Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Problems setting the directory
by Rosalia Dacosta Aguayo 18 Oct '18

18 Oct '18

External Email - Use Caution Dear Free Surfer team, Surely this is a basic question but I am having a trouble setting the subjects_dir in my terminal and, as a result, any of the commands work. This is how I have my Free Surfer configurated in my computer: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 -------------------------------------------------------------------------------------------------------- As it is, I cannot work in the SUBJECTS_DIR, as it is protected. I tried to set a new subjects_dir: export SUBJECTS_DIR=/home/rosalia/Desktop Then I try to run the first step (autorecon1) with one subject, and it appears the following error: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s 001 -autorecon1 *ERROR: cannot find /usr/local/freesurfer/subjects/001* rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ I have even changed my .bashrc file...but it seems I am doing something wrong as my terminal keeps pointing to the same subject_dir. I have tried to use sudo so in order to move my folder and subfolders to the subjects_dir set by default, and I am experiencing problems as well. I would much appreciate any help with this basic question. Kind regards, Rosalia

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Computing relative cortical measures maps instead of absolute cortical measures maps
by Angela Martina Mueller 18 Oct '18

18 Oct '18

External Email - Use Caution Hi, I am referring to a paper of Vuoksimaa et al. 2016. The authors used relative instead of absolute cortical measures (cortical thickness and surface area) to compute individual vertex-cognitive ability correlations throughout the cortex. To compute individual relative cortical thickness and surface area maps of each individual subjects, the authors divided the surface area value at each vertex by the total surface area (sum across all vertices for each subject) and subtracted the mean cortical thickness value (for each subject) from the thickness at each vertex. I would like to use the same approach (relative CT and SA maps instead of absolute maps) for one of the projects of our lab. In the Freesurfer mailing list, I found that the command "fscalc" can be used for simple mathematical transformations of mgh files. Therefore my question: Would it be correct to use “fscalc” with the option “sub” resp “div” to compute these relative cortical measures maps for each of my subjects? Thank you for helping me with this question Angela

1 0

autorecon1 with skull stripped image
by Rosalia Dacosta Aguayo 18 Oct '18

18 Oct '18

External Email - Use Caution Dear Free Surfer's team, I have a doubt. I have a sample of patients in which I already have done the skull stripping using specific options with bet, so the skull stripping has been successful. I wonder if I could feed autorecon1 with the skull stripped image instead of the T1 image with skull. Thank you very much for your time, Rosalia

2 3

Adding longitudinal time points to clean dataset {Disarmed}
by Molly Prigge 17 Oct '18

17 Oct '18

External Email - Use Caution Hello Freesurfer experts, We have a large longitudinal dataset (n=~200) of up to 4 time points per participant. All images were processed using Freesurfer v6.0 and have already undergone QA, and editing the cross, Base or long where needed. We are finishing up collection of a 5th time point and will begin collecting a 6th time point next year (average interscan interval 2.5 years). We are running the new scans through the same Freesurfer v6.0 and same workstation as the previous time points. Is it appropriate to use the Bases already created with Times 1-4 for the 5th and 6th timepoint long file creation? We are hoping to avoid losing all the QA editing already done on the Base and long files from Times 1-4 and not have to redo all QA on Times 1-5 long files when time 6 is complete. We appreciate any guidance. Thanks! Molly --------------------------- Molly DuBray Prigge, PhD Research Associate Department of Pediatrics molly.prigge at hsc.utah.edu MRI Study Phone: 801.585.9061

2 1

Raw Data for Clusters
by WON JONG CHWA 17 Oct '18

17 Oct '18

External Email - Use Caution Dear FreeSurfer Experts, I am running Qdec 1.4 and I want to extract raw data (in this case, volume) from the significant clusters after Monte-Carlo simulation. In this particular case, the summary file shows 5 significant clusters after correction: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2018/10/16-23:28:21-GMT # cmdline mri_surfcluster --in /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh --csd /Users/user/MyInstall/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm18/abs/th13/mc-z.csd --mask /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/mask.mgh --cwsig /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.mgh --vwsig /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.vertex.mgh --sum /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.summary --ocn /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.mgh --oannot /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.annot --csdpdf /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.pdf.dat --annot aparc --cwpvalthresh 0.05 --o /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.masked.mgh --surf white # cwd /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only # sysname Darwin # hostname N-Volunteer-iMac.local # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only # SearchSpace_mm2 64328 # SearchSpace_vtx 149926 # Bonferroni 0 # Minimum Threshold 1.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 1.300000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 2.06685 at vertex 34785 # Overall min -4.82491 at vertex 356 # NClusters 5 # Total Cortical Surface Area 64328 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.825 356 2272.51 60.8 -9.4 -1.7 0.00010 0.00000 0.00020 3745 superiortemporal 2 -4.419 146292 2658.98 19.8 52.0 -5.7 0.00010 0.00000 0.00020 3104 rostralmiddlefrontal 3 -4.267 138330 1525.99 35.6 35.2 7.0 0.00460 0.00370 0.00550 1936 rostralmiddlefrontal 4 -3.304 140353 1712.65 34.9 -30.2 56.6 0.00220 0.00160 0.00280 3540 postcentral 5 -3.050 28351 1096.87 19.6 -34.8 -8.7 0.04530 0.04260 0.04800 1687 parahippocampal ------ However, when I run the command to extract the raw data from these clusters using this line: mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0 The terminal window outputs this: rh-Diff-SZ-HC-Intercept-volume user$ mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0 sysname Darwin hostname N-Volunteer-iMac.local machine x86_64 user user UseRobust 0 Loading mc-z.abs.th13.sig.cluster.mgh Loading y.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 4 segmentations Computing statistics for each segmentation 0 -4 6849 6849.000 1 -2 5476 5476.000 2 -1 1687 1687.000 Reporting on 3 segmentations Computing spatial average of each frame 0 1 2 Writing to mc-z.abs.th13.cluster.ocn.dat mri_segstats done ----- So I get a .dat file that only has 3 columns, which does not match up to the 5 that I originally observed after the correction. If you could let me know what the problem is that would be greatly appreciated. Thank you. William

