Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

issue with mris_ca_label and mrisReadTriangleFile
by Caspar Schwiedrzik 27 Sep '22

27 Sep '22

External Email - Use Caution Hi! I am having issue with mris_ca_label while trying to apply the Yeo 2011 atlas to single subject surfaces. Specifically, I am getting "surface doesn't match" from mrisReadTriangleFile and "could not read spherical coordinate system" from mris_ca_label. lh.smoothwm and lh.sphere.reg both exist in the specified places. It does not matter from where I run the below command. I also tried adding -sdir, which did not change anything. It happens with v5.3 and v7. I have seen a couple of bug reports on this specific error, but no solution other than re-running recon all, which is not an option in my case. Any advice would be appreciated. Thank you! Caspar mris_ca_label -l /home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/label/lh.cortex.label \ 9152127433 lh /home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/surf/lh.sphere.reg \ /home/local/GWDG/cschwie3/ukme11/common/Software/YeoParcellation/lh.Yeo2011_17Networks.gcs \ /home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/label/lh.Yeo2011_17Networks_N1000.annot $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /home/local/GWDG/cschwie3/ukme11/common/Software/YeoParcellation/lh.Yeo2011_17Networks.gcs... reading color table from GCSA file.... average std = 8.4 using min determinant for regularization = 0.705 0 singular and 246 ill-conditioned covariance matrices regularized mrisReadTriangleFile(/home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/surf/lh.sphere.reg): surface doesn't match /neuro_tools/freesurfer/subjects/9152127433/surf/lh.smoothwm No such file or directory mrisReadTriangleFile failed. No such file or directory mris_ca_label: could not read spherical coordinate system from /home/local/GWDG/cschwie3/ukme11/cschwie3/patients/ecog/9152127433/recon/surf/lh.sphere.reg for 9152127433 No such file or directory

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Re: [Freesurfer] FSFAST first level covariates
by Emily Iannazzi 27 Sep '22

27 Sep '22

External Email - Use Caution Hi Doug, Thanks for the reply! We basically want to test an equation like y = age + sex + age*sex. How would you set up the par files for that? ________________________________ 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 <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Friday, September 23, 2022 6:58 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 223, Issue 39 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/1IzCHemGL_AtVnb1hKsNw_yrWd8f7jBmtqch_lhK5jVhdF… 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. Re: Running v7 with recon-all v6 files (fsbuild) 2. Fwd: Error (Ahmad Khan) 3. Re: Error (fsbuild) 4. dcmunpack (O'Dor, Sarah,PHD) 5. Re: Fwd: Error (Douglas N. Greve) 6. Re: dcmunpack (Douglas N. Greve) 7. Re: FSFAST first level covariates (Douglas N. Greve) ---------------------------------------------------------------------- Message: 1 Date: Fri, 23 Sep 2022 08:00:38 +0200 From: fsbuild <fsbuild(a)contbay.com> Subject: Re: [Freesurfer] Running v7 with recon-all v6 files To: freesurfer(a)nmr.mgh.harvard.edu Cc: brouillard.alexandra(a)gmail.com Message-ID: <9bf58e7024ed99c7c06379a6876dda10(a)trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Alexandra Please let us know if you are on an Intel or a newer Mac with an arm processor, e.g., M1, M2 chip.  You could send along a screen shot of what "About this Mac" displays. Per the "Important Note" at the bottom of the freesurfer release page, https://secure-web.cisco.com/1h8voqUHNsdhi9ys-CwoL0SIgr1DmXws2WTt1cB7SmS2bk… , you may not get exactly the same (floating point) results when running v6 on a different/newer version of MacOS. - R. On 9/22/22 09:36, Alexandra Brouillard (brouillard.alexandra(a)gmail.com) wrote:         External Email - Use Caution         Hi   I ran recon-all on an external server using the version 6. I recently downloaded the v6 on my Mac v12.6. I was able to set a home directory but get a ?permission denied? error when typing ?$FREESURFER_HOME? (but have the permissions/sudo). I also can?t open Freeview: by double clicking on the app, the GUI crashes, or by typing ?freeview? in the terminal I get a PETSC error.  According to some previous forum threads, I?m thinking of downloading the v7 but would like to validate that it?s OK when using recon-all v6 files.   Thank you for your support,   Alexandra   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1UxrIgfDDA9rvsB1mbWDnICuSG7lAKZ6_Kt-F6dmE_ycb_… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/10QK0DJSELj6A0Z9B7SeJ4Pw4ytHDHx4VqJvPiItIOo3UK… <https://secure-web.cisco.com/1ODrGbxxaKclPvtjL5GjXY28DLLx66WIe0MpKi9TvUrgA8yMpuw9Az1UEiKz3ZEmzQpPFJG0aY3eyRv4dPWc9saAi1lUcF95WyDKOpsHv_Y8Xk3G7-ZOxKTawTeRD9-VR4KByLwX7H2kRY-ZnveKcN0X7_NUJXbbOL2AaWNT4ARXvFJvMfxxYfgsRWeJ9MdfSesCBSrK7h5QUfeznYTFoHltKLZz4if2ZnSC2xBb1GTu_3fl0kQDPF6AU2VXE5eh6_E8-ewZouLRn3aliC42pz78wQbC_8zqvqd3RGg5eoZvN5w1DRhsO6s85wf870GKj/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1QEu65hJzFz0Qlr-f85ovtCCFPcEQTuVjkATuX8Dzuz3-aNImRz08NXygo1pKr2Wbp8Y7ERP6XX_QXuwwA7OQtL95Jy8KMvQkj8V15v6C3snSGsuYEymHIorCwk50lasrKb8M0DVESSb7lpsfhGW7Z8XrutrhY2vETqwYjoknqZ2L7coJdB9m0JwsRPxH88FkJaPyuapnujCIKZ0QiH7JLW_PxPUN1xjG8C0rI2ClwPd8PHXFdDo4ft_5ujxHY0YquA5UdKOwf3hc1himt1m2KKha9Xl8__;!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC7hKRKUCg$ cwmMraWndDu5-S3ei8hubimZcdWjlXmybq7wVZ40Jt_OHoyghzrMyO1mZg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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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Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than
by Nederpelt, D.R. van (David) 27 Sep '22

