Freesurfer December 2023

freesurfer@nmr.mgh.harvard.edu

52 participants
65 discussions

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by Fargol Rezayaraghi 11 Dec '23

11 Dec '23

External Email - Use Caution confirm 9409585a645272fb88d533c84bc48f62063467b6 -- Kind Regards, *Fargol R. Araghi (Rezayaraghi)* Ph.D. Candidate, University of Washington Department of Mechanical Engineering http://secure-web.cisco.com/1z5zqpTtSp3691W2lP50ZDEzYaCGRVNvntr3001fktP80Uo… <https://secure-web.cisco.com/1ArdYpUJQ6TCYtxW-5pkUVyVFSwYPtirrqOkTYF65PO_q7…>

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FreeSurfer release for Redhat Linux 9.x and its clones
by Li, Mingyi 11 Dec '23

11 Dec '23

External Email - Use Caution Will there be a binary release of FreeSurfer for Redhat Linux 9.x clones such like Rocky Linux 9.x or Oracle Linux 9.x? Thanks, Mingyi [1C766421] Mingyi Li, Ph.D. | Director of Scientific Computing | Imaging Institute 9500 Euclid Ave. | Cleveland, OH 44195 | 216-444-8112, 216-401-8585 Please consider the environment before printing this e-mail Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://secure-web.cisco.com/1G1FHl8o-c0952oHfiUYZctzucCRahko4Lbt_u3kQEogLp2… 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.

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Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled
by fsbuild 10 Dec '23

10 Dec '23

External Email - Use Caution   Hello Sophie, Just FYI, there is no matlab distribution included in the 7.4.1 release and we so not support using R2023b.  So I presume someone at your site installed R2023b separately via a Mathworks matlab installer.  We do provide a script, fs_install_mcr, to install either the R2014b or R2019b matlab runtime environment into the freesurfer tree for use.  I don't know if running R2019b would affect what you report below, but you could try it via the commands below.. - R. $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1                  <--- linux install path $ source $FREESURFER_HOME/SetUpFreeSurfer.sh <... output showing SUBJECTS_DIR and other environment variables> $ cd  $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b I believe this sets things up so the libmwm* libraries are installed under $FREESURFER_HOME/MCRv97/bin/glnxa64.  You can try adding that path (or any path the script output recommends) to the start of LD_LIBRARY_PATH.  You should remove any other entries to a different MATLAB distribution. On 11/23/23 20:42, Sophie Matis (sophie.matis(a)sydney.edu.au) wrote:         External Email - Use Caution         Hello FreeSurfer experts!   I have carried out some analysis of changes in cortical thickness over time using the LME Matlab (R23b) Toolbox distributed within Freesurfer (7.4.1) in line with the instructions on this page:  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16TbMFKCSxY9QLMDkUoKiHpONPO8cJ5IumheTtc9oNl4e8…   At this stage I just want to look at changes over time within each of three groups. For two groups I have been able to proceed through the steps fine and have my significance files which look normal. For the last group I am running into an error on the “[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3); “ step. MATLAB returns “Warning: Matrix is singular, close to singular or badly scaled” and lhTh0 and lhRe are created as matrices with only NaN values.   Has anyone run into this error before or have any tips for troubleshooting it?   I haven’t had any errors on the longitudinal processing steps and visual QC on my files looks normal. No errors on mris_preproc or mri_surf2surf.  An aparcstats2table for thickness doesn’t reveal any NaNs.   My design matrix is created with X = [ones(length(M),1) M] after following the suggested sortData code from the wiki Contrast is [0 1] This is my qdec file:   fsid    fsid-base       yearsfromBL 108_MR1       108   0.00 199_MR1       199   0.00 199_MR2       199   1.10 199_MR3       199   2.25 202_MR1       202   0.00 204_MR1       204   0.00 204_MR2       204   1.16 204_MR3       204   2.30 223_MR1       223   0.00 0821_MR1      0821  0.00 0931_MR1      0931  0.00 1010_MR1      1010  0.00 1010_MR2      1010  1.84 1031_MR1      1031  0.00 1031_MR2      1031  1.00 1031_MR3      1031  2.13 1064_MR1      1064  0.00 1064_MR2      1064  2.01 1125_MR1      1125  0.00 1134_MR1      1134  0.00 1134_MR2      1134  1.17 1134_MR3      1134  2.28 1233_MR1      1233  0.00 1233_MR2      1233  1.05 1373_MR1      1373  0.00 1439_MR1      1439  0.00 1439_MR2      1439  1.14 1439_MR3      1439  2.28 1475_MR1      1475  0.00 1475_MR2      1475  1.04 1475_MR3      1475  2.03 1522_MR1      1522  0.00 1522_MR2      1522  2.07 1541_MR1      1541  0.00 1541_MR2      1541  1.47 1551_MR1      1551  0.00 1551_MR2      1551  0.98 1551_MR3      1551  2.05 1572_MR1      1572  0.00 1572_MR2      1572  1.03 1625_MR1      1625  0.00 1625_MR2      1625  1.06 1637_MR1      1637  0.00 1641_MR1      1641  0.00 1656_MR1      1656  0.00 1656_MR2      1656  0.94 1656_MR3      1656  2.26 1755_MR1      1755  0.00 1755_MR2      1755  1.04 1755_MR3      1755  2.01 1829_MR1      1829  0.00 09154_MR1     09154 0.00 09154_MR2     09154 1.01 09154_MR3     09154 2.01 12110_MR1     12110 0.00 12110_MR2     12110 1.04     Any help appreciated!   Thank you,   Sophie Matis | Data Management & Research Officer School of Health Sciences & Brain and Mind Centre  Faculty of Medicine and Health    The University of Sydney   Brain and Mind Centre, 94-100 Mallett Street, Camperdown (M02G) | The University of Sydney | NSW | 06  sophie.matis(a)sydney.edu.au  | sydney.edu.au   CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments.   Please think of our environment and only print this email if necessary.   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1JpB2M6srxvOJofQQKW2x6xhujK5Mdwvp75j2I-8SrFl7M… Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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PETSurfer
by Emma Tinney 07 Dec '23

