Freesurfer January 2025

freesurfer@nmr.mgh.harvard.edu

44 participants
67 discussions

Neuroimaging Analyst Position at University of Seville
by PATRICIA POMBO SEGURA 07 Jan '25

07 Jan '25

External Email - Use Caution We’re hiring! 🚀 Are you passionate about neuroimaging, MRI, brain charts, or genetics? 📊🧠 * Join our research team at the Neuroimaging Lab, University of Seville, and work on "Resil-net: Resilience and vulnerability—from neural circuits to networks". 🌐✨ Resil-Net is a European project bringing together 6 research groups to explore how brain reorganization relates to vulnerability and resilience. Predoc and postdoc candidates will be considered! https://secure-web.cisco.com/1zve6DjfggQCRWhak2xSLQJiOa-i-Br7WUB4WQ-IGtvMoh… https://secure-web.cisco.com/12-gDglo7g1H8gccIBBRTxKETQjKjNfUl5FAq_nwB-DLW0… https://secure-web.cisco.com/1srEdi67CckI8YYhEok8zLTL4YWZyVb2kf3Iab3sQYMLUS… https://secure-web.cisco.com/1s2RdRBBD3pTutq7jv6nfU-ctalIdDqqcu2PO6O3utKciw…

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Re: [Freesurfer] Freesurfer Digest, Vol 251, Issue 6
by 黄月虹 06 Jan '25

06 Jan '25

External Email - Use Caution Thanks，please don't send emails！ > -----原始邮件----- > 发件人: freesurfer-request(a)nmr.mgh.harvard.edu > 发送时间:2025-01-06 22:12:15 (星期一) > 收件人: freesurfer(a)nmr.mgh.harvard.edu > 主题: Freesurfer Digest, Vol 251, Issue 6 > > 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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_Bv… > 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: [ext] Re: Freeview crash (Tietze, Anna) > 2. How to Plot Surface with ROI Boundaries Using Harvard-Oxford > Brain Atlas? (Zeng, Xinglin) > 3. Re: [ext] Re: Freeview crash (Wang, Ruopeng) > 4. Re: [ext] Re: Freeview crash (Dicamillo, Robert) > 5. registration error (Ramesh Babu) > 6. Re: [External] Re: Assistance with mri_vol2surf: Missing > Surface Values in Output (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Jan 2025 20:58:14 +0000 > From: "Tietze, Anna" <anna.tietze(a)charite.de> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <89FA2C60-63FF-4959-8039-0724E56EF3CC(a)charite.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Ruopeng, > > It works with the app when I move the licence.txt! It doesn?t work from the terminal so far, but this helps a lot. Thank you very much! > > Best, Anna > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4(a)MGH.HARVARD.EDU> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Date: Friday, 3. January 2025 at 18:17 > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > > I mean /Applications/freesurfer/license.txt. > > > On Jan 3, 2025, at 11:36 AM, Tietze, Anna <anna.tietze(a)charite.de<mailto:anna.tietze@charite.de>> wrote: > > > It?s there: > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) > Or do you mean /Applications/freesurfer/license.txt? > > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> Im Auftrag von Wang, Ruopeng > Gesendet: Freitag, 3. Januar 2025 16:58 > An: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Betreff: Re: [Freesurfer] [ext] Re: Freeview crash > > To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data. > > On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze(a)charite.de<mailto:anna.tietze@charite.de>> wrote: > > External Email - Use Caution > Yes, I?ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent?sometimes I can load a file without any issues, but most of the time, it crashes in the same way. > I?ve this problem on two different Macs: > > * System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. > * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0. > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu<mailto:RWANG4@mgh.harvard.edu>> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, 2. January 2025 at 19:04 > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [ext] Re: [Freesurfer] Freeview crash > > Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this: > > $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview > > On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze(a)charite.de<mailto:anna.tietze@charite.de>> wrote: > > > Hi, > > When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me? > > Operating system: Mac, Sonoma 14.7.1 > Fressurfer version 7.4.0 > XQuatz 2.8.5 > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) > environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh > > When I run the command freeview, the following message is given: > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Or trying to open a file: > freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Attached is a detailed error report. > > What did I overlook?? Thank you so much for help! > > Best, Anna > <problem report freeview.rtf> > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr…<https://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34i…> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr…<https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQit…> > > <smime.p7s> External Email - Use Caution > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr… > 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/1C3Rm_EJQFroDFSeUXGwlWJGelS12bb9i0uJ0bBhV30bmw… <https://secure-web.cisco.com/1C3Rm_EJQFroDFSeUXGwlWJGelS12bb9i0uJ0bBhV30bmw… > EvnvCxt9TqD/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . > 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. > > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr… > > >

