Freesurfer

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30132 discussions

(No Subject)
by KennethSPrice 11 May '20

11 May '20

External Email - Use Caution Hello Freesurfer friends! I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \ --osgm \ --surf fsaverage lh I am getting an ERROR: DOF = 0. MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR. What is the cause of the error? Thanks, Ken Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as one of the nation’s top hospitals by U.S. News & World Report (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 5

tkmedit in FreeSurfer 7.0
by Dincer, Aylin 11 May '20

11 May '20

External Email - Use Caution Hi FreeSurfer Experts, We are unable to use tkmedit using FreeSurfer 7.0 (centos 7). In the .xdebug_tkmedit file, it outputs the following error: "Tcl_Init returned 1: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4" It looks like when we manually set the environmental variable TCL_LIBRARY to point to the tcl location in the $FREESURFER_HOME folder, tkmedit will open. Is there a way to fix this so it automatically sets this environmental variable? Thanks! Aylin _____________________________ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging Core, Benzinger Lab 314-362-3629 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

Re: [Freesurfer] Hippocampus
by Iglesias Gonzalez, Juan E. 11 May '20

11 May '20

Dera Elisabetta, Can you please give us some more detail on what you mean by “I am trying to translate the same subdivision to MRI acquisition for spectroscopy purposes.”? 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 "Del Re, Elisabetta" <Elisabetta_DelRe(a)hms.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, May 11, 2020 at 09:42 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampus Dear Freesurfer team, I have analyzed the anterior/posterior hippocampus successfully utilizing FS6.0. I am trying to translate the same subdivision to MRI acquisition for spectroscopy purposes. Do you have suggestions? Thank you very much, regards, Elisabetta

3 7

Downloading Matlab runtime - ubuntu
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 11 May '20

11 May '20

External Email - Use Caution Dear Freesurfer experts, I'm trying to download runtime for ubuntu using the instructions on the website and I'm struggling to resolve this error (seen below). Any ideas on how to fix this? Thank you and hope everyone is safe! cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_inst… -o fs_install_mcr && chmod +x fs_install_mcr % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file fs_install_mcr: Permission denied 68 1988 68 1371 0 0 4436 0 --:--:-- --:--:-- --:--:-- 4422 curl: (23) Failed writing body (0 != 1371) alex@ubu19:/usr/local/freesurfer/bin$ fs_install_mcr R2012b % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 177 100 177 0 0 77 0 0:00:02 0:00:02 --:--:-- 77 Archive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive. unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period. Thank you, Alex Job Said

3 3

Get Atlas surfaces in subject space
by Ian 11 May '20

11 May '20

External Email - Use Caution Hi Freesurfers. I have a subject S with recon-all having been run on it. I have the subject-specific surface files /surf/lh.pial, rh.pial, lh.white, and rh.white. I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in subject space. Any helpers on how to achieve this? Thanks, Ian -- *Ian Hardingham*

5 29

Re: [Freesurfer] Recon-all exited WITH errors
by Mason Wells 11 May '20

11 May '20

External Email - Use Caution Hi Doug, Not sure if my email below got to you? I sent the terminal outputs of the command you told me to run. Any idea what’s going on or how to fix it? Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, 4 May 2020 at 20:01 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} External Email - Use Caution Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below: mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz... reading input surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white... reading input pial surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial... reading input white surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white... reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1698 1132 3274 2.730 0.526 0.130 0.032 26 2.4 caudalanteriorcingulate 4375 2908 8369 2.594 0.599 0.127 0.040 46 7.0 caudalmiddlefrontal 3883 2464 5378 2.087 0.498 0.149 0.082 74 9.4 cuneus 546 373 1423 2.817 0.999 0.154 0.087 11 1.9 entorhinal 5411 3506 10979 2.768 0.567 0.137 0.059 101 14.8 fusiform 6159 4159 11629 2.543 0.520 0.133 0.045 86 11.0 inferiorparietal 5973 3945 13736 2.965 0.705 0.138 0.060 130 13.4 inferiortemporal 1536 934 2788 2.725 0.838 0.164 0.090 50 5.1 isthmuscingulate 6953 4476 11030 2.320 0.542 0.147 0.055 110 15.3 lateraloccipital 3897 2512 7780 2.641 0.630 0.147 0.077 99 13.1 lateralorbitofrontal 5273 3237 7567 2.161 0.603 0.151 0.956 191 20.8 lingual 2015 1290 4210 2.576 0.773 0.157 0.084 64 6.5 medialorbitofrontal 6073 4091 14456 3.026 0.553 0.130 0.043 80 11.0 middletemporal 1012 711 2254 2.886 0.735 0.133 0.112 16 6.3 parahippocampal 2182 1401 4296 2.690 0.669 0.128 0.044 26 4.5 paracentral 3247 2175 6722 2.682 0.501 0.121 0.038 34 5.1 parsopercularis 1195 793 2520 2.549 0.514 0.138 0.045 21 2.1 parsorbitalis 2780 1882 5377 2.457 0.608 0.131 0.043 37 5.0 parstriangularis 2229 1444 2359 1.685 0.476 0.155 0.067 41 6.1 pericalcarine 7692 4818 11728 2.218 0.657 0.130 0.053 114 16.0 postcentral 1983 1360 4109 2.902 0.617 0.167 0.079 44 6.1 posteriorcingulate 7681 4765 13220 2.521 0.549 0.123 0.056 119 15.1 precentral 6240 4189 11573 2.532 0.576 0.145 0.052 104 13.3 precuneus 1613 992 3166 2.820 0.661 0.136 0.055 54 3.6 rostralanteriorcingulate 6644 4495 12118 2.347 0.579 0.144 0.052 117 13.9 rostralmiddlefrontal 12967 8768 28469 2.839 0.612 0.132 0.047 170 25.1 superiorfrontal 7963 5213 12201 2.095 0.481 0.125 0.053 125 16.2 superiorparietal 9021 6069 20753 3.059 0.612 0.130 0.050 183 19.9 superiortemporal 7970 5269 15543 2.684 0.502 0.149 0.074 910 17.4 supramarginal 702 454 1432 2.844 0.618 0.133 0.046 8 1.3 transversetemporal 2953 1947 6539 3.228 0.801 0.124 0.056 33 6.4 insula Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, 4 May 2020 at 19:56 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} Something else has gone wrong. wm.mgz should have been there in order to get as far as it did. Is your SUBJECTS_DIR set properly? On 5/4/2020 2:49 PM, Mason Wells wrote: External Email - Use Caution Hi, Terminal output is below: /Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz... mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 From: <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, 4 May 2020 at 18:54 To: "freesurfer(a)nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited WITH errors Unfortunately, the log file does not indicate what went wrong. But it does show that the error happened on the LH (so it is not just RH). Run the command below and send all terminal output cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white On 5/4/2020 1:34 PM, Mason Wells wrote: External Email - Use Caution Hi Experts, I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…>

