Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

QDEC error Two Groups three covariates
by Mikael Novén 21 May '20

21 May '20

External Email - Use Caution Dear FreeSurfer Developers, I’m attempting to run a cortical thickness correlation analysis regressing out the effect of brain size, age and gender. However, when attempting to run this analysis in qdec (or trying to use mri_glmfit separately) I get the following error: "MatrixMultiplyD(): m2 is null break matrix.c:415 No such file or directory” Full output from the mri_glmfit call is last in this mail. The first lines of my fsgd files look like this: "GroupDescriptorFile 1 Title RTfMRI Class M Class F Variables RT eICV Age Input 101 M 36.767 1046505.93 25 Input 102 F -58.589 955597.34 30 Input 103 M 68.883 1107660.32 22” My contrast matrix looks like this: "+0.00000 +0.00000 +1.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000” Any help is much appreciated. Kind regards, Mikael mri_glmfit --y lh.thickness.fMRIRT_revision.10.mgh --fsgd fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex --glmdir fMRIRT_revision_test2 gdfRead(): reading fMRIRT_age_gender_eICV.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 RT 82.6508 76.4669 1 eICV 980394 122148 2 Age 24.5294 3.23797 Class Means of each Continuous Variable 1 M 97.4687 1037828.2188 25.0000 2 F 74.5684 949066.0966 24.2727 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Applications/freesurfer/subjects cmdline mri_glmfit.bin --y lh.thickness.fMRIRT_revision.10.mgh --fsgd fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex --glmdir fMRIRT_revision_test2 sysname Darwin hostname LUMAC1089 machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh logyflag 0 usedti 0 FSGD fMRIRT_age_gender_eICV.fsgd labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir fMRIRT_revision_test2 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory fMRIRT_revision_test2 Loading y from /Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to fMRIRT_revision_test2/Xg.dat Computing normalized matrix Normalized matrix condition is 3815.6 Matrix condition is 1e+08 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149078 voxels in mask Saving mask to fMRIRT_revision_test2/mask.mgh Reshaping mriglm->mask... search space = 74130.630564 DOF = 9 Starting fit and test Fit completed in 0.0511667 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995881, ar1std=0.003426, gstd=6.299149, fwhm=14.833361 Writing results RT_covNI_cp maxvox sig=-4.61019 F=62.3686 at index 156731 0 0 seed=1590285961 MatrixMultiplyD(): m2 is null break matrix.c:415 No such file or directory

2 1

Recon-all error in CA Normalize (FreeSurfer V 7.1)
by Schranzer René 21 May '20

21 May '20

External Email - Use Caution Dear Freesurfer experts, I'm trying to recon-all (-hires) for a new subject (mp2rage image) using the FreeSurfer Version 7.1. However, the recon-all exited with errors at the "mri_ca_normalize". I also processed the same subject from different timepoints and they finished without errors. The error log is as following: #@# CA Normalize Sat May 16 12:43:31 CEST 2020 /data/disk_1/IP/MS/freesurfer/MS_MRS_03_TP1_MP2RAGE/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (74, 87, 47) --> (250, 243, 247) finding center of left hemi white matter using (133, 139, 147) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (111,120,122) --> (154, 158,171) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 108 +- 4.3 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246437 sample points... INFO: compute sample coordinates transform 0.82947 -0.03916 0.01418 -3.56121; 0.02560 0.95026 0.20358 -65.47982; -0.02149 -0.16312 0.83311 18.21485; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (162, 90, 50) --> (242, 211, 245) double free or corruption (out) Command terminated by signal 6 @#@FSTIME 2020:05:16:12:43:32 mri_ca_normalize N 8 e 52.08 S 0.30 U 41.78 P 80% M 793644 F 0 R 213860 W 0 c 1239 w 3 I 0 O 0 L 10.49 12.64 12.79 @#@FSLOADPOST 2020:05:16:12:44:24 mri_ca_normalize N 8 10.29 12.25 12.65 Linux twodogs 4.15.0-88-generic #88-Ubuntu SMP Tue Feb 11 20:11:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MS_MRS_03_TP1_MP2RAGE exited with ERRORS at Sat May 16 12:44:24 CEST 2020 I am thankful for any help. Best, René