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registration error
by Ramesh Babu 06 Jan '25

06 Jan '25

External Email - Use Caution Hello, I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local subject space. For this, I want to generate a registration.dat file which will be used for registration with local subject image. But I am facing an issue which I pasted below. echo $SUBJECTS_DIR /usr/local/freesurfer/subjects bbregister --ss sample-001.mgz --mov /usr/local/fsl/data/atlases/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz --reg registration_matrix.dat --init-fsl --dti ERROR: Flag --ss unrecognized. --ss sample-001.mgz --mov /usr/local/fsl/data/atlases/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz --reg registration_matrix.dat --init-fsl --dti I tried with -s flag, but still the same error. Could you please provide me a solution? Regards Ramesh

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How to Plot Surface with ROI Boundaries Using Harvard-Oxford Brain Atlas?
by Zeng, Xinglin 06 Jan '25

06 Jan '25

External Email - Use Caution Dear Community, I am currently working on visualizing ROI boundaries on the brain surface using the Harvard-Oxford brain atlas. My goal is to generate a surface plot that overlays ROI boundaries from the atlas in a clear and accurate manner. I also tried visualizing in Freeview, connectome_workbench, and I could plot the surface but I was unable to plot the boundaries correctly. Specific challenges I’m facing: I don’t know how to combine the ROI boundaries with a functional surface overlay while keeping the boundaries visible. [image]<https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJF…> image800×330 95 KB<https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJF…> I would really appreciate any tips, example commands, or references to similar workflows. Thank you in advance for your help!

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Freeview crash
by Tietze, Anna 03 Jan '25

03 Jan '25

Hi, When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me? Operating system: Mac, Sonoma 14.7.1 Fressurfer version 7.4.0 XQuatz 2.8.5 licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh When I run the command freeview, the following message is given: /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Or trying to open a file: freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Attached is a detailed error report. What did I overlook?? Thank you so much for help! Best, Anna External Email - Use Caution

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Re: [Freesurfer] [ext] Re: Freeview crash
by fsbuild 03 Jan '25