07 Dec '23

External Email - Use Caution Hi I am reaching out to ask some questions about PetSurfer. I am working with an open access dataset (ADNIDOD<https://secure-web.cisco.com/1CEWzN2wc2OketK1X9ZfAONKbe4S8QwQqJbEzc-uLebpb5…>) to analyze neurobiological differences in veterans with a history of TBI. I am hoping to use the PET data (there are the raw dicoms and preprocessed PET data) to segment the choroid plexus using a specific segmentation software.<https://secure-web.cisco.com/1UhF7rhtSZAlDXzE9N3KqTGlmagy96emXFw2bQ51_0Eb0I…> I have already done the segmentation on the T1 images, but am hoping to apply the masks to the preprocessed PET images. I was looking at using the “mri_gtmpvc” command to segment the choroid plexus using the mask I already created but was hoping for some guidance. There are also several options of preprocessed PET data I can chose from, including “co-registered averaged standardized image and voxel” including “co-registered averaged standardized image and voxel with unform resolution” and “co-registered averaged” or “co-registered dynamic”. If anyone are willing to help or can connect me to someone how might have time to reply or quickly chat, that would be great. I appreciate the support and am looking forward to using PetSurfer.

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Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b
by Na, Xiaoxu 07 Dec '23

07 Dec '23

External Email - Use Caution Thank you for your information! However, even though I appended the temporary paths that were generated right after running mcr installation. While running, I first printed out the $ LD_LIBRARY_PATH, it seems right. However, the same error occurred. I didn’t install the freesurfer in the default folder, if that may be a problem. I used neurodocker to build the base image with freesurfer 7.3.1 running correctly. Is there anything else I can try? Thank you so much! Regards, Xiaoxu :/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv84/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv84/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64/libmwlaunchermain.so:/usr/lib/x86_64-linux-gnu/:opt/freesurfer-7.3.1/MCRv84/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv84/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64/libmwlaunchermain.so:/tmp/tmp.s91tLX1Jfv/install-target/v84/runtime/glnxa64:/tmp/tmp.s91tLX1Jfv/install-target/v84/bin/glnxa64:/tmp/tmp.s91tLX1Jfv/install-target/v84/sys/os/glnxa64::/.singularity.d/libs recon-all -s BL-101 -localGI fs-check-version --s BL-101 --o /tmp/tmp.UQALDw Thu Dec 7 15:57:37 UTC 2023 setenv SUBJECTS_DIR /home/xna/fmri/data_BF_str cd /home/xna/fmri/data_BF_str /opt/freesurfer-7.3.1/bin/fs-check-version --s BL-101 --o /tmp/tmp.UQALDw -rwxrwxr-x 1 root root 18565 Dec 7 15:31 /opt/freesurfer-7.3.1/bin/fs-check-version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 $Id$ Linux xbt090 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pid 107005 Current FS Version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 bstampfile exists /home/xna/fmri/data_BF_str/BL-101/scripts/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/xna/fmri/data_BF_str Actual FREESURFER_HOME /opt/freesurfer-7.3.1 -rw-rw-r-- 1 xna xna 1220527 Dec 7 13:57 /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log Linux xbt090 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ~/fmri/data_BF_str/BL-101/mri/transforms ~/fmri/data_BF_str/BL-101 ~/fmri/data_BF_str/BL-101 #@# white curv lh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Thu Dec 7 15:57:43 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /home/xna/fmri/data_BF_str/BL-101/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Dec 7 15:57:43 UTC 2023 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux xbt090 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BL-101 exited with ERRORS at Thu Dec 7 15:57:43 UTC 2023 For more details, see the log file /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/19z1ocn0OehHUGM4w6oiRnM6yr0UPgIGAZZxoya2UA2h4t8… finish From: fsbuild <fsbuild(a)contbay.com<mailto:fsbuild@contbay.com>> Sent: Wednesday, December 6, 2023 9:14 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Na, Xiaoxu <XNA(a)uams.edu<mailto:XNA@uams.edu>> Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b I believe the assumption is the freesurfer 7. 3. 1 distribution has already been installed (under /usr/local/freesurfer/7. 3. 1 by the *. deb or *. rpm linux installer file) and that FREESURFER_HOME is set in the environment (/usr/local/freesurfer/7. 3. 1). ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd I believe the assumption is the freesurfer 7.3.1 distribution has already been installed (under /usr/local/freesurfer/7.3.1 by the *.deb or *.rpm linux installer file) and that FREESURFER_HOME is set in the environment (/usr/local/freesurfer/7.3.1). You should be able to download and run the 7.3.1 freesurfer installer using one of the 7.3.1 links from https://secure-web.cisco.com/1xzEw_39iMXyKuBpdo8UKsiKydPO1Z-ipCErkgZpMyG6GU…<https://secure-web.cisco.com/1fU-Lgo7fC-rWXRP-ehuSHyAmpBhqQCNi_30XNCdY1ywXy…>. After running the freesurfer installer, the steps - which it looks like you are already using - are listed below from a bash terminal window, $ export FREESURFER_HOME=/usr/local/freesurfer/7.3.1 $ cd $FREESURFER_HOME/bin .... you can try using either R2019b or R2014b ... $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b I'm not sure the paths generated by the Maltab installer for use in LD_LIBRARY_PATH are always the same. They may not be if it uses some temporary path naming mechanism. So you may need to capture the output from the matlab installer, parse out the LD_LIBRARY_PATH setting each time it is run, and set it in the environment. - R. On 12/6/23 13:58, Na, Xiaoxu (XNA(a)uams.edu<mailto:XNA@uams.edu>) wrote: External Email - Use Caution Dear Freesurfer Experts, I’m building a docker file with freesurfer and matlab run time. May I know if freesurfer 7.3.1 should be compatible with matlab run time 2019b? If so, what else can I make the environment setting correct in order to run localGI? I tried to run “cd $FREESURFER_HOME/bin && sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b” and it finished successfully and I also appended the “/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so” to "$LD_LIBRARY_PATH". On the target computer, append the following to your LD_LIBRARY_PATH environment variable: /tmp/tmp.T0m3Pxj9fW/install-target/v97/runtime/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/bin/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/sys/os/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/extern/bin/glnxa64 If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable. (Dec 06, 2023 17:26:10) Exiting with status 0 (Dec 06, 2023 17:26:10) End - Successful. Finished R2019b installed successfully in /opt/freesurfer-7.3.1/MCRv97 Removing intermediate container afe25e3801f1 ---> ae8788b3fa89 Step 13/14 : ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so ---> Running in e3601f8c33c4 Removing intermediate container e3601f8c33c4 ---> 404199efd51a Step 14/14 : RUN echo "$LD_LIBRARY_PATH" ---> Running in ac3754cb24bb :/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so Removing intermediate container ac3754cb24bb ---> 9e9c3e2e0051 Successfully built 9e9c3e2e0051 However, when I run “recon-all -s BL-101 -localGI” on the subject BL-101 that was successfully finished was recon-all previously, it yelled Malab was not available. Could you please help where I did wrong? Thank you so much! start /usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64/libmwlaunchermain.so:/.singularity.d/libs recon-all -s BL-101 -localGI fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn Wed Dec 6 18:51:08 UTC 2023 setenv SUBJECTS_DIR /home/xna/fmri/data_BF_str cd /home/xna/fmri/data_BF_str /opt/freesurfer-7.3.1/bin/fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn -rwxrwxr-x 1 root root 18565 Dec 6 17:50 /opt/freesurfer-7.3.1/bin/fs-check-version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 $Id$ Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pid 106796 Current FS Version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 bstampfile exists /home/xna/fmri/data_BF_str/BL-101/scripts/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/xna/fmri/data_BF_str Actual FREESURFER_HOME /opt/freesurfer-7.3.1 -rw-rw-r-- 1 xna xna 1158857 Dec 6 18:24 /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ~/fmri/data_BF_str/BL-101/mri/transforms ~/fmri/data_BF_str/BL-101 ~/fmri/data_BF_str/BL-101 #@# white curv lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/lh.white .../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/lh.white .../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/rh.white .../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/rh.white .../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /home/xna/fmri/data_BF_str/BL-101/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Dec 6 18:51:09 UTC 2023 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BL-101 exited with ERRORS at Wed Dec 6 18:51:09 UTC 2023 For more details, see the log file /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/19z1ocn0OehHUGM4w6oiRnM6yr0UPgIGAZZxoya2UA2h4t8…<https://secure-web.cisco.com/1v2hZu1ivO7aHp4s4Z4ec6Itn5kVU3XRJrHypkr2l429bA…> Regards, Xiaoxu ________________________________ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1o8KMA-6zF6Lep6khhWfOHNu5D19D131-YyTZ_2EcGvXYl…<https://secure-web.cisco.com/19SzGZflgcFR90JJ11fhJKew5mKZkW6XKAgxeaTV5IZDgZ…> Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

