Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

Longitudinal LME matlab error - Matrix singular or badly scaled
by Sophie Matis 28 Nov '23

28 Nov '23

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: https://secure-web.cisco.com/1T0jceJqjr8o0YltVDmmB4EAlEhKr0pMp8gIavJ6vaUX1H… 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<mailto:shona.brinley@sydney.edu.au> | sydney.edu.au<http://secure-web.cisco.com/1TuWK5WUev2Fb_3Y4GMAFPyrgRjl5K2o4Isb-heH5rrBUMM…> 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.

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Fwd: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label
by Suman Saha 27 Nov '23

27 Nov '23

External Email - Use Caution Regards, *Suman Saha* ---------- Forwarded message --------- From: Suman Saha <ecesuman06(a)gmail.com> Date: Sat, Nov 25, 2023 at 8:21 AM Subject: Fwd: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label To: <freesurfer(a)nmr.mgh.harvard.edu> Regards, *Suman Saha* ---------- Forwarded message --------- From: <freesurfer-owner(a)nmr.mgh.harvard.edu> Date: Sat, Nov 25, 2023 at 8:18 AM Subject: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label To: <ecesuman06(a)gmail.com> You are not subscribed to this mailing list, and your message has been automatically rejected. Please subscribe to the list following the instructions at: https://secure-web.cisco.com/1GUd1hdBRPxgF-mL_r8NbneNA4m_Qy5_5__TuOpcP6Rr01… IMPORTANT: Make sure you are sending your message using the same email address that was used to subscribe to the list! Further, registering for a FreeSurfer license does not mean you have been subscribed to the list! If you think that your messages are being rejected in error, contact the mailing list owner at freesurfer-owner(a)nmr.mgh.harvard.edu ---------- Forwarded message ---------- From: Suman Saha <ecesuman06(a)gmail.com> To: freesurfer(a)nmr.mgh.harvard.edu Cc: Bcc: Date: Sat, 25 Nov 2023 08:17:35 +0530 Subject: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon-all command, but I get the following error when I run the "recon-all -i sub.mgz -s sub1 -all" command: ERROR: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label Linux cbdl 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s my_sub exited with ERRORS at Fri Nov 24 23:43:39 IST 2023 Does anyone have any thoughts on how to trouble-shoot this one? I've attached the recon-all.log. 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 22.04.1 3) recon-all.log: see attached 4) recon-all.error : see attached

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Re: [Freesurfer] recon-all error - MRISlabel2Mask()
by Mark Wagshul 27 Nov '23

27 Nov '23

External Email - Use Caution Here is the log file, thanks for the help! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately. -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Wednesday, November 22, 2023 1:22 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 237, Issue 26 CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the "Phish Alert" button on the top right of the Outlook dashboard to report any suspicious emails. Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1rJkZ5uxySrpWhsLGjGTDASTPuao4nugI2v8ucy4w4t46S… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Help (Xincen Wu) 2. Re: freesurfer results QC (yunus soleymani) 3. Unable to add FGATIR during thalamic segmentation (Pal, Amrita) 4. issue with mri_vol2surf (Atena Akbari) 5. Re: Unable to add FGATIR during thalamic segmentation (Iglesias Gonzalez, Juan E.) 6. Re: run recon-all with already skull-stripped data (Douglas N. Greve) 7. Re: total intracranial volume (Douglas N. Greve) 8. Re: Fwd: About Mean LGI value (Douglas N. Greve) 9. Re: Transformation of volume images (Douglas N. Greve) 10. Re: Distance Measurement After recon-all (Douglas N. Greve) 11. Re: recon-all error - MRISlabel2Mask() (Douglas N. Greve) 12. Re: Boundary based registration on partial FoV to MNI space (Douglas N. Greve) 13. Re: Errors in recon-all command (Douglas N. Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Nov 2023 08:44:18 -0500 From: Xincen Wu <xlwu25(a)groton.org> Subject: [Freesurfer] Help To: Freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CADAiWu4jbXuW22WA9OWD5E0sdrXA9ZJw5Eo-K+z3y7s0CsPRNA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, I am using freesurfer. I have gone through with the installation and diagnostics and everything works fine. FOr example, using the command recon-all --help in terminal yields a bunch of directions. Yet, when I enter something like: recon-all -s bert -autorecon1 an error pops up saying my python3 is problematic. However, I regularly use python3 and redownloaded it after. Please advise on the issue at hand. Thanks, Lucas

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Functional data analysis with longitudinal data
by Akkoyunlu, Beyza 26 Nov '23