2 7

averaging timecourses
by Nasiriavanaki, Zahra 11 May '20

11 May '20

Hi Freesurfer experts I have extracted the time course of a task fMRI data in a specific contrast and within a specific ROI, in 7 subjects. Consider my specific ROI has 1200 voxels and I extracted the time course for a duration of 5 TRs. After extracting the timecourse, I have a matrix of 1200x5 for each subject. To calculate the average timecourse, I concatenated the matrices for the 7 subjects and made one matrix of 8400x5. Then I averaged across columns which gives me one mean per column. I also calculated the standard error for each column. My question is if this voxel wise way of averaging and calculating the standard error is statistically correct or not. I deeply appreciate any comments on this. Thanks a lot Mona

2 1

T1 recon -all error "XL defect detected"
by Zeng, Qi 11 May '20

11 May '20

External Email - Use Caution Hi, I've conducted longitudinal T1 recon-all. One subject's last-scan ran into error in the first independent recon all step: " recon-all -s SUBJ1 -SUBJ1.nii -all'. Error: "CORRECTING DEFECT 0 (vertices=14101, convex hull=2297, v0=1419) XL defect detected...". Log file attached below. I've increased the memory usage limit as some suggestions did, but no help. Also T1.nii looks fine, same parameter setting as first scan, also attached below. Subject first scan and all the other subjects were finished without errors. Can you help figure out what has caused it? Thank you so much! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

3 12

segmentHA_T1.sh outputs "Error using myMRIread (line 16)"
by Soichi Hayashi 11 May '20

11 May '20

External Email - Use Caution Hello. I am testing freesurfer 7.0.0 with segmentHA processing. I've run recon-all successfully, and now I am trying to run "segmentHA_T1.sh". When I do, it generates the following error message. $ segmentHA_T1.sh output . > ------------------------------ > USER user > HOST slurm3-compute2 > PROCESSID 14892 > PROCESSOR x86_64 > OS Linux > ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 > Linux slurm3-compute2 4.15.0-99-generic #100-Ubuntu SMP Wed Apr 22 > 20:32:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux > ------------------------------ > > freesurfer-linux-centos7_x86_64-7.0.0-20200429-3a03ebd > > setenv SUBJECTS_DIR . > cd /export/prod/5eb5c3986d02b3164bd1ad8b/5eb5c8506d02b3677ed1add8 > /usr/local/freesurfer/bin/segmentHA_T1.sh output . > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Sat May 9 00:23:06 UTC 2020 > ------------------------------------------ > Setting up environment variables > --- > LD_LIBRARY_PATH is > .:/lib64:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/.singularity.d/libs > Registering imageDump.mgz to hippocampal mask from ASEG > Error using myMRIread (line 16) > Error in myMRIread: temporary directory does not exist > Error in segmentSubjectT1_autoEstimateAlveusML (line 157) > Linux slurm3-compute2 4.15.0-99-generic #100-Ubuntu SMP Wed Apr 22 > 20:32:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux > T1 hippocampal subfields exited with ERRORS at Sat May 9 00:23:16 UTC 2020 I am not sure what it means by "temporary directory does not exist", but I see that it's written some files under my freesurfer subject output directory. [image: image.png] Could you help me troubleshoot this problem? Thank you! Soichi Hayashi

2 1

Regarding OS
by Rahul Sharma 11 May '20

11 May '20

External Email - Use Caution Can anyone please help me out which OS will be suitable for using freesurfer from now onwards. Regards: Rahul Sharma Research Scholar NIT Silchar (Assam) 9827834360

1 0

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