/lIFG//Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.125 Pruning voxels by thr: 1.175494e-38 Found 512 voxels in mask Saving mask to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atC S+E/outputFiles/lIFG//mask.nii.gz Reshaping mriglm->mask... search space = 222.026773 DOF = 15 Starting fit and test Fit completed in 0.0002 minutes Computing spatial AR1 on surface Residual: ar1mn=0.987586, ar1std=0.043927, gstd=3.620916, fwhm=8.526606 Writing results groupDiff MRImask(): AllowDiffGeom = 1 INFO: MRImask() using MRImaskDifferentGeometry() maxvox sig=-0 F=4.36504 at index 391 0 0 seed=1632900996 mri_glmfit done

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Confusion about mean CT measures after registration
by Dongyue Zhou 08 Oct '21

08 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I use the command recon-all qcache to get filesub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file. I want to know mean CT measures of every ROI after registraion in one subject. And I know mean CT is calculated by dividing CT of all vertices by the number of vertices. Can I use fsaverage/label/?.annot as atlas to calculate mean cortical thickness of every ROI directly? Or should I transfer sub_01/label/?.annot to fsaverage ?

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Thalamus-proper gone?
by Cubillo, Ana 08 Oct '21

08 Oct '21

External Email - Use Caution Dear Freesurfer community, I am using the freesurfer version through a singularity container (https://secure-web.cisco.com/1j_Zv2QItcuWtdQRfU3BocTH20Tz0V5FYnvMZKQNUHVHrS…) in a HPC cluster. It all ent well until I extracted the subcortical regions, where I see that for all of my subjects the values of Thalamus-proper are 0. When I look further into it, I see that my FreeSurferColorLUT.txt file only includes Thalamus but not Thalamus-proper. I found this thread which mentions that the thalamus-proper was removed from recent FreeSurfer versions: https://secure-web.cisco.com/1_BT-tajm4M7yDBVb5BfWwjdB0iHk_Liz1vM5WOL3zLziL… Unfortunately, when I try to look for information online on whether they are exactly the same or whether they differ, I only found the FreeSurfer wiki page about the FreeSurferColorLUT<https://secure-web.cisco.com/1i1A_DRuhjTo1dIQFd0ggAD58K_mWkVlkDzs4I3ydFj4x2…>(i.e., look up table) which includes this note: “* Thalamus-Proper is the correct segmentation for the Thalamus.” But this is a page from 2015 so might not be up to date anymore. In this thread<https://secure-web.cisco.com/1IMfKsWyLM9gWH6vW81VZUrGlkiDnwKUtLgzVagH0ZHERn…> from 2017it was also discussed that the thalamus-proper is the correct one but it is also stated that name should be changed, so maybe they have done this now. Basically - do I need to re-run the recon-all with a different freesurfer version to extract Thalamus-proper or has this been replaced by Thalamus now? Thanks!! A

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Confusion Working with Longitudinal and Group Analysis Tutorials
by Giuseppe Miranda 08 Oct '21

08 Oct '21

External Email - Use Caution Hello, I have been looking through tutorials on the website and referencing the freesurfer mail archives, but I am a bit unsure if I am following the correct procedures for my analysis. The main source of confusion on my end stems from trying to apply tutorials (and in some cases the tutorials they reference) to my longitudinal data. I appreciate your help in advance. I have longitudinal data with scans from two time points. My variables were all collected at time point 1 (TP1). I am interested in change in cortical thickness in relation to these variables as well as interacting effects on cortical thickness; some of these variables are continuous (e.g. suvr) and some are categorical (e.g. alleles). My initial goal was to use QDEC, but I quickly learned that should use glmfit. For the purpose of understanding, I am writing in focusing on age and suvr as my variables. I started with the longitudinal tutorial. 1.) The first point of confusion came near the end of the tutorial at "long_stats_slopes". The command runs for me, but I'd appreciate a second look on whether this is correct: long_stats_slopes --qdec $SUBJECTS_DIR/long.qdec.table.dat --stats lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1 --do-spc --do-stack --time years --stack-avg [desired path]/stack-avg --stack-rate [desired path]/stack-rate --stack-pc1 [desired path]/stack-pc1 --stack-spc [desired path]/stack-spc >From there, the tutorial says to run my data through the glm tutorial. I have several points of confusion here - the first being that I'm concerned that I may not have my data set up correctly. 2.) I looked at the FSGD examples and built my file from them, and I also referenced the mail archives for similar projects to mine. I am unsure as to whether I should be using the [LONG] files created or the [BASE] files created with the longitudinal tutorial in my FSGD file. For example, if I am just looking at age and another factor (suvr) should my FSGD look like this... GroupDescriptorFile 1 MeasurementName thickness Class subject Variables age suvr Input Subject1_TP1 subject 57 0.93 Input Subject1_TP2 subject 57 0.93 Input Subject2_TP1 subject 64 1.22 Input Subject2_TP2 subject 57 1.22 Or should it point to the directories made during the [BASE] step of the longitudinal tutorial like this? GroupDescriptorFile 1 MeasurementName thickness Class subject Variables age suvr Input Subject1_base subject 57 0.93 Input Subject2_base subject 56 1.06 3.) From there, I understand that I need an individual contrast matrix for each contrast that I'd like to run. Here is what I have been using: Age: 0 1 0 Suvr: 0 0 1 Age x Suvr: 0 1 -1 4.) Next, I ran through the rest of the GLM tutorial to assemble the data and run glmfit, followed by a clusterwise comparison for multiple comparisons mris_preproc --fsgd file_name.fsgd \ --target fsaverage \ --hemi lh \ --meas thickness \ --out lh.file_name.thickness.00.mgh mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.file_name.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.file_name.thickness.10.mgh mri_glmfit \ --y lh.file_name.10.mgh \ --fsgd file_name.fsgd dods\ --C age.mtx \ --C suvr.mtx \ --C age_suvr.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.directory_name.glmdir mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces 5.) My last question is, if I want to run glmfit to analyze my data with other variables, is there anything that I have to delete or re-run on my end? From what I understand, I would only have to run glmfit and its' corrections again. I appreciate your help - I just want to make sure that I am, and that I am following these tutorials properly. Vince

