Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Freesurfer Digest, Vol 238, Issue 7
by Spapens, Jeltje (NP) 21 Dec '23

21 Dec '23

External Email - Use Caution Hi I have not received a response to my question yet I think __ On 13/12/2023, 08.53, "freesurfer-bounces(a)nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu>" <freesurfer-bounces(a)nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/13w96AyqB5Nk5Zlu_uq8_qAk6WErZ9a6rflAusUqF0Icp2… <https://secure-web.cisco.com/13w96AyqB5Nk5Zlu_uq8_qAk6WErZ9a6rflAusUqF0Icp2…> or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu <mailto:freesurfer-owner@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. FW: Boundary based registration (Spapens, Jeltje (NP)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 13 Dec 2023 07:48:55 +0000 From: "Spapens, Jeltje (NP)" <j.spapens(a)maastrichtuniversity.nl <mailto:j.spapens@maastrichtuniversity.nl>> Subject: [Freesurfer] FW: Boundary based registration To: "freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <802B8CE8-CF05-4066-809E-1B14866460CB(a)maastrichtuniversity.nl <mailto:802B8CE8-CF05-4066-809E-1B14866460CB@maastrichtuniversity.nl>> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Freesurfer developers, I want to register an MRI slap to a full FoV UNI scan of the same subject, but I get a false reorientation with my code (see attached image). I have tried multiple input and tried the script on different subjects. I also changed som flags such as -init-header and --cubic, but all seem to give the same results. bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --t2 --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_acpc_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat ?trilin I would appreciate to hear your thoughts on this problem. Have a nice weekend and kind regards, Jeltje Spapens

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Re: [Freesurfer] Freesurfer/Freeview Version Compatibility
by fsbuild 20 Dec '23

20 Dec '23

External Email - Use Caution The freesurfer 6.X and 7.x release release notes summarize some changes for Freeview (listed below) since version 5 was released in 2013.   If none of the improvements in features/stability are relevant to what you are doing, then I don’t see why you could not revert to the older 5.X software.  But if you run into issues with a now ~10 year old version of Freeview, we may tell you to use the latest 7.4.1 release from June of 2023. - R. - - - - -  • New: interface for x virtual frame buffer (fsxvfb). When you run freeview from fsxvfb, no X server is needed. This is good for taking a bunch of pictures when you don't want freeview popping up all the time. Eg, fsxvfb freeview orig.mgz -ss mypic.png —quit • The filled.mgz can now be edited instead of the wm.mgz. The advantage to this is that filled.mgz is slightly further in the process and it is more intuitive. The filled.mgz is actually a segmentation of the subcortical mass. In Freeview, you can view it in outline mode, meaning that the edges of the segmentations are actually the surface that you are editing. After that, run recon-all with the -autorecon2-wm -autorecon3 options, just as you would if you had edited the wm.mgz..Landmark-based repositioning of surfaces. Did you ever want to just make the surface move through a certain point? You can do that now by creating point sets in freeview. Create a separate point set for each surface (lh, rh, white, and pial), then save it in subject/surf with a file name repos.$hemi.$surf.json where $hemi is either lh or rh and $surf is either white or pial. Then run recon-all with the -autorecon2-surfonly -autorecon3 options. Note that you can do this interactively inside of FreeView as well; look under Tools->Resposition Surface. If you do it interactively, the surface may be overwritten next time recon-all is re-run, but it gives you a chance to play with the repositioning.freeview - can now load and visualize diffusion orientation distribution function (ODF) data.FreeView changes: surfce path and label editing, surface annotation editing, automatic segmentation assisted by Geodesic Matting algorithm, displaying two time courses at the same time, better support for Mac (petsc error fixed on Mac) On Dec 20, 2023, at 14:07, Edwards, Vincent <Vincent.Edwards(a)utdallas.edu> wrote:        External Email - Use Caution        Hi, I'm following up on my quick question from this time last week. I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able to do recon-all through Freesurfer 7?  Years ago, someone asked if they could do recon-all in an older version of Freesurfer and edit in a newer GUI. Doug said that was fine. My question is basically the inverse of their problem. I assumed that since Freeview is a GUI, the version used shouldn't have any actual impact on things as long as we returned to version 7 to recon-all. I just want to confirm that my assumption is correct?The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all for pial/wm/cp's)Thanks,Vincent Edwards_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Evaluating the Reliability of Optic Chiasma Analysis in Freesurfer
by Knut J Bjuland 20 Dec '23

