Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Re: [Freesurfer] annex repository missing a lot of files
by fsbuild 04 Oct '22

04 Oct '22

External Email - Use Caution Hello Ahmed, Maybe you could further explain what you are trying to accomplish, e.g., you don’t need the annex files to compile the freesurfer source. - R. On Oct 4, 2022, at 04:33, Ahmed Abou Aliaa <ahmed.s.aboualiaa(a)gmail.com> wrote:        External Email - Use Caution        Good day everyone,I did a clean clone of the annex repository for my local workflow to check that I have all files. Unfortunately there are a lot of missing (or maybe stale/private/copyrighted) files which are not available. I've appended the output of the "git annex get" command below.Is there a way to fix this?-- kind regards,Ahmed Abou-Aliaa<annex.txt>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

annex repository missing a lot of files
by Ahmed Abou Aliaa 04 Oct '22

04 Oct '22

External Email - Use Caution Good day everyone, I did a clean clone of the annex repository for my local workflow to check that I have all files. Unfortunately there are a lot of missing (or maybe stale/private/copyrighted) files which are not available. I've appended the output of the "git annex get" command below. Is there a way to fix this? -- kind regards, Ahmed Abou-Aliaa

1 0

Re: [Freesurfer] Freeview does not display image
by fsbuild 04 Oct '22

04 Oct '22

External Email - Use Caution Hello Justina, We need to know what your setup is on Windows for running Linux in order to help with running freeview.  It reads like you are not using VirtualBox to run the Linux Ubuntu OS,  I do not have VirtualBox installed ... So it’s not clear to me how you are currently running Ubuntu Linux on your Windows machine in order to run freeview or other freesurfer commands.  Are you running Ubuntu linux with the Windows Subsystem for Linux (WSL)?  Maybe you are connecting remotely to a linux machine via VNC or the like from your Windows machine ? If you don’t mind running freesurfer 7.2.0 (instead of the newest 7.3.2 release), there is a smaller version of the VM to download from https://secure-web.cisco.com/1YWO9PWAWb2dUg45HhJ8-Uf5BVRKini-Plt5…; with setup instructions under that link.   But you would still need to download and install VirtualBox on your Windows machine and then download and install the Freesurfer Software. - R. On Oct 3, 2022, at 09:35, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        To whom that can provide any insight,I am currently using Ubuntu on windows to open freeview to show some data. My issue at hand is that freeview does not show any images, despite changing the window levels (contrast and brightness). Using the command freeview -v works, and I am able to run it smoothly. When I try to open an mgz file, it runs fine, but I am unable to see anything.  I do not have VirtualBox installed and tried to take this advice from previous but I ran across the problem of downloading the course Virtual Machine. I do think that I do not need to download the VirtualBox and can continue using Ubuntu on Windows.What could be the issue with this? Should I be downloading the Virtual machine to run Freeview?Thank you so much for your time and I hope that my issue is not too big of a problem to solve.Sincerely,Justina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Freeview does not display image
by Justina Lee 03 Oct '22

03 Oct '22

External Email - Use Caution To whom that can provide any insight, I am currently using Ubuntu on windows to open freeview to show some data. My issue at hand is that freeview does not show any images, despite changing the window levels (contrast and brightness). Using the command freeview -v works, and I am able to run it smoothly. When I try to open an mgz file, it runs fine, but I am unable to see anything. I do not have VirtualBox installed and tried to take this advice from previous but I ran across the problem of downloading the course Virtual Machine. I do think that I do not need to download the VirtualBox and can continue using Ubuntu on Windows. What could be the issue with this? Should I be downloading the Virtual machine to run Freeview? Thank you so much for your time and I hope that my issue is not too big of a problem to solve. Sincerely, Justina

1 0

mri_glmfit error
by fernanda rohrsetzer 03 Oct '22

03 Oct '22

External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C Contrasts/LR-HR_testcov.mtx --C Contrasts/LR-MDD_testcov.mtx --C Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir lh.groupteste.thickness.glmdir --eres-save But it gives me an error (attached below) indicating a formatting problem in my FSGD file (attached). I have been trying to figure that out for a while. But I am unable to debug it. Could someone please help me resolve it? Thanks for your time.

