Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

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…

2 5

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!

2 1

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.

1 0

Segmentation error with T2w
by Litsch, Jakob Benjamin 06 Dec '23

06 Dec '23

External Email - Use Caution Dear Freesurfer Team, I am a master student from Berlin and pretty new to preprocessing MRI data, so please bear with me. I am attempting to use Freesurfer as Part of my fMRIprep pipeline to preprocess patient data. When running fmriprep with only the T1w and the BOLD image it works fine. As soon as I put in my T2w image as well recon-all crashes at some point. My patient data has lesions like brain tumors, just in case this could make freesurfer struggle. Starting loop over 250145 vertices vno = 0, t = 5.16114 error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image Segmentation fault 1) Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 2) platform: Windows 11, Ubuntu 22.04.2 LTS (GNU/Linux 5.15.133.1-microsoft-standard-WSL2 x86_64) 3) recon-all log: see attached Looking forward to hear from you, Jakob Litsch

2 1

Saving more than one label in a single volume file
by Aurora Orazi 06 Dec '23

06 Dec '23

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to save more than one label in as a single volume file from the aseg.mgz file obtained with the infant FreeSurfer pipeline. However, given the lack of tutorials I'm finding it difficult to do so. I hope you can help me with this problem. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Platform: Ubuntu 22.04 Hoping to hear from you soon, Best regards, Aurora

2 1

Reopen issue 898: mri_binarize --replace misbehavior
by Nick Schmansky 04 Dec '23

04 Dec '23

External Email - Use Caution I have encountered the problem that chrisadamsonmcri<https://secure-web.cisco.com/1xWGWxoOiHrVvr8AONbdJmSDQHTmtv9-28Mk5n8yl42uZZ…> describes in issue 898<https://secure-web.cisco.com/1m61bxpBwgxqKDi9Ogsq79O03id3L1GGsM-889UgjAYymO…>. The last time I used mri_binarize was using FS v6, where it behaves like this: mri_binarize --replace A B --replace B C Label A would become B in the output. Label B would become C in the output. here's an example: --replace 11 15 # map "4th Ventricle" -> "4th-Ventricle"\ --replace 15 72 # map "5th Ventricle" -> "5th-Ventricle"\ i want to convert a seg where the LUT maps 11 as 4th ventricle and 15 as 5th ventricle. i want to convert these to the FS LUT (using the replacements shown, 15 and 72). But this results in 4th ventricle getting labeled as 5th ventricle! Four years ago i ran a script performing 230 replace functions to map Neuromorphometrics labels to FS, and it worked fine (evidenced by Dice testing and inspection). Today i ran the same script on the same data and get funky results on a half dozen or so structures that follow the example replacement scheme. My current workaround is to use mri_binarize from v6. ---------------------------------------------------------------------- The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately with a copy to lfoster(a)radnet.com and destroy this message. Please be aware that e-mail communication can be intercepted in transmission or misdirected. Your use of e-mail to communicate protected health information to us indicates that you acknowledge and accept the possible risks associated with such communication. Please consider communicating any sensitive information by telephone, facsimile or regular U.S. mail. If you do not wish to have your information sent by e-mail, please contact the sender immediately.

4 3

outer_skin.surf
by Diksha Srishyla 04 Dec '23

04 Dec '23

External Email - Use Caution Hello, I am trying to generate the surfaces ‘brain.surf’, ‘inner_skull.surf’, ‘outer_skull.surf’ and ‘outer_skin.surf’. When I use ‘mne watershed bem’, I obtain surfaces that are in the wrong order (eg. brain.surf is outside of the inner_skull.surf’) I viewed previous queries on the archive was able to generate properly ordered ‘brain.surf’ and ‘inner_skull.surf’ by using the following commands: mri_binarize --i brainmask.mgz --min 0.5 --surf brain.surf mris_expand brain.surf 3 inner_skull Are there similar commands I can use to generate ‘outer_skin.surf’ ? From that, I understand I would just need to shrink the surface by 3 mm to get ‘outer_skull.surf’. Thank you for your time. Best, Diksha

1 0

skull stripping error
by yunus soleymani 04 Dec '23

04 Dec '23

External Email - Use Caution Hello Freesurfers, I recently analyzed about 600 subjects from HCP database using the Freesurfer recon-all algorithm. However, I noticed that in almost one third of the subjects, the software did not perform the skull stripping correctly when I checked the results in Freeview. To address this issue, I repeated the skull stripping step for each subject using the code "recon-all -skullstrip -wsthresh 35 -clean-bm -s <subject name>". The skull stripping went well, and then I repeated the analysis using the code "recon-all -autorecon-pial -subjid <subject name>". When I compared the pre and post-correction stats folder, I noticed that some volumetric values had changed, especially in the specific areas related to the initial skull stripping error. However, my concern is that when I loaded the .pial and .aseg files into Freeview, there was no change compared to before the correction visually. Is this okay, or should I take additional steps? I would appreciate your help. Thank you,YunusBellow is an example. NumberS 1 and 2 are brain masks before and after correction. Numbers 2 and 3 are superimposed .aseg files before and after correction.

2 5

tracula using FS 7.2
by Alexopoulos, Dimitrios 30 Nov '23

30 Nov '23

External Email - Use Caution We'd like to use FS7.2 to generate hi-re surfaces on 0.8mm data on 6yo subject. However, we'd like to be able to generate the white matter tracts that are produced with older versions (specifically 6.0), not the new 42 tracts with 7.2. Can a FS 6.0 dmrirc config file be used with 7.2 to get the WM tracts generated from the older tracula versions? Jim ________________________________ 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

Converting register.dat file to reg.lta
by Mirsol Choi 30 Nov '23

30 Nov '23

External Email - Use Caution Hello there, I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data. I have tried to perform bbregister, but the alignment is completely off. Thank you so much for your time! Mirsol

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