03 Jan '25

External Email - Use Caution  Below are the commands I used to run freeview from the Freesurfer 7.4..0 release on a silicon Mac with an M2 processor running MacOS Sonoma 14.7.2 with Xquartz 2.8.5.  I put the freesurfer license.txt file under my home directory and set the FS_LICENSE environment variable to its path.  (If you add that FS_LICENSE setting to your shell initialization file, then you should not need to worry about setting up the license again no matter what freesurfer release/build you end up using).   I then ran freeview with no arguments to make sure it could open an empty window.  Then I had freeview display one of the volume files included with the example subject data. The old 7.4.0 release contains only Intel binaries and so has to run under Rosetta on silicon Macs with M processors.  While this should work for freeview, it will not work to run some of the other commands in the 7.4.0 distribution on a silicon Mac.  If you plan to use the freesurfer mri* commands, then you would be better off installing a native build of freesurfer compiled for the silicon Macs.   You can use this installer package to install a recent stable development build from 09/2024, https://secure-web.cisco.com/1mYajo-Nb3fUswwrx78iSXy97lDpj0Dp… If you want to try that development build, I would first remove the 7.4.0 release with the command,$ sudo bash /Applications/freesurfer/7.4.0/uninstall.sh With that development build, then FREESURFER_HOME would be set as in the commands below as,$ export FREESURFER_HOME=/Applications/freesurfer/dev - R. - - - - - - -  $ bash… output deleted …$ export FREESURFER_HOME=/Applications/freesurfer/7.4.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.4.0-20230510-e558e6e --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.0FSFAST_HOME       /Applications/freesurfer/7.4.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.4.0/subjectsMNI_DIR           /Applications/freesurfer/7.4.0/mni$ which freeview/Applications/freesurfer/7.4.0/bin/freeview$ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou(a)somewhere.com      <—— email address you used to register for license$ freeview     <—— check that freeview opens an empty window$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz  <--- try opening one of the included volume files On Jan 3, 2025, at 00:49, Tietze, Anna <anna.tietze(a)charite.de> wrote:        External Email - Use Caution         M3 max processor Anna Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von fsbuild <fsbuild(a)contbay.com> Gesendet: Donnerstag, 2. Januar 2025 19:46 An: freesurfer@nmr.mgh.harvard.edu Betreff: [ext] Re: [Freesurfer] Freeview crash         External Email - Use Caution         Are you running on an old Intel Mac or a Mac with one of the newer M1, M2, M3, M4 processors ? - R. On Jan 2, 2025, at 13:02, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this: $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview  On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze(a)charite.de> wrote: Hi, When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me? Operating system: Mac, Sonoma 14.7.1Fressurfer version 7.4.0XQuatz 2.8.5licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works)environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh When I run the command freeview, the following message is given:/Applications/freesurfer/7.4.0/bin/freeview: line 2:  6615 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Or trying to open a file:freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2:  6765 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2:  6799 Segmentation fault: 11  $FREESURFER_HOME/Freeview..app/Contents/MacOS/freeview "$@" Attached is a detailed error report. What did I overlook?? Thank you so much for help! Best, Anna<problem report freeview.rtf>        External Email - Use Caution        _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1QHuUffDuUmCT6Kur8brjyEtinGdgVAQ8kT19o… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1QHuUffDuUmCT6Kur8brjyEtinGdgVAQ8kT19o05mNUMnZ… _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview crash
by fsbuild 03 Jan '25

03 Jan '25

External Email - Use Caution  Are you running on an old Intel Mac or a Mac with one of the newer M1, M2, M3, M4 processors ? - R. On Jan 2, 2025, at 13:02, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this: $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview  On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze(a)charite.de> wrote: Hi, When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me? Operating system: Mac, Sonoma 14.7.1Fressurfer version 7.4.0XQuatz 2.8.5licence.txt located in: /Applications/freesurfer/7.4.0/license..txt (can be read, as recon-all works)environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh When I run the command freeview, the following message is given:/Applications/freesurfer/7.4.0/bin/freeview: line 2:  6615 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Or trying to open a file:freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2:  6765 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2:  6799 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Attached is a detailed error report. What did I overlook?? Thank you so much for help! Best, Anna<problem report freeview.rtf>        External Email - Use Caution        _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/18V4CVl0pNi04RSRcHVGUZZ2grg3UExn--vRzoOrrkkJKL…

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Issues with MRI and PET Registration to fsaverage Template
by 문준호 02 Jan '25

02 Jan '25

External Email - Use Caution Hello, I am currently working on registering MRI and PET data from the ADNI dataset, processed using our custom preprocessing pipeline, to the fsaverage template. My goal is to align both the MRI and PET data to the fsaverage template. To achieve this, I followed these steps: *Step 1:* I used mri_coreg to create an LTA file for registering the MRI data to the fsaverage template. Then, I used mri_vol2vol to perform the registration of the MRI data to the fsaverage template. Commands Used: mri_coreg --mov $MRI_PATH --targ $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg ${OUTPUT_DIR}/mri${num}_reg.lta mri_vol2vol --mov $MRI_PATH --targ $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg ${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/mri${num}_to_atlas.nii.gz *Step 2:* I used the LTA file generated in Step 1 and applied mri_vol2vol to register the PET data to the MRI data. Commands Used: mri_vol2vol --mov $PET_PATH --targ ${OUTPUT_DIR}/mri${num} _to_atlas .nii.gz --reg ${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/pet${num}_to_atlas.nii.gz However, when visualizing the results using Freeview, I noticed that the registration of both the MRI and PET data to the fsaverage template is not accurate. (The MRI and PET data were successfully co-registered.) I have attached some images of the results and the output from the mri_info command for your reference. # freeview results ## Example 1[image: 6f1a5a16-f77f-493c-8802-925ef33a7f98.png] ## Example 2 [image: image.png] ## Example 3 [image: 37a638c7-944d-424c-af84-4fa1860560dc.png] # mri_info results ## T1w MRI niiRead(): detected input as 64 bit double, reading in as 32 bit float Volume information for {my_mri_data} type: nii dimensions: 128 x 128 x 128 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 128.000 dof: 1 xstart: -64.0, xend: 64.0 ystart: -64.0, yend: 64.0 zstart: -64.0, zend: 64.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -13.0000 : x_a = -0.0000, y_a = 1.0000, z_a = -0.0000, c_a = 16.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 11.5000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -1.0000 -0.0000 0.0000 51.0000 -0.0000 1.0000 -0.0000 -47.5000 0.0000 0.0000 1.0000 -52.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 51.0000 -0.0000 1.0000 -0.0000 47.5000 -0.0000 -0.0000 1.0000 52.5000 -0.0000 -0.0000 -0.0000 1.0000 ## brain.mgz Volume information for /usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/brain.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : /usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000 Could you please help me identify any potential issues with my approach or the commands I used? I would greatly appreciate any guidance you can provide. Thanks a lot! Best regards, Junho Moon

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LME pipeline for individual ROIs
by Bondi, Daniel 02 Jan '25

02 Jan '25

External Email - Use Caution Hello FreeSurfer experts, I am using a mass-univariate pipeline to assess cortical thickness changes longitudinally at a regional level (based on the D-K atlas), and have been following this thread: https://secure-web.cisco.com/1gfQ9eWAEqDZ3DGmI9NL7F2WPKbHBLsM60VyuP_LVR3dT1… My pipeline is set up so that lme_mass_fit, lme_mass_F, and lme_mass_FDR are all run independently in a for-loop for each individual ROI, rather than altogether. Is this correct? As well, would using FDR2 be more advantageous than FDR? Best, Daniel Bondi

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(no subject)
by Tommaso Mariani 02 Jan '25

02 Jan '25

External Email - Use Caution Dear authors, I'm trying to reconstruct a model of a brain from an MRI, and after completion of recon-all (without any errors) the results are truly poor. By looking through your tutorials I am quite confident to say that the problem is either one of intensity normalisation or of white matter segmentation (possibly, both), as you can see in the images attached. My first attempt is to insert some control points, though I wonder if I might need instead to fix the segmentation with the brush tool. Could it be possible to receive some feedback about this issue? Another issue regards the freeview software, as whenever I move with the arrows from a slice to another the loaded surfaces suddenly disappear and won't reappear unless I delete and reopen them, and it makes it really hard to insert control points if I can't see the surfaces' outlines. Also, I was wondering if the computational cost of the autorecon2-cp is dependent significantly on the number of control points. The pictures shows the lh.white, rh.white files over the T1.mgz file and the wm.mgz and control.dat files over the brain mask.mgz file. Thanks in advance for your help, Tommaso Mariani

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