2 6

Re: [Freesurfer] FSFAST first level covariates
by Emily Iannazzi 03 Oct '22

03 Oct '22

External Email - Use Caution Apologies, that was a bad example! Yes, like you said we want to have two variables (one binary & one continuous) that represent different aspects of the same stimulus. We’re wondering if we can rescale the values to incorporate both responses – do you know whether Freesurfer allows negative modulation values in the par files? We would essentially make negative values represent the valence ratings of stimuli with “no” responses and positive values represent those with “yes” responses. Additionally, do you have any advice for debugging the “design is ill-conditioned” error we received before? We still don’t know why our XCond was calculated to be so high at 5.45e16. Here was our setup: 1 SelfRelevant (=1, included only for trials rated as self-relevant) 2 ValenceOffset (=1, included only for trials rated as self-relevant) 3 ValenceSlope (=valence rating) 4 SelfIrrelevant (=1, included only for trials rated as self-IRrelevant) 5 ValenceOffset (=1, included only for trials rated as self-IRrelevant) 6 ValenceSlope (=valence rating) 0 Other 0 Case 0 Fixation Thank you very much for your continued help! ------------------------------ Message: 2 Date: Tue, 27 Sep 2022 09:51:58 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <d4a6ad9a-6463-6e7e-1c19-e951622915e7(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" See https://secure-web.cisco.com/1p1LwpSgcETesv4kjUKw_dC03qPRgQywmg0EAB7vjcgsoO…<https://secure-web.cisco.com/18_XTBGtGCKWwG3rq2kI81hxXtDx-uxj7639kO0xJN6cc4…> where group1=female, group2=male, and variable=age On 9/26/2022 10:45 PM, Emily Iannazzi wrote: > > ????????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 > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1WCS_x94kVz8QXVOecVfY7eRj6O05PqvwIbbUxk-BOZiKo…<https://secure-web.cisco.com/1uhSofRCBHzEwOVNvZAcm8rKoTjVfBVXE277darP8MyDhD…> > <https://secure-web.cisco.com/1Rba_aZxOkZUlSMnOdqT1LxdC3ROZ9V_xXtNg8xpYG12MU… > > > 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, > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1G0PkeFaLvOIRrn1MIK2_iZ9z6soqbvDnv5IRSAtAu0Vjk…<https://secure-web.cisco.com/1J_qi8yBmzKfxh4irpKkAx2HOSBPQb6Sep4ufVusAmr6D0…> > <https://secure-web.cisco.com/1xGoLsU1v9x_WJOz_jz46yX4Kqn77z6kQ5d1UM97vcLfuM… > > , 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 > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/14kn_bB-iqSxYYBorx6tYbCA2oF3qeUI4Wx92HackpsboZ…<https://secure-web.cisco.com/1gbLJj5Ss62qOQb_h0V-5Hjd2rYPJDtwniatKhJz7qsIvi…> > <https://secure-web.cisco.com/12Xm2UG55yhwvp_SD445TSDlYU7qDkQtbcAxgAa1hPxmu6… > > > 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 *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1XLqiQGGciftaJJf4IEmMwzFtnbd4PwcOuGsPas_-_8FSy…<https://secure-web.cisco.com/1ClrBOcX09ZV8oxYPLZnM6bfotSY4GjrBndnqvUT1oax8m…> > <https://secure-web.cisco.com/1VfHcQd78F8lWAln7dxGeqsla_w1QLy6b-qHUpK9i8Gf1j… > > <https://secure-web.cisco.com/1DBaRDxd12iOhxclW6Qeu-Qisec-Dz6mXPSrXki6ba2--4aP-1KUZOHTmn4djjjdndA9X9awKPiD1OBkULr__Lq7CBVhYBhC2dfDHkgvi83IrDtBDTkL3fHDuidZyLsKppjsl4b5boiolVj_GOvpmkY6fZpboqD0klywe80BrAeC7cTHNFz2p97AhioWI8BZSAXsNTm3-j9MyP0k5sbDjXd7IF0I-qNWhTcgC3AAT1VBGBBItmHGf-66q3EighSvYErFAGVakpGdOgUVNkMyrNRjlfyHt-fBkDrQHIIuKArHFAzi3ehd0vj9ppxhfLpcs/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. > > > >