2 8

Cortical Thickness Measurement in Cortical Lesion ROI
by 李浩 07 Dec '23

07 Dec '23

External Email - Use Caution Dear Freesurfer Experts, I am currently engaged in a project where I need to measure the cortical thickness of a segmented cortical lesion (ROI) in the volume space. After running recon-all for my subjects, i employed 'mri_vol2surf' function to project my ROI from the native T1 space to indiviaul surface space to project the ROI from the native T1 space to the individual surface space. My command was as follows: $chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz --hemi rh --surf white --projfrac-avg -0.1 1 0.05 --interp nearest --o "$sub"_chronic-CMI_4-1_rh.mgh --regheader "$sub" --trgsubject “$sub” However, I encountered an issue where I could not locate the ROI in the individual surface space, as the values in "$sub"_chronic-CMI_4-1_rh.mgh were all zero. I suspect this might be due to a registration error or possibly the small size of my ROI (only 4 voxels). Do you have any suggestions on how to address this issue? Additionally, I am wondering whether it's possible to register the cortical thickness map from the surface space back to the individual volume space, then calculate the mean cortical thickness of my ROI there. Alternatively, is it feasible to convert the coordinates of my ROI's center point to the MNI152 coordinate and then surface-based coordinates and directly create an ROI in the surface space? Any feedback on these questions would be greatly appreciated. Thanks in advance. Bests, Hao Li