27 Sep '22

External Email - Use Caution Thank you for the response. I've attached the log files for each cross sectional analysis separately and the longitudinal as one log file. Cross-sectional commandline: run_samseg -I sub-001_tp1_T1.nii.gz --threads 4 -o result_sub-001 longitudinal commandline: mri_robust_template --mov sub-001_tp1_T1.nii.gz sub-001_tp2_T1.nii.gz sub-001_tp3_T1.nii.gz --template mean_sub-001.mgz --satit --mapmov sub-001_tp0_T1.mgz sub-001_tp1_T1.mgz sub-001_tp2_T1.mgz run_samseg_long --timepoint sub-001_tp0_T1.mgz --timepoint sub-001_tp1_T1.mgz --timepoint sub-001_tp2_T1.mgz --threads 4 -o result_sub-001_long I believe this was the command line suggested by https://secure-web.cisco.com/1oqDIm79n7D7QLNKEDd942zigkcTJZXoH4tRx3rNojVf-E… Thank you, David Message: 3 Date: Mon, 26 Sep 2022 22:14:37 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than cross-sectional To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <34a07418-b022-160b-bfac-39c493226f28(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Can you send your command line and log file? In particular, how did you register the time points? On 9/26/2022 6:46 AM, Nederpelt, D.R. van (David) wrote: > > ????????External Email - Use Caution > > Dear SAMSEG developers, > > We have a dataset with 55 subjects (MS patients and controls) scanned > on three timepoints with yearly intervals. > > When we ran the (SAMSEG) longitudinal pipeline we noticed that the > sbTIV always had an increased volume (between 0.5 and 3.5% larger) > compared to the sbTIV computed cross-sectionally. Do you have any idea > how and why we may see these effects? > > Thank you in advance! > > Best regards, > > David van Nederpelt | Amsterdam UMC > > ______________________________________________________ > VUmc disclaimer : http://secure-web.cisco.com/1EbjEQdohUHHbwqoXgtELvuZtoJbA4FpYVDb696sqA2OCCM… > AMC disclaimer : http://secure-web.cisco.com/1OKBQzdi-SpM4JCdLoqAd96KeYXkbEWuzJHlDAdSqXAevsH… > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1BSAqf9q22bDxY2klFhioiJ1vAOoopvo6KQDUssTUdioRp…

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SAMSEG longitudinal sbTIV bigger than cross-sectional
by Nederpelt, D.R. van (David) 26 Sep '22