20 Dec '23

External Email - Use Caution Dear FreeSurfer experte I am currently engaged in a detailed volume analysis project where I am utilizing the optic chiasma as a key focal point. In this context, I'm specifically interested in understanding how reliable the optic chiasma measurements are when analyzed using Freesurfer software. This includes assessing the accuracy of volumetric data, the precision of segmentation processes, and the overall consistency of results obtained across different datasets. Given the critical role of the optic chiasma in neuroanatomical studies, it's imperative to ensure that the tools we use provide dependable and repeatable outcomes. Therefore, any insights into the efficacy of Freesurfer in handling optic chiasma data would be greatly appreciated, as it will significantly impact the interpretation and validity of our research findings. Knut Jørgen Bjuland

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Clinical research coordinator position II at MGH - Boston
by Jacobs, Heidi I.,PHD 18 Dec '23

18 Dec '23

Clinical Research Coordinator II position at the Department of Radiology, Massachusetts General Hospital / Harvard Medical School Are you passionate about neuropsychology and eager to contribute to a clinical trial focused on individuals at risk for Alzheimer’s disease? JOIN US! The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, is hiring a clinical research coordinator to work with Dr. Heidi Jacobs (www.heidijacobs.org<http://www.heidijacobs.org>). The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers and cognitive assessments. In this position, you'll play a crucial role in our clinical trial exploring the potential of transcutaneous vagus nerve stimulation on memory. Responsibilities include neuropsychological testing, 7T MR-imaging, physiological and pupil measurements, administering the intervention, conducting phlebotomy, and overall organizational tasks. More information and application: https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3261238&tz=G… For this position we seek someone with a B.A/B.S./MS with background in pre-med, psychology, neuroscience or related field required and with one year of experience in a related field. Dr. Heidi Jacobs Associate Professor of Radiology Massachusetts General Hospital Harvard Medical School Department of Radiology Gordon Center for Medical Imaging 149 13th Street Charlestown, MA 02129 hjacobs(a)mgh.harvard.edu www.heidijacobs.org<http://www.heidijacobs.nl> twitter: @HeidiJacobsLab Linkedin: https://www.linkedin.com/in/heidijacobs/

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aparcstats2table - append option
by Horn, Mitchell Jacob 18 Dec '23

18 Dec '23

Hi FS Devs, Would it be possible to add an "append" flag for use with aparcstats2table and asegstats2table? If I understand their usage correctly, each time one of them are run they will create (or overwrite) a new file. Not urgent but would be useful. Thanks, Mitch

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Convert Scanner RAS to Vertex RAS
by Eric Tsang 18 Dec '23

18 Dec '23

External Email - Use Caution Dear All, I have great deal of trouble converting scanner RAS to vertex RAS. I have tried a couple of formula (in the following) which had failed to produce accurate coordinate. [tkR tkA tkrS] = [ScannerRAS 1] / (vox2ras * inv(tkrvox2ras))[tkR tkA tkrS] = [ScannerRAS 1] * inv(vox2ras0) Both of these formula produced distorted coordinates. Please help! Thanks,Tim

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cannot read nifti-2 files in freesurfer - files ok in AFNI
by Patricia Pais Roldan 15 Dec '23

15 Dec '23

External Email - Use Caution Dear Freesurfer team, I am having problems reading files with nifti-2 header, the error I get is something like "error: No such file or directory; error: niiRead(): bad number of dimensions (31488) in $file*". I get this error with any FS function (e.g., with mri_info $file), so I cannot work with these files in FS at all. The original files were nifti-1 (and readable by FS) but after processing them in AFNI, they were converted to nifti-2 (and now FS cannot read them). I contacted the AFNI team and everything seems to be alright with the files (AFNI functions can work with them and they can be displayed in the AFNI viewer). Does FS have the requirement of files being nifti-1? Thank you very much in advance. Best regards, Patricia ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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aparcstats2table - IndexError
by Laura Willers de Souza 15 Dec '23

15 Dec '23

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to get the cortical thickness values for a list of subjects using aparcstats2table and I'm encountering this error: aparcstats2table --fsgd subjects.test1.fsgd --meas thickness --hemi lh --common-parcs --tablefile lh.aparc.thickness.table SUBJECTS_DIR : /mnt/wsl/PHYSICALDRIVE1/FS_OUTPUTS Traceback (most recent call last): File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 376, in <module> subj_listoftuples = assemble_inputs(options) File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 273, in assemble_inputs if splitline[0].upper() == 'INPUT': IndexError: list index out of range The fsgd file only contains the list of subjects, as illustrated below: GroupDescriptorFile 1 Title subjects.test1 Input 002_S_0295_S13408 Input 002_S_0413_S13893 Input 002_S_0559_S14875 I have successfully executed the same command for an individual subject. For other measurements (surface area, volume) this error also occurs. It's worth noting that the images and files for the subjects and recon-all are stored on an external hard drive that I have mounted on Linux, emulated on Windows. Could this be the source of the problem? I appreciate any assistance you can provide with resolving this issue. Thanks in advance! Laura Willers de Souza PhD Student in Pharmacology and Therapeutics Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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The Corpus Callosum parcellation
by FMU 14 Dec '23