1 0

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b
by fsbuild 06 Dec '23

06 Dec '23

External Email - Use Caution   I believe the assumption is the freesurfer 7.3.1 distribution has already been installed (under /usr/local/freesurfer/7.3.1 by the *.deb or *.rpm linux installer file) and that FREESURFER_HOME is set in the environment  (/usr/local/freesurfer/7.3.1).  You should be able to download and run the 7.3.1 freesurfer installer using one of the 7.3.1 links from https://secure-web.cisco.com/1JcyAuFpIReuF1zXqp8tlLsd3XWfOZVJNAxAaV1v1-OILt… After running the freesurfer installer, the steps - which it looks like you are already using - are listed below from a bash terminal window, $ export FREESURFER_HOME=/usr/local/freesurfer/7.3.1 $ cd  $FREESURFER_HOME/bin .... you can try using either R2019b or R2014b ... $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b I'm not sure the paths generated by the Maltab installer for use in LD_LIBRARY_PATH are always the same.   They may not be if it uses some temporary path naming mechanism.  So you may need to capture the output from the matlab installer, parse out the LD_LIBRARY_PATH setting each time it is run, and set it in the environment. - R. On 12/6/23 13:58, Na, Xiaoxu (XNA(a)uams.edu) wrote:         External Email - Use Caution         Dear Freesurfer Experts,   I’m building a docker file with freesurfer and matlab run time. May I know if freesurfer 7.3.1 should be compatible with matlab run time 2019b? If so, what else can I make the environment setting correct in order to run localGI?   I tried to run “cd $FREESURFER_HOME/bin && sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b” and it finished successfully and I also appended the “/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so” to  "$LD_LIBRARY_PATH".   On the target computer, append the following to your LD_LIBRARY_PATH environment variable:   /tmp/tmp.T0m3Pxj9fW/install-target/v97/runtime/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/bin/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/sys/os/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/extern/bin/glnxa64   If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable.   (Dec 06, 2023 17:26:10) Exiting with status 0 (Dec 06, 2023 17:26:10) End - Successful. Finished R2019b installed successfully in /opt/freesurfer-7.3.1/MCRv97 Removing intermediate container afe25e3801f1 ---> ae8788b3fa89 Step 13/14 : ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so ---> Running in e3601f8c33c4 Removing intermediate container e3601f8c33c4 ---> 404199efd51a Step 14/14 : RUN echo "$LD_LIBRARY_PATH" ---> Running in ac3754cb24bb :/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so Removing intermediate container ac3754cb24bb ---> 9e9c3e2e0051 Successfully built 9e9c3e2e0051     However, when I run “recon-all -s BL-101 -localGI” on the subject BL-101 that was successfully finished was recon-all previously, it yelled Malab was not available. Could you please help where I did wrong? Thank you so much!   start /usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64/libmwlaunchermain.so:/.singularity.d/libs recon-all -s BL-101 -localGI fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn Wed Dec  6 18:51:08 UTC 2023   setenv SUBJECTS_DIR /home/xna/fmri/data_BF_str cd /home/xna/fmri/data_BF_str /opt/freesurfer-7.3.1/bin/fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn -rwxrwxr-x 1 root root 18565 Dec  6 17:50 /opt/freesurfer-7.3.1/bin/fs-check-version   freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 $Id$ Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pid 106796 Current FS Version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 bstampfile exists /home/xna/fmri/data_BF_str/BL-101/scripts/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/xna/fmri/data_BF_str Actual FREESURFER_HOME /opt/freesurfer-7.3.1 -rw-rw-r-- 1 xna xna 1158857 Dec  6 18:24 /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ~/fmri/data_BF_str/BL-101/mri/transforms ~/fmri/data_BF_str/BL-101 ~/fmri/data_BF_str/BL-101 #@# white curv lh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv    Update not needed #@# white area lh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area    Update not needed #@# pial curv lh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial    Update not needed #@# pial area lh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial    Update not needed #@# thickness lh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness    Update not needed #@# area and vertex vol lh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness    Update not needed #@# white curv rh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv    Update not needed #@# white area rh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area    Update not needed #@# pial curv rh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial    Update not needed #@# pial area rh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial    Update not needed #@# thickness rh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness    Update not needed #@# area and vertex vol rh Wed Dec  6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness    Update not needed /home/xna/fmri/data_BF_str/BL-101/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Dec  6 18:51:09 UTC 2023   mris_compute_lgi --i lh.pial   ERROR: Matlab is required to run mris_compute_lgi! Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux   recon-all -s BL-101 exited with ERRORS at Wed Dec  6 18:51:09 UTC 2023   For more details, see the log file /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1nEcknYcMHcSToXzS7wgrg4Q4X9FG-5ASqRyq8IAxcH_CcV…   Regards, Xiaoxu   Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1S_1PtE6PLv0H4cPPs4tL__MHbe4c8exiUR72xwXIQoipP… Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

1 0

Automatic prompt reply for freesurfer subsegmentations
by Gool, J.K. (Jari) 06 Dec '23

