Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

How to verify that cortical surface orientation volume w/ respect to b0 is accurate?
by Bansal, Krishan Chandra 28 Sep '22

28 Sep '22

External Email - Use Caution I have created a volume which is supposed to have the cortical surface orientation with respect to b0 at each voxel. To do this I got the 6 frame overlay file from mris_convert. Then I isolated the first 3 values from each row in Matlab to create an Nx3 matrix, then from this I calculated the angle between each row vector and the b0 vector (which was just [0 1 0]) using the usual angle between two vectors formula. The result was an Nx1 matrix.I then saved it as an .mgh surface file (using save_mgh) and projected it back onto the original volume using surf2vol. I believe that I did this correctly, however the professor that I am developing this method for told me he wants me to verify that the results are correct. He was not very specific in how to do this, all he told me was that I could use volumes of the individual scanner x,y,z angles to help me figure out if my b0 results are right. What I assume he meant is: since the b0 axis goes vertically down the middle of the brain when in coronal view I can tell if the b0 angles are correct by seeing where the cortical surface is with respect to the z scanner direction and seeing if the b0 angle at the corresponding location makes sense. My problem is that I can’t tell if my results make sense. In theory I believe that at the locations where the cortex appears to be orthogonal to the B0 (z scanner) axis, the overall B0 angle of the cortical surface should be closer to 90 degrees. I still don’t understand what pattern I should be seeing in the values of the z scanner volume compared to the b0 angles volume. Comparing my z scanner volume results to the B0 angle volume the only pattern I can see is that the cortical surface with respect to B0 is closer to 90 degrees when the z scanner volume is closer to 0 degrees. No B0 angle I got is actually greater than 89 though. I can’t tell if this is the right pattern or enough to verify the results in the way the professor I’m working for wants. Any help here would be GREATLY appreciated. So far I have been able to get pretty far in teaching myself Freesurfer, but the some of the underlying mathematics about how to verify my results are unclear. I can send pictures of my results if someone wants to look at them.

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Assistant Professor in Cognitive Neuroscience at UW-Milwaukee
by Caitlin R Bowman 28 Sep '22

28 Sep '22

External Email - Use Caution The University of Wisconsin-Milwaukee (UWM) is seeking applicants for a tenure-track faculty position in Cognitive Neuroscience. UWM is a Carnegie “Research 1” institution located in Wisconsin’s cultural and economic center. We are interested in recruiting outstanding scientists that will build directly on the current strengths of our program (http://secure-web.cisco.com/1k866Hj6O0LlrfeDn8tfH4EdKsnTmoH6F2ktOgucr0s8Ck9…) We expect to make an appointment at the Assistant Professor level. Responsibilities include developing an independent extramurally funded research program and teaching graduate and undergraduate courses in the neurosciences and experimental psychology. Successful applicants will have access to two research-dedicated MRI scanners maintained by the Center for Imaging Research (https://secure-web.cisco.com/13spGP24aK2sb8fPfNu2ykeT0PNJZJAabHc-QLtSPpbbMD…) and should be actively conducting novel, theory-based research in the domain of cognitive neuroscience. Outstanding individuals who use cutting-edge neuroimaging and/or computational methods to address questions about perception, attention, memory, aging, emotion, decision-making, or any combination of these cognitive domains are encouraged to apply. Individuals from minoritized, underrepresented communities are particularly encouraged to apply. See full job posting: https://secure-web.cisco.com/1cPlunNEn-50PO-A_IKfS2IE4eWAFUpiXPigrsu7QTG1F9… Contact Caitlin Bowman (bowman2(a)uwm.edu<mailto:bowman2@uwm.edu>) with questions. -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee

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How can I get a code to unzip the image for Freesurfer?
by Marisa Smith 27 Sep '22

27 Sep '22

External Email - Use Caution

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Job Ad: Professor of Biopsychology
by Katharina von Kriegstein 27 Sep '22

27 Sep '22

External Email - Use Caution The Faculty of Psychology at TU Dresden, Germany, invites applications for the Chair (W2) of Biopsychology to be filled on April 1, 2024. TU Dresden is one of eleven German Universities of Excellence. The Faculty of Psychology currently has eighteen chairs covering a broad spectrum of psychology and human neuroscience. It provides an outstanding scientific infrastructure and ideal environment for interdisciplinary cooperation. The Faculty of Psychology is member of several large-scale funding schemes and also houses a state-of-the-art human neuroscience center with 3-Tesla MRI, neurostimulation (TMS, tFUS, tDCS), EEG, and a wet lab. We are looking for a scientifically outstanding personality (m/f/x) with international visibility who will strengthen the institute's profile in both research and teaching. More information on the post can be found here (PDF): https://secure-web.cisco.com/1S2bXVTPk0w19EvBKdImAJ6Vp5wpmKlaYJ9rSdHlXrSYy2… _ _ Katharina von Kriegstein Professor of Cognitive and Clinical Neuroscience Vice-Dean Faculty of Psychology Technische Universität Dresden Bamberger Str. 7, 01187 Dresden, Germany Phone +49 (0) 351-463-43145 https://secure-web.cisco.com/1G_nIYC6x1SmWHCj16HQigz4I1hlUzjs9vePO1-TsePxnT… https://secure-web.cisco.com/17hxGRVbbU1_mm71iu4AN1dxHwvJ0yJebo0Mnn3GJTG7FB…

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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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