14 Dec '23

External Email - Use Caution Hi everyone. What is the background or rationale behind the five segments of the Corpus Callosum that we see in the aparc files? What is the segmentation based on? I would appreciate any reference you can give me. Mudathir

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Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled
by fsbuild 11 Dec '23

11 Dec '23

External Email - Use Caution I don’t think there is any GUI or graphical interface with the runtime environment (which does not require a Matlab license).  Neither does it contain the matlab compiler to build matlab executables, etc.  So if you still need to create Matlab executables either with the GUI or from the command line, you would need to have your own site or personal installation of Matlab with a license.  The Matlab runtime environment in freesurfer subsequently allows you to run what has already been built with Matlab. - R. On Dec 10, 2023, at 21:31, Sophie Matis <sophie.matis(a)sydney.edu.au> wrote:        External Email - Use Caution        Hi there, Thanks for the advice, I have followed these suggestions and used the fs_install_mcr command and can see the the libmwm* libraries are installed under $FREESURFER_HOME/MCRv97/bin/glnxa64. I also added the path the script suggested once finished to LD_LIBRARY_PATH. I’m now not sure how to open matlab now though as I can’t find any executable matlab file? There were no error with the command but it doesn’t look like matlab was installed… Thanks again for the help, Sophie Matis | Data Management & Research OfficerSchool of Health Sciences & Brain and Mind Centre Faculty of Medicine and Health  The University of Sydney  Brain and Mind Centre, 94-100 Mallett Street, Camperdown (M02G) | The University of Sydney | NSW | 2006 sophie.matis(a)sydney.edu.au  | sydney.edu.au CRICOS 00026AThis email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this email if necessary. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of fsbuildSent: Saturday, November 25, 2023 6:43 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled         External Email - Use Caution         Hello Sophie,Just FYI, there is no matlab distribution included in the 7.4.1 release and we so not support using R2023b.  So I presume someone at your site installed R2023b separately via a Mathworks matlab installer.  We do provide a script, fs_install_mcr, to install either the R2014b or R2019b matlab runtime environment into the freesurfer tree for use.  I don't know if running R2019b would affect what you report below, but you could try it via the commands below.- R.$ 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  R2019bI 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 behttps://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels 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 wikiContrast is [0 1]This is my qdec file: fsid    fsid-base       yearsfromBL108_MR1       108   0.00199_MR1       199   0.00199_MR2       199   1.10199_MR3       199   2.25202_MR1       202   0.00204_MR1       204   0.00204_MR2       204   1.16204_MR3       204   2.30223_MR1       223   0.000821_MR1      0821  0.000931_MR1      0931  0.001010_MR1      1010  0.001010_MR2      1010  1.841031_MR1      1031  0..001031_MR2      1031  1.001031_MR3      1031  2.131064_MR1      1064  0.001064_MR2      1064  2.011125_MR1      1125  0.001134_MR1      1134  0.001134_MR2      1134  1.171134_MR3      1134  2.281233_MR1      1233  0.001233_MR2      1233  1.051373_MR1      1373  0.001439_MR1      1439  0.001439_MR2      1439  1.141439_MR3      1439  2.281475_MR1      1475  0.001475_MR2      1475  1.041475_MR3      1475  2.031522_MR1      1522  0.001522_MR2      1522  2.071541_MR1      1541  0.001541_MR2      1541  1.471551_MR1      1551  0.001551_MR2      1551  0.981551_MR3      1551  2.051572_MR1      1572  0..001572_MR2      1572  1.031625_MR1      1625  0.001625_MR2      1625  1.061637_MR1      1637  0.001641_MR1      1641  0.001656_MR1      1656  0.001656_MR2      1656  0.941656_MR3      1656  2.261755_MR1      1755  0.001755_MR2      1755  1.041755_MR3      1755  2.011829_MR1      1829  0.0009154_MR1     09154 0.0009154_MR2     09154 1.0109154_MR3     09154 2.0112110_MR1     12110 0.0012110_MR2     12110 1.04  Any help appreciated! Thank you, Sophie Matis | Data Management & Research OfficerSchool 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 00026AThis 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 listFreesurfer@nmr.mgh..harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1p2Xe7gNwGMHP6pOnr2RizRPipeaYfciNCVH_GRWyTs7Kk… 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.  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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