26 Nov '23

External Email - Use Caution Hi, I am doing a longitudinal experiment and I already run the longitudinal anatomical pipeline. I am not sure which anatomical data I should register my functional data to? My first idea was to use base anatomical image, but when I checked results I realised that the white gray matter boundaries are not so good with the subject’s base. Do you have a suggestion whether I should use subject’s base data or base.long.post data? FYI, we are using MEMPRAGE as our anatomical pipeline. Thanks Best, Beyza

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Freesurfer's Matrice for reading a nifti Image
by Yazdan Rezaee Jouryabi 26 Nov '23

26 Nov '23

External Email - Use Caution Dear all, Hi I'm looking for the convention of freesurfer which is used for reading a nifti Image, as we are familiar with a nifti Image is saved as an array which then the Voxel Space obtained from that from these "Voxel Space" evey method (as FreeSurfer, FSL, ANTS, ...) will use One Matrice to convert these "Voxel Space" to the Anatomical Space taking care of orientation, Origin Definition, voxel size, ... . I'd appreciate it if you could show me the parts of FreeSurfer's source code which are responsible for this action. Bests, Yazdan

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Extracting Beta Values from FSFAST
by Deyan Mitev 25 Nov '23

25 Nov '23

External Email - Use Caution Hello Freesurfer Developers, I want to extract the beta values for an fMRI dataset that I analyzed with FSFAST, so that I get one beta map (in the ras space) per condition/regressor. The dataset has 5 conditions/regressors specified in the paradigm file and each participant has 4 runs. I used the following commands when running FSFAST (example for left hemisphere): mkanalysis-sess -analysis localiser.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm parbench.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -nskip 4 -TR 2 -nconditions 5 -per-run -fsd bold mkcontrast-sess -analysis localiser.sm5.lh -contrast right-vs-left -c 3 -c 5 -a 2 -a 4 selxavg3-sess -sf sessid -analysis localiser.sm5.lh >From the output when I navigate to PARTICIPANT_FOLDER/bold/localiser.sm5.lh and examine the beta file with mri_info, I get: mri_info beta.nii.gz --dim 163842 1 1 33 My understanding is that the first number is the actual beta values for a given regressor in ras space and the last number (33) is the different betas. From an archived post I found that the first N betas represent the first N conditions. Is that per run, or collapsed over runs? Or is it that the first five betas are the five conditions for run 1, the second five for run 2, etc until 20? What are the other nuisance regressors used to make the rest of the betas then? Kind Regards, Deyan Mae croeso i chi gysylltu gyda'r Brifysgol yn Gymraeg neu Saesneg. Ni fydd gohebu yn Gymraeg yn arwain at oedi. You are welcome to contact the University in Welsh or English. Corresponding in Welsh will not lead to delay. Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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Transformation of volume images
by P Pieperhoff 25 Nov '23

25 Nov '23

External Email - Use Caution Dear developers, please, may I ask you how I can transform volume images (containing discrete region labels) from the fsaverage space into the space of a given subject, and vice-versa? I tried the following command: mri_vol2vol --interp nearest --mov fsaverage/mri/aseg.mgz --o test_mask.mgz --s test001 --targ test001/mri/orig.mg or mri_vol2vol --interp nearest --mov fsaverage/mri/aseg.mgz --o test_mask.mgz --targ test001/mri/T1.mgz --lta test001/mri/transforms/talairach.lta --m3z talairach.m3z --s test001 but there was always a large mismatch between the transformed images and the target image. Best regards, Peter

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No ROI name in summary of MNI305 group analysis
by wangzhiwei3233 25 Nov '23

25 Nov '23

External Email - Use Caution Dear Freesurfer Experts, I did group-level analysis in MNI305 space. Then I output the summay via command 'mri_volcluster' as follows: mri_volcluster --in ./sig.nii.gz --thmin ${thvoxel} --sign ${sigsignTemp} --cwpvalthresh 0.05 --minsize 273 --fwhm 6--no-adjust --sum ${nameout}.cluster.summary --out ${nameout}.cluster.nii.gz --ocn ${nameout}.ocn.nii.gz --labelbase $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label --mask /mnt/hgfs/G/work/MetaCog/Human/subjects/fsaverage/mri.2mm/subcort.mask.mgz the output is as follows. there are no ROI names in the table. Is it because I missed the option '--reg' in the command line? Which register file shoul I use if I should add it? I can't find the 'register.dat' file in fsaverage folder. Very appricated if you can help me. Best, zhiwei ------------------------------------------------------------- # Reporting Coordinates in Voxel Indices # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ Max GRFCWP 1 5270 42160.0 33.00 35.00 60.00 6.04524 0.0000001 2 1995 15960.0 15.00 65.00 24.00 4.32869 0.0008543 3 1429 11432.0 51.00 64.00 17.00 3.72032 0.0036314 4 690 5520.0 55.00 56.00 49.00 -3.22358 0.0488862

