Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

xhemi
by Joost Janssen 06 Mar '24

06 Mar '24

External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks. surfreg --s $subject --t fsaverage_sym --lh --no-annot surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg $subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg $subject/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg $subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg $subject/xhemi/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0 $subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o $subject/surf/li.thickness.lh.fsaverage_sym.mgh mri_segstats --annot fsaverage lh aparc --i $subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum $subject/stats/li.thickness.aparc.stats -joost

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Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 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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mri_watershed and improvements of skullstripping
by Michelangelo Fabbrizzi 01 Feb '24

01 Feb '24

External Email - Use Caution Dear Freesurfer experts, I am new to FS, and I would have couple of questions. I used in sequence: A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1 B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon The brainmask.mgz obtained is good (no skull, brain is okay), however if I now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not used and it is created a new one called ws.mgz that still contain some piece of skull that generate wrong BEM surfaces; even using -h 5 the result is not optimal: mri_watershed -h 5 -useSRAS -surf /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz I am wondering: - how can I force the mri_watershed command to use the brainmask.mgz already created after step C above, instead of creating a new one? - is it possible to use the -gcut command also for mri_watershed? Thanks, appreciated, Miche

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Infant_recon_all generated surface does not align well with the provided aseg file
by Yanbin Niu 11 Jan '24

11 Jan '24

External Email - Use Caution Hi Freesurfers, I'm currently working on running infant_recon_all with our edited aseg.nii.gz for newborn data. However, we've encountered an issue where the generated surface does not align well with the provided aseg file. I have attached some screenshots as an example, in which a fold that infant_recon_all is failing to fully recognize. This problem seems consistent across the brain and subjects. I'm reaching out to inquire if anyone has experience with this issue and if there are specific parameters that we can adjust to address this issue. Here is the command we've been using: infant_recon_all --s sub-1041 --age 1 --inputfile ${SUBJECTS_DIR}/sub-1041/mprage.nii.gz --segfile ${SUBJECTS_DIR}/sub-1041/aseg.nii --masked ${SUBJECTS_DIR}/sub-1041/brain_mask.nii.gz Thank you, Yanbin Niu

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Use of infantFS and FS in the interval 2 - 4.5 years of age
by Michelangelo Fabbrizzi 11 Jan '24

11 Jan '24

External Email - Use Caution Dear FS experts, I see it is recommended to use infantFS below 2 years of age, whereas FS has been used for 4.5 years and above. I was wondering what could be used in the interval 2 - 4.5 years of age: which are benefits and drawbacks of both? Thanks, appreciated, Mic

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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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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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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.

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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.

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Freesurfer November 2023