06 Dec '23

External Email - Use Caution Dear, I would like to run the different available Freesurfer subsegmentations (brainstem, amygdala/hippocampus, thalamus, hypothalamus and ScLimbic) on a large sample of 150 subjects (code below). I want to run multiple subjects in parallel using the sbatch command on the linux server I am working on. Because of previous recon-all processing in 7.3.2 I would like to also perform the subsegmentations in this version and ScLimbic in 7.4.0. The problem is that the "segmentBS.sh", "segmentThalamicNuclei.sh" and "segmentHA_T1.sh" halfway prompts for user input: "mv: replace 'imageDump.mgz', overriding mode 0444 (r--r--r--)?". The imageDump.mgz file is made within this same subsegmentation script and I have no problem with replacing this file. When I run the code interactively I just reply with "y" and the subsegmentation finishes without any errors. When I want to submit my script as a job and in batch, I am unable to provide this user input and the subsegmentation gets stuck at the prompt. I have tried to change my code of the subsegmentations with yes and echo (such as "yes | segmentBS.sh ${subj}_ses-EEGfMRI1 /home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/" or "echo "y" | segmentBS.sh ${subj}_ses-EEGfMRI1 /home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/") but the script still gets stuck on the prompt. Do you know how I can fix this? We would also like to perform these subsegmentations in a large consortium and hope to be able to automate this problem so sites will not have to manually provide the user input every time. Thank you in advance for your help, it is much appreciated. Kind regards, Jari Gool | MD-PhD candidate Department of Anatomy & Neurosciences, Amsterdam UMC Location VUmc #!/bin/bash #SBATCH --job-name=subsegmentations_ams #SBATCH --mem=16G #SBATCH --partition=luna-cpu-long #SBATCH --qos=anw-cpu #SBATCH --cpus-per-task=1 #SBATCH --time=03-00:00:00 #SBATCH --nice=2000 #SBATCH --array=1-37%3 #SBATCH --output=slurm-%A.%a.out module load FreeSurfer/7.3.2-centos8_x86_64 #make list of subjects SUBJECTS_DIR=/scratch/anw/jkgool/freesurfer_rick/input/ cd ${SUBJECTS_DIR} ls -d sub-* > subjects.txt subj=$(sed "${SLURM_ARRAY_TASK_ID}q;d" subjects.txt) #1 hypothalamus (doc: https://secure-web.cisco.com/1onztiawxb5qsVvLHN8f5XCv2KtGSQGWg_dK2SaFV6PqzO…) echo "running hypothalamus segmentation..." mri_segment_hypothalamic_subunits --s ${subj}_ses-EEGfMRI1 --sd /home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/ --write_posteriors #2 brainstem (doc: https://secure-web.cisco.com/1yA5iB2C_fQBajVg9CMfEqeSaXWvxL5h6YNRFRhGqg70rv…) echo "running brainstem segmentation..." segmentBS.sh ${subj}_ses-EEGfMRI1 /home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/ #3 thalamus (doc: https://secure-web.cisco.com/12Cjw5kv1gZcMaSw-FGtq5Rj_H-W8Ti_S-0G1z5Q3RcGYA…) echo "running thalamic nuclei segmentation..." segmentThalamicNuclei.sh ${subj}_ses-EEGfMRI1 /home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/ #4 hippocampal subfields and amygdala (doc: https://secure-web.cisco.com/1msow8_UAwH0qjnlyynpNAamisXbwaGhA9aKGjqT8cxwFY…) echo "running hippocampal subfields and amygdala segmentation..." segmentHA_T1.sh ${subj}_ses-EEGfMRI1 /home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/ module load FreeSurfer/7.4.0-centos8_x86_64 #5 subcortical limbic structures (doc: https://secure-web.cisco.com/1BzoZbanMMDeo_3lpTpcyI0wfALp7CjhwdsuIj1cE8JFgb…) echo "running limbic structures segmentation..." mri_sclimbic_seg --i /home/anw/jkgool/my-scratch/freesurfer_rick/input/${subj}/ses-EEGfMRI1/anat/ --o /home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/${subj}_ses-EEGfMRI1/output_sclim --write_volumes --write_qa_stats ______________________________________________________ AmsterdamUMC disclaimer : http://secure-web.cisco.com/1td9AygoAleVUgM8ZzmybSU3puYBZUmWaYHhLwS0mlie9Na…

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Faces and vertices error !
by Sahil Bajaj 06 Dec '23