26 Sep '22

External Email - Use Caution Dear SAMSEG developers, We have a dataset with 55 subjects (MS patients and controls) scanned on three timepoints with yearly intervals. When we ran the (SAMSEG) longitudinal pipeline we noticed that the sbTIV always had an increased volume (between 0.5 and 3.5% larger) compared to the sbTIV computed cross-sectionally. Do you have any idea how and why we may see these effects? Thank you in advance! Best regards, David van Nederpelt | Amsterdam UMC ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/16dTwUt-h5YvffeeNV0QbLNceQ9UsGTEg6beKJRQ5xjRAWt… AMC disclaimer : http://secure-web.cisco.com/1wCLBitXY1OL0ukuyAU5hlAWzXE9ch8WHFXFMugOT_u3oSI…

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PETSurfer tutorial images?
by daedalus39＠aol.com 26 Sep '22

26 Sep '22

External Email - Use Caution Dear FreeSurfer/PETSurfer experts, I am beginning to explore the functionality of PETSurfer, and in the Wiki there is reference to a set of 18 folders (" called s01, s02, etc"), and I am wondering if that dataset is publicly available (and if so, where?). I am particularly interested in an example of the format/layout of the file: "frame.time.dat -- text file indicating the time at which each frame was acquired." In order to test my syntax, it would be very useful to have a set of explicit volumes and text files. Sincerely, -Randy

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Help with group analysis
by fernanda rohrsetzer 26 Sep '22

26 Sep '22

External Email - Use Caution Hi Freesufer's, I need to run a group analysis but I don't know how to do it, the error always appears (print below). There are 3 groups ( risk_group) that I would like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3) and I would like to control for sex, age and total brain measure. Please, if anyone can help me understand what I'm doing wrong, I'd really appreciate it. The FSG file is attached Thank you.

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mri_sclimbic_seg: --conform not conforming?
by Markus Handal Sneve 26 Sep '22

26 Sep '22

External Email - Use Caution Hi, I’m testing mri_sclimbic_seg in the new FS version (7.3.2). My structurals are 0.8mm isotropic, so I’m adding the —conform flag, but still get this error: [cid:6758653C-0371-4C06-8D50-100648474ED0] Any ideas? And, BTW, I had to set the environmental variable HDF_USE_FILE_LOCKING to FALSE to get the tool running. Perhaps a tip to add to the wiki, if not people can now see it here. Thanks for your great work! Cheers, Markus Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo

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Re: [Freesurfer] segment_subregions failed
by Markus Handal Sneve 26 Sep '22

26 Sep '22

External Email - Use Caution Hi, Sorry if this ends up in the wrong place, had to reactivate my FS-mailing list account. So I get the exact same error as reported by Mamun Al-Amin when running segment_subregion (FS v7.3.2). Fresh terminal, no other FS version running in the background, build-stamp.txt shows the correct version. Hopefully you can see the screenshot below, sadly cannot ctrl-c text out of our cluster [cid:02AE0EFB-80BC-4895-B44D-AC05CB77D890] Thanks! Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo

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Tracula statistics outputs
by King-Wai Chu 26 Sep '22

26 Sep '22

External Email - Use Caution Hi, I have 3 questions on tracula statistics outputs. 1) There are duplicate points in pathstats.byvoxel.txt, is it normal? I didn't try it on all 42 tractcs. For the few I've looked at, they all have duplicate points. I used the default setting in the config file to run trac-all. 2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D files. When embed the sig.mgh and z.mgh statistical maps from the analysis into the template .trk (*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't have enough information to give *.display.trk the voxel values for the *.overlay.trk. There is no one-to-one voxel corresponding between sig.mgh and *.display.trk. What am I missing? Or what's the embedding process do? 3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using dmri_trk2trk or mri_convert the voxel values of the .trk file don't get converted into the .nii.gz or ascii file, only the x,y,z coordinates are converted. Is there a way to get the voxels values of the .trk file when converting to .nii.gz or ascii format? Thanks, King-Wai -- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. Peters Dept. of Veterans Administration Medical Center (OOMH) 130 W. Kingsbridge Road Bronx, NY 10468

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intrareg: Undefined variable
by miracle ozzoude 26 Sep '22

26 Sep '22

External Email - Use Caution Hello, I am trying to run TRACULA using FreeSurfer version7.2. I followed the instructions on the tutorial website for cross-sectional study with 1 scan (see link below). However, I keep getting "intrareg:Undefined variable" error whenever I run the first step "trac-all -prep -c tracula.file". I checked my config file and I did set intrareg = 3. Any suggestions on what the issue is/how to fix it? I have attached my config file in the email below, in addition to the log file. The participants' recon-all were processed using freesurfer v6.0 Many thanks, Paul

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