2 1

-T2pial after white matter edits
by Octavian Lie 21 May '20

21 May '20

External Email - Use Caution Dear All, I ran recon-all on the 1st run using the -T2pial flag. After wm.mgz edits, when running recon-all autorecon2-wm -autorecon3 -T2pial volT2.mgz it throws an error ~ 'flag volT2.mgz not recognized'. When reruning recon-all as above, do we need to include the T2pial flag to make use of the t2 pial information? If not, is the previous T2pial output used to regenerate the pia? Thank you, OL

2 3

Problem with single subject retinotopy visualization using tksurfer-sess
by Kasia Siuda-Krzywicka 21 May '20

21 May '20

External Email - Use Caution Dear FreeSurfer community, I am running a retinotopy analysis using FSFAST and I encountered a problem with data visualisation. To perform my analysis I followed the official guidelines found here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis and the following tutorial: https://kylemathewson.com/retinotopy-in-freesurfercnl-protocol/#FUNC The pipeline worked and I didn't get any error messages. I now want to visualise my single subject data to make sure that everything worked fine. As suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I run a command: tksurfer-sess -s 2016_09_23_NBI_AMJU -hemi lh -analysis retino.self.lh Unfortunately, it doesn't work and returns the following error message: /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' I attached in this mail a print screen with the logs of the operation. I believe that the program is supposed to create a file: retino.self.lh/tksconcat.nii but I don't find it in my analysis folder. Could anyone help me resolve this issue? Thank you! Kasia [image: image.png]

2 1

the result of '1 -1' and '1 -1 0 0 0 0' are different
by John 21 May '20

21 May '20

External Email - Use Caution Hi friends, (1) I have two groups, I set '1 -1' in .mtx file. (2) I add two variables in the .fsgd file, and set '1 -1 0 0 0 0' in the corresponding .mtx file. While, after run mris_preproc, mri_glmfit, I found the result of (1) and (2) are different. [e.g. freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh] I think the result of '1 -1' and '1 -1 0 0 0 0' will be same, right? Thanks John

2 1

FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z"
by Safi Ullah . 21 May '20

21 May '20

External Email - Use Caution Dear Freesurfer, Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using the command below ls *.nii | parallel -jobs 8 recon-all -s {.} -I {} -all –qcache (also checked with this one find . -name '*.nii' | parallel -j 8 recon-all -s {.} -i {} -all -qcache) but each time i face the same error as attached with the mail. I checked the transformation folder, but the said file, talairach.m3z, is not there. the error is not same for all cases, some cases showed a different errors, stating "IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH:" as attached file recon-all(2nd type).log Regards

3 6

Volume timeseries to native and fsaverage
by özenç taskin 21 May '20

21 May '20

External Email - Use Caution Hello Freesurfer developers, I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer. I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation: 1 - Create a register.dat by using fsl identity matrix since I am already in the native space: tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat> 2 - Then, using this register.dat to make surfaces from the 4D timeseries with: mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz> I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this. Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ? Best, Ozzy

3 5

qdec and mris_anatomical_stats help
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 21 May '20

21 May '20

External Email - Use Caution Dear Freesurfer experts, Hope everyone is doing well! Could someone please clarify some things about mris_anatomical_stats, done after running qdec + mapping label to all subjects? From what I can understand, the following code should be used: mris_anatomical_stats -l lh.supramarg.label \ -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh But if I created the ".label" file directly on qdec, by "mapping label to all subjects", and didn't use the mri_label2label code for "target subjects", how should I work around this to perform mris_anatomical_stat correctly? Also, I'm confused on when + where this "lh.thickness" file is created and stored. Please let me know if you need any other information about my code or my qdec output. Thank you, Alex Job Said

2 2

question on partial volume correction
by Barletta, Valeria 21 May '20

21 May '20

Dear Freesurfers, We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white matter and outside the pial surface? Thanks a lot, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823

1 0

longitudinal trac -prep missing outputs
by Zeng, Qi 21 May '20

21 May '20

External Email - Use Caution Hi, I was running longitudinal trac-all. After the 3rd step -path was finished, I found that multiple pathways were missing (e.g. fminor). I traced back, realizing outputs from its first step trac-prep were missing corresponding pathways in SUBJ_base/dlabel/mni/fminor. However, the scripts of SUBJ_base_long_ses-1 and ses-2 both claimed "trac-preproc finished without error". I double checked the bval, bvec and DTI and increased the memory limit, the same problem still exists. So I was wondering how to fix it. Attached the compressed log file of SUBJ_base of trac -prep (too big). Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Freesurfer May 2020