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Re: [Freesurfer] Help
by fsbuild 24 Nov '23

24 Nov '23

External Email - Use Caution  It reads like something is not right with your setup/shell environment.   Once you have setup the freesurfer environment via, e.g.,  $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetupFreesurfer.sh-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.4.1 FSFAST_HOME       /usr/local/freesurfer/7..4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjects MNI_DIR           /usr/local/freesurfer/7.4.1/mni FSL_DIR           /usr/pubsw/packages/fsl/current - then the head or start of your PATH has on purpose been modified to contain paths pointing to binaries in the freesurfer tree, $ echo $PATH | tr -s ':' '\n'/usr/local/freesurfer/7.4..1/bin /usr/local/freesurfer/7.4.1/fsfast/bin /usr/local/freesurfer/7..4.1/tktools /usr/local/freesurfer/7.4.1/mni/bin…. rest of output deleted … All python scripts in the freesurfer distribution are automatically run with fspython - which in turn runs the python distribution included in freesurfer.  Any, e.g., system, python3 otherwise found in your path should not be used.  We do not recommend activating a conda environment, or other python (virtual) environment that will change PATH or set PYTHONPATH after setting up the freesurfer environment. $ which fspython/usr/local/freesurfer/7.4.1/bin/fspython$ which python3 /usr/bin/python3        <--- not used by freesurfer$ echo $PYTHONPATH… no output ... - R. Subject:[Freesurfer] HelpDate: Wed, 22 Nov 2023 08:44:18 -0500From: Xincen Wu <xlwu25@groton.org>Reply-To:Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>To: Freesurfer@nmr.mgh.harvard.edu        External Email - Use Caution        Hi,I am using freesurfer. I have gone through with the installation and diagnostics and everything works fine. FOr example, using the command recon-all --help in terminal yields a bunch of directions. Yet, when I enter something like: recon-all -s bert -autorecon1an error pops up saying my python3 is problematic. However, I regularly use python3 and redownloaded it after. Please advise on the issue at hand.Thanks,Lucas<Attached Message Part.txt>

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Yeo's 17 Network atlas: label mismatch and volume stats extraction
by 최지혜(영상의학과) 24 Nov '23

24 Nov '23

External Email - Use Caution Hello FreeSurfer experts, I'm attempting to obtain volume values for the ROIs, each corresponding to a specific network based on Yeo's 17 Network atlas. Here are the steps I've done so far: 1. Transform from fsaverage to subject's surface (LH, RH) mri_surf2surf --srcsubject fsaverage5 --trgsubject sdas/sub052 --hemi lh --sval-annot 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/sub052/label/lh.Yeo_17Network_native.annot 2. Transform from subject's surface into my subject's volume mri_aparc2aseg --s sub052 --o $SUBJECTS_DIR/sub052/mri/Yeo17.mgz --annot Yeo_17Network_native --annot-table Downloads/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt Upon inspecting the output file (Yeo17.mgz) overlaid with 17Networks_ColorLUT_freeview.txt before extracting the volume values, I observed that the actual ROI doesn't match the label. ex) The label indicates "DefaultB_IPL" when I point the caudate nucleus Is there something I might be missing? And would you let me know how to extract the volumes of the ROIs for each of the 17 Networks? So I would be getting volumes for 114 ROIs in total. I would greatly appreciate your help. Jihye 상기 메일은 지정된 수신인 만을 위한 것이며 부정경쟁 방지 및 영업비밀보호에 관한 법률을 포함하여 관련 법령에 따라 보호의 대상이 되는 영업비밀, 산업기술 등을 포함하고 있을 수 있습니다. 본 문서에 포함된 정보의 전부 또는 일부를 무단으로 제3자에게 공개, 배포, 복사 또는 사용하는 것은 엄격히 금지됩니다. 본 메일이 잘못 전송된 경우, 발신인에게 알려주시고 즉시 삭제하여 주시기 바랍니다. The above message is intended solely for the named addressee and may contain trade secret, industrial technology or privileged and confidential information otherwise protected under applicable law including the Unfair Competition Prevention and Trade Secret protection act. Any unauthorized dissemination, distribution, copying or use of the information contained in this communication is strictly prohibited. If you have received this communication in error, please notify the sender by email and delete this communication immediately.

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Freesurfer November 2023