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number of seeds in fcseedcor
by Nasiriavanaki, Zahra,M.D. 08 Oct '21

08 Oct '21

Hi Freesurfer experts, I was wondering how many seeds we can use in fcseedcor command? I have more than 100 seeds and when I use all those seeds in the below command, I get this error: Command: fcseedcor -s $subj -fsd rest -seed 1.dat -seed 2.dat -xreg global.waveform.dat 1 -xreg vcsf_mean.dat 1 -xreg wm_mean.dat 1 -xreg mcprextreg 6 -hpf .01 -lpf 0 -nskip 0 -sim 1000 -o cor_all.dat Error: Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.768795e-22. > In ^COperation terminated by user during fast_glmfit (line 35) Appreciate your help, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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A question regarding a Freeview command
by inbal paran 08 Oct '21

08 Oct '21

External Email - Use Caution Dear FreeSurfer developers, I am trying to run a group analysis to test for an association between *gray matter volume* and a behavioral measure of interest. reacon-all ran OK for all my subjects as well as mris_preproc followed by mri_surf2surf, and finally glmfit. Finally, I wanted to visualize the significant voxels using freeview and followed the command line in the tutorial of the group analysis ( https://secure-web.cisco.com/1_d3qazq-_19W6y1XEkeVPINXH5vgktFtuM1FrpU_HJNr4…) However, since I am talking about volume and not surface, I wasn't sure how to edit the final command to visualize my results in freeview. I want to make sure it will include significant voxels both in subcortical + cortical regions. Should I use a stats.table file as an input? As you probably understand, working with Linux and FreeSurfer are both very new to me, if it's possible, any help would be greatly appreciated. If it's relevant, these are the details of the version and platform I'm using: 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 20.04.1 LTS 3) uname -a: Linux inbal-paran 5.11.0-37-generic #41~20.04.2-Ubuntu SMP Fri Sep 24 09:06:38 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) I also attached the mris_preproc log files in case it can help Kind regards, Inbal Paran -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1TCV1fAKzZJ5GOMgMi06jDdgf5mlDmrjtvqzBaNtTAOycuW…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

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Comparing volumes before and after editing
by Kang, Jee Won 08 Oct '21

08 Oct '21

External Email - Use Caution Hello all, I'm very new to Freesurfer and have started with quality-checking recons. I wanted to know if there is a way to compare volumes before and after edits were made before recon-all has been re-run. For example, if we have brainmask.mgz that has been edited and brainmask_ORIG.mgz before any edits were made, is there a way to create a volume overlay and extract the areas where edits were made (perhaps parsed from aparc+aseg)? Thank you for your assistance on this! -Jee Won

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matlab: command not found - How can I solve this?
by Camila Fernandes da Silva 08 Oct '21

08 Oct '21

External Email - Use Caution Hey, I'm totally new into Freesurfer and I need some help with my Matlab. I tried to do "recon-all -s <.....>/ -lgi But as you can see, It shows an error related to matlab... I tried everything! But nothing is working. I have heard that we should modify the startup.m file... But, what am I supposed to do with it? I'm using the Freesurfer 7.1.0 version ----------------------------------------------------------------------- #@# Local Gyrification Index lh Fri Oct 1 15:25:01 EDT 2021 mris_compute_lgi --i lh.pial *matlab: Command not found.matlab5: Command not found.* ERROR: *Matlab is required to run mris_compute_lgi!* Command exited with non-zero status 1 @#@FSTIME 2021:10:01:15:25:01 mris_compute_lgi N 2 e 0.01 S 0.00 U 0.01 P 94% M 2784 F 0 R 736 W 0 c 11 w 15 I 0 O 0 L 0.05 0.12 0.10 @#@FSLOADPOST 2021:10:01:15:25:01 mris_compute_lgi N 2 0.05 0.12 0.10 Linux developer-VirtualBox 5.4.0-87-generic #98~18.04.1-Ubuntu SMP Wed Sep 22 10:45:04 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s controle01_T1 exited with ERRORS at Fri Oct 1 15:25:01 EDT 2021 For more details, see the log file /home/developer/freesurfer/controle01_T1/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1cisSzDB61L2V_wjkzh5VutTxw6cDnzHhZoLYWlTI2KVRLa… -- Atenciosamente, Camila Fernandes Licenciatura em Física - IFUSP

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Freesurfer October 2021