2 1

Using a .asc file as overlay in freeview/tksurfer
by Worker, Amanda 17 Oct '18

17 Oct '18

External Email - Use Caution Hello, I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck. As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command: % mris_convert -c lh.thickness lh.white lh.thickness.asc I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message: % mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc. If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New Interestingly, I can load the file as a curvature file, but then can't play around with the threshold. Do you have any idea what I'm doing wrong? Any help would be appreciated! Thanks, Amanda

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license format error
by Georg Schramm 17 Oct '18

17 Oct '18

External Email - Use Caution Dear FreeSurfer Developers, I have a installed freesurfer (6.0.0-centos6_x86_64) on 2 of our linux servers. One the first server: platform: ubuntu 16.04 uname -a: Linux fermi 4.4.0-133-generic #159-Ubuntu SMP Fri Aug 10 07:31:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux It runs fine. On the second server: platform: CentOS 7.4.1708 uname -a: Linux r23g36 3.10.0-862.11.6.el7.x86_64 #1 SMP Tue Aug 14 21:49:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I get the following license format error when running recon-all: -------------------------------------------------------------------------- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 ... -------------------------------------------------------------------------- The license files are new (downloaded this week) and exactly the same on both servers (I compared the hexdumps). I also checked that I have read permissions to the license file in $FREESURFER_HOME on the 2nd server. Do you have any idea what could go wrong on the 2nd server? Bests, Georg

1 0

create label from cluster obtained with mri_glm-fit-sim
by Ting Li 16 Oct '18

16 Oct '18

External Email - Use Caution Dear Freesurfer Experts, I really need your attention and help. Thanks a lot. We want to create label through the mri_glm-fit-sim cluster results. We have found the same topic in 2013 and tried the method you have provided. However, it doesn’t work. If you think it is not the right way, could you give me an example to do it right. I really appreciate your great help. Thanks a lot. Here is my code: mri_annotation2label --subject F999 --hemi lh --annotation cache.th20.neg.sig.ocn.annot --labelbase lh.test_label Here is my error information: subject = F999 annotation = cache.th20.neg.sig.ocn.annot hemi = lh labelbase = lh.test_label surface = white Reading surface /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white Loading annotations from /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot could not read annot file /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot No such file or directory INFO: could not load from /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot, trying /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot could not read annot file /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot No such file or directory ERROR: MRISreadAnnotation() failed This is the annot files in my directory F999: ls F999/label/*.annot F999/label/cache.th20.neg.sig.ocn.annot F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot F999/label/lh.aparc.a2009s.annot F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot F999/label/rh.BA_exvivo.thresh.annot F999/label/lh.aparc.DKTatlas.annot F999/label/rh.aparc.annot

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FreeSurfer Errors (2)
by Sparsh Jain 16 Oct '18

16 Oct '18

External Email - Use Caution Hey! I sent two responses on Friday. The second response was bigger than 1 MB so it awaited moderator approval. I don't know if you received it eventually. Following up to that mail, my reconstruction on the subject with 176 images crashed after about 32 hours of execution with the error 'could not read label' and 'too many symbolic links' in fsaverage. I have attached the entire command line output. Please help me understand what I'm doing wrong ! Thanks Sparsh

2 2

fsfast preproc-sess: viewing preproc surface outputs
by Jacob Matthews 16 Oct '18

16 Oct '18

External Email - Use Caution Hi FS Team, We are running our first fsfast pipeline, and starting with a single subject to test everything. We successfully ran preproc-sess with the following command: preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -sliceorder odd -fsd bold We wanted to check the outputs. It was clear how to view most intermediate outputs, but we didn't know how to view the surface space outputs: fmcpr.odd.sm5.fsaverage.rh.nii.gz fmcpr.odd.sm5.fsaverage.lh.nii.gz Loading them into freeview as surfaces fails. We thought perhaps they needed to be loaded on top of an fsaverage surface, but didn't know where to start this process. Thanks, Jacob Matthews MRI Specialist Rotman Research Institute Baycrest Hospital 416-785-2500 ext. 3322

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