2 3

Postdoc Position in Social and Affective Neuroscience
by Jiang, Jing 02 Oct '22

02 Oct '22

External Email - Use Caution Postdoc Position in Social and Affective Neuroscience The Jiang Lab at University of Iowa Carver College of Medicine (PI: Dr. Jing Jiang, https://secure-web.cisco.com/1kOcSJkyo1xCVO1eLJX_lrVfYy2-aYQoxsJT_jedzPuGSI… ) is looking for a two-year postdoctoral fellow (with a possibility of extension) to conduct social and affective neuroscience research. Research topics are flexible and could include: (1) determining causal neural circuits relevant to social and emotional deficits and treatment effects using brain lesion or brain stimulation methods (transcranial magnetic stimulation [TMS], intracranial electrical stimulation [es]) in combination with neuroimaging methods (e.g., functional magnetic resonance imaging [fMRI], intracranial electroencephalography [iEEG]) in neuropsychiatric/neurological populations, (2) identifying neuromarkers of social and emotional skills acquisition during typical and atypical development using functional near-infrared spectroscopy [fNIRS] in infants and children. We are an interdisciplinary team and welcome applicants from various research backgrounds! Our lab is situated in the Departments of Pediatrics and Psychiatry and maintains active collaborations with faculty and teams from the Departments of Neurology, Neurosurgery, Psychological and Brain Sciences, and Biomedical Engineering at the University of Iowa, the Iowa Neuroscience Institute, and the Intellectual and Developmental Disabilities Research Center. The lab has access to the University of Iowa’s cutting-edge imaging facility (https://secure-web.cisco.com/1_kdTAIej9w2FpqXquWutkqCb3drPeo_FKTxkOdm2lvaav…) the world-renowned Iowa Neurological Patient Registry including neuroimaging and neuropsychological testing data from over 3500 patients with focal brain lesions, as well as state-of-the-art portable fNIRS, concurrent TMS-fMRI, concurrent TMS-iEEG, and concurrent es-fMRI systems. The University of Iowa (UI) is an internationally recognized leader in neuropsychology and cognitive neuroscience. The UI Roy J. and Lucille A. Carver College of Medicine is consistently one of the nation’s top-ranked medical schools (#39 on research by the 2022 U.S. News & World Report). The UI Stead Family Children’s Hospital is listed among the nation’s best in seven specialties in the 2022-23 “Best Children’s Hospitals” rankings by U.S. News & World Report (#38 in pediatrics neurology). Iowa City ranks among the best places to live in America (e.g., #1 Best College Town by Reviews.org) Iowa City, Johnson County, and the state of Iowa all routinely appear on national “best of” lists for low cost of living, safety, access to world-class health care, and more. Responsibilities and what you will achieve The goal of postdoctoral training in our lab is to help you become an independent researcher. To achieve this goal, you will work with Dr. Jiang to develop a plan (e.g., independent projects, mentorship experience, grant application, job hunts, networking) that meets your career development. You will receive theoretical and methodological training and resources through ongoing projects and independent projects, mentor students and research assistants, publish impactful papers, and apply for eligible research grants. You will be provided networking opportunities and guidance for job hunts. Required Qualifications - PhD or MD/PhD degree in Psychology, Neuroscience, Cognitive Science, Computer Science, electrical or biomedical engineering, or a related field - A track record of peer-reviewed scientific journal publications in human neuroscience Desired Qualifications - Experience with scripting/programming languages (preferable MATLAB and/or Python) - Experience with one or several of the following human neuroscience techniques: fNIRS, fMRI, iEEG, TMS, brain lesion, etc. - Self-motivated, able to work independently, strong written and interpersonal communication skills To apply, please submit (1) a cover letter describing your research interests and (2) your CV to https://secure-web.cisco.com/1qCAntHvjWTUZfmