Freesurfer

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30064 discussions

Freesurfer white matter overestimated
by Luisa Klahn 23 Feb '24

23 Feb '24

External Email - Use Caution Hello! I am processing structural data from a 3T scanner using Freesurfer version 7.3.2. For some subjects, the grey matter looks very thin, and the white matter looks overestimated. I'll attach screenshots of the brainmask, wm mask, and T1 including wm and pial surface lines. I have tried to set control points into the wm but this did not change the results. Does anyone have an idea? Would it be possible to change the intensity settings in the recon-all command? Thanks for helping! Luisa

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Fixing intensity normalization issue which leads to gray matter classified as WM
by Maya Yablonski 23 Feb '24

23 Feb '24

External Email - Use Caution Hello, I am running freesurfer v7.3.2 reconall with -synthseg on a pediatric sample, and for one specific subject I keep getting a lot of gray matter classified as white matter, which leads to the ?h.white surfaces being too close to the pial surface. I have tried running with and without the --robust option but the issue recurs. Are there any expert options that I can play with before manually editing the WM.mgz? The issue is pervasive throughout the brain so will require heavily editing every single slice. The values for the misclassified gray matter are 85-97 in the brainmask.mgz and 100-110 in the WM.mgz and the T1 image looks ok by eye. When trying to run the same subject with the default pipeline (no synthseg), it crashes with the following error: reading 1 input volumes... logging results to talairach.log reading '/share/software/user/open/freesurfer/7.3.2/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... error: mghRead(/MYPATH/freesurfer/sub-2341/mri/brainmask.mgz, -1): could not open file error: mri_em_register: could not open mask volume brainmask.mgz. I wonder if there's any parameter I can tweak in the expert.opts? Thanks for any leads, Maya

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Grey Matter Intensities
by ERNEST KISSI 21 Feb '24

21 Feb '24

External Email - Use Caution Hi Freesurfer team, Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities. Thank you.

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Help with Recon-all Errors
by Perumalla, Sucika 21 Feb '24

21 Feb '24

Hello FreeSurfer Support, My name is Sucika Perumalla and I hope you can please help me with troubleshooting recon-all. I’m getting multiple frames errors when trying to run recon-all with my dicoms even after extracting the multiple frames. I was wondering if you can please help resolve this issue. Please refer to the attachment with my recon-all log. Thanks _____________________________ Sucika Perumalla Clinical Research Assistant I Department of Neurology, Division of Movement Disorders Brigham and Women’s Hospital 60 Fenwood Road, Boston, MA 02115 sperumalla1(a)bwh.harvard.edu<mailto:sperumalla1@bwh.harvard.edu> | 508-414-2601

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Errors with Recon-all
by Perumalla, Sucika 21 Feb '24

21 Feb '24

Dear Freesurfer Support Services, My name is Sucika Perumalla and I get the multiple frames errors when trying to run recon-all with my dicoms even after extracting the multiple frames. I was wondering if you can please help resolve these issues. Thanks _____________________________ Sucika Perumalla Clinical Research Assistant I Department of Neurology, Division of Movement Disorders Brigham and Women’s Hospital 60 Fenwood Road, Boston, MA 02115 sperumalla1(a)bwh.harvard.edu<mailto:sperumalla1@bwh.harvard.edu> | 508-414-2601

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postdoc position at Karolinska Institutet (Sweden)
by daniel ferreira padilla 20 Feb '24

20 Feb '24

External Email - Use Caution Dear everyone, We are recruiting a postdoc with expertise in neuroimaging (PET and/or MRI). Please see announcement here. Last day for submitting your application is 23rd of February. https://secure-web.cisco.com/1vVDjWQTc49asVod0AwGjaQgTeUpNJConsZgW_WT7VGOM7… [https://secure-web.cisco.com/1k7ZG4EQGIYP_4wb9sxv-IR-zIj9LfC1Wb_V9GYXiBs6Jx…]<https://secure-web.cisco.com/1vVDjWQTc49asVod0AwGjaQgTeUpNJConsZgW_WT7VGOM7…> Postdoctoral Researcher in neuroimaging in aging and dementia<https://secure-web.cisco.com/1vVDjWQTc49asVod0AwGjaQgTeUpNJConsZgW_WT7VGOM7…> Do you want to contribute to top quality medical research? We are looking for a postdoctoral fellow for studies of brain degeneration in Lewy Body dementia (DLB) using advanced brain imaging methods. ki.varbi.com All the best Dani -- Daniel Ferreira, PhD, Docent (Associate Professor) Director of Center for Alzheimer Research Karolinska Institutet, Sweden Department of Neurobiology, Care Sciences and Society (NVS) Center for Alzheimer Research Division of Clinical Geriatrics NEO floor 7th, SE 141 83 Huddinge daniel.ferreira.padilla(a)ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/1N82OsVZfbL6tc69_tJ91s2Fb22PUAN8UekFfodgpRrBl4…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1HBPUsdG40yRZJSAKuTROqyF-SgSZqmGX671qFGlFwaTlb…>.

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Re: [Freesurfer] Mac OS M2 M3 computers
by fsbuild 17 Feb '24

17 Feb '24

External Email - Use Caution If you don’t have a license.txt file setup to read, then freeview will not run. If you have not already done so, I would set the environment variable FS_LICENSE to point to the license.txt file you downloaded after registering, e.g., if license.txt is in your home directory and your user name is “cstevens” then $ export FS_LICENSE=/Users/cstevens/license.txt$ head -1 $FS_LICENSEyou(a)somewhere.com  <——  email you used to register You can put that define in your shell initialization file so you do not have to set it again when you login. If you are doing long term work, we recommend you download and install the 7.4.1 release from June 2023.  Those are Intel binaries, but they should run.  You should use the standard Mac .pkg file.  Right click on the .pkg file icon, select open with installer.app (default) which should provide some security exemptions. June 2023 7.4.1 releasehttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesur… There is a native Silicon Mac development build, but it is unstable and has not been tested as a full release has been.  But if you are only running freeview, then you could try that instead..  Install the same way as listed above by right clicking. Development buildhttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-… - R. On Feb 17, 2024, at 22:09, Charles Leger <charlie.stevens.leger(a)gmail.com> wrote:       External Email - Use Caution        Really. I have a Mac Mini M2 (16GB), 8 cores. I downloaded FreeSurferMac OS 7.4.1. Then tried freeview and loaded a T1 image. Freeviewimmediately closed. I tried this 3 times with the same result. PerhapsI should try a different version, ideally a version that allows CPUrather than a GPU install.Best,COn Sun, Feb 4, 2024 at 12:50 AM Fatima Karim <fatimakareem128(a)gmail.com> wrote:       External Email - Use CautionI have been using free surfer for a year nowon Mac m2 max and it's working fine.On Sat, Feb 3, 2024, 23:42 Charles Leger <charlie.stevens.leger(a)gmail.com> wrote:       External Email - Use CautionThere seems to be some contention if FreeSurfer will support Mac OSsilicon (M2, M3) computers. In the technical requirements section, itis clearly specified that a " 3D graphics card with its own graphicsmemory & accelerated OpenGL drivers" is required. But in the emailarchive (caution suggested) it is noted that "binaries should run oncurrent Macs with M1, M2, M3 arm64".Currently. Apple has not indicated plans to support eGPUs, which, onpaper, makes all newer non-intel Mac computers not compatible withFreeSurfer.Any suggestions would be greatly appreciated.--*********************************************Dr. Charles Stevens LegerPhD Psychology, Neuroscience diplomaDepartment of PsychologyConcordia University7141 Sherbrooke Street W.Montreal, Quebec, CanadaH4B 1R6_______________________________________________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/1swIjR2PdKJ-tGWCqLlTzXXnPbNpDqwl7lVLV9r_aC1CVB… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Wm-LbShKwZnggMKu70mgCrqBikmdTG-n5C_oMDoGIo-ej… <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Wm-LbShKwZnggMKu70mgCrqBikmdTG-n5C_oMDoGIo-ej… ._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1swIjR2PdKJ-tGWCqLlTzXXnPbNpDqwl7lVLV9r_aC1CVBUJA9_RbBE2kgRn27WfUcfa0ggUCmkIDbEh5doMeoCe1P1Mk7ghtCPlKlYtnO5Zpt_AMCNWKbCAq1gO2xF3do-4bLQlHAPuH1lO4gThEIdMNph7vL60Q-8JTr6lHaTmsQ_Bxmay7wliyd9s6gDjjdsCgkpZ-GCqgn4lrHXwblfrqSuxp5cQcUlTFTtTKKd4TN-pSA2mgucdW5BUqJPL85hZQD0PRkI4ma_5IQl8LvhmTx35KbeRK_BGGAZ79hBFzJUDa7uPFA00JL3JU0yR9ZcqQjDMwXSK5VhCeaHlbxA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferThe 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/1Wm-LbShKwZnggMKu70mgCrqBikmdTG-n5C_oMDoGIo-ej… <https://secure-web.cisco.com/1Wm-LbShKwZnggMKu70mgCrqBikmdTG-n5C_oMDoGIo-ejXMLmE2pFp7238dDpRA2syCMdftPNjnUOrYcZ8cmnRIzfpzY_rE_wLEOfKpAAGG1l6kX9P6Dprr429zr_W2w1jOtkms_ju5oFqQvNqNqbdCyxwlPkLCXzOvVwmHi95JNqQvnKgIq0WEi-fDv43ynu7kong2lixS68Lo2a-ypmZ-dpbIpC6Ozqc0AbWK9WdfEX-Mhbl_c3UKyYPwy7bq_1mntvGjp7ODhT48aZslEosjaesH_uTF8iLKWhDmCvmzkkmVE3mm_Qmk7DJd0kHimGOuTb5LZmggNpsh-GiyTUQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> ._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mac OS M2 M3 computers
by Charles Leger 17 Feb '24

17 Feb '24

External Email - Use Caution There seems to be some contention if FreeSurfer will support Mac OS silicon (M2, M3) computers. In the technical requirements section, it is clearly specified that a " 3D graphics card with its own graphics memory & accelerated OpenGL drivers" is required. But in the email archive (caution suggested) it is noted that "binaries should run on current Macs with M1, M2, M3 arm64". Currently. Apple has not indicated plans to support eGPUs, which, on paper, makes all newer non-intel Mac computers not compatible with FreeSurfer. Any suggestions would be greatly appreciated. -- ********************************************* Dr. Charles Stevens Leger PhD Psychology, Neuroscience diploma Department of Psychology Concordia University 7141 Sherbrooke Street W. Montreal, Quebec, Canada H4B 1R6

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Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option
by Stefano Delli Pizzi 17 Feb '24

17 Feb '24

External Email - Use Caution Thank you. Stefano Binarizing based on threshold min 1e-09 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149926 values in range Counting number of voxels in first frame Found 149925 voxels in final mask Writing output to /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/masks/brain.fsaverage.rh.pr.nii.gz Count: 149925 149925.000000 163842 91.505841 mri_binarize done 1/1 003_S_6014 001 lh --------- Mar 13 Feb 2024 10:28:12 CET ERROR: could not determine file for /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.even if ( $status ) exit 1 ; if ( 1 ) exit 1 exit 1

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