06 Dec '23

External Email - Use Caution Hi FreeSurfer community, I am trying to map subject-specific cortical thickness map to standard fsaverage space and I ran the following command where sub1_filled is my individual subject in native: mri_surf2surf --srcsubject sub1_filled --srcsurfreg thickness --trgsubject fsaverage --trgsurfreg thickness --hemi lh --sval sub1/surf/lh.thickness --tval fsaverage/surf/lh.thickness After I run the above command, I am getting the following output and error. I am not sure how to resolve this and whether there is something wrong with my command line or with the data. I would greatly appreciate any help. Source registration surface changed to thickness Target registration surface changed to thickness 7.4.1 setenv SUBJECTS_DIR /Users/sbajaj/FS_Projects/ cd /Users/sbajaj/FS_Projects mri_surf2surf --srcsubject sub1_filled --srcsurfreg thickness --trgsubject fsav1 --trgsurfreg thickness --hemi lh --sval sub1/surf/lh.thickness --tval fsav1/surf/lh.thickness sysname Darwin hostname MDACM0CL9004107 machine x86_64 user sbajaj srcsubject = sub1_filled srcval = sub1/surf/lh.thickness srctype = trgsubject = fsav1 trgval = fsav1/surf/lh.thickness trgtype = srcsurfreg = thickness trgsurfreg = thickness srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/sbajaj/FS_Projects//sub1_filled/surf/lh.thickness nquads=4456450, nvertices=341 error: ERROR: MRISread: file '/Users/sbajaj/FS_Projects//sub1_filled/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface!

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Freesurfer 7.3.1 MCR 2019b
by Na, Xiaoxu 06 Dec '23

06 Dec '23

External Email - Use Caution Dear Freesurfer Experts, I'm building a docker file with freesurfer and matlab run time. May I know if freesurfer 7.3.1 should be compatible with matlab run time 2019b? If so, what else can I make the environment setting correct in order to run localGI? I tried to run "cd $FREESURFER_HOME/bin && sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b" and it finished successfully and I also appended the "/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so" to "$LD_LIBRARY_PATH". On the target computer, append the following to your LD_LIBRARY_PATH environment variable: /tmp/tmp.T0m3Pxj9fW/install-target/v97/runtime/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/bin/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/sys/os/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/extern/bin/glnxa64 If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable. (Dec 06, 2023 17:26:10) Exiting with status 0 (Dec 06, 2023 17:26:10) End - Successful. Finished R2019b installed successfully in /opt/freesurfer-7.3.1/MCRv97 Removing intermediate container afe25e3801f1 ---> ae8788b3fa89 Step 13/14 : ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so ---> Running in e3601f8c33c4 Removing intermediate container e3601f8c33c4 ---> 404199efd51a Step 14/14 : RUN echo "$LD_LIBRARY_PATH" ---> Running in ac3754cb24bb :/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so Removing intermediate container ac3754cb24bb ---> 9e9c3e2e0051 Successfully built 9e9c3e2e0051 However, when I run "recon-all -s BL-101 -localGI" on the subject BL-101 that was successfully finished was recon-all previously, it yelled Malab was not available. Could you please help where I did wrong? Thank you so much! start /usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64/libmwlaunchermain.so:/.singularity.d/libs recon-all -s BL-101 -localGI fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn Wed Dec 6 18:51:08 UTC 2023 setenv SUBJECTS_DIR /home/xna/fmri/data_BF_str cd /home/xna/fmri/data_BF_str /opt/freesurfer-7.3.1/bin/fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn -rwxrwxr-x 1 root root 18565 Dec 6 17:50 /opt/freesurfer-7.3.1/bin/fs-check-version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 $Id$ Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pid 106796 Current FS Version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 bstampfile exists /home/xna/fmri/data_BF_str/BL-101/scripts/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/xna/fmri/data_BF_str Actual FREESURFER_HOME /opt/freesurfer-7.3.1 -rw-rw-r-- 1 xna xna 1158857 Dec 6 18:24 /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ~/fmri/data_BF_str/BL-101/mri/transforms ~/fmri/data_BF_str/BL-101 ~/fmri/data_BF_str/BL-101 #@# white curv lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Wed Dec 6 18:51:09 UTC 2023 cd /home/xna/fmri/data_BF_str/BL-101/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /home/xna/fmri/data_BF_str/BL-101/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Dec 6 18:51:09 UTC 2023 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BL-101 exited with ERRORS at Wed Dec 6 18:51:09 UTC 2023 For more details, see the log file /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/10JlU9uC5Jx9CmqgAZa_0KlYFqyorcNvk6q66KAYmJMeQk0… Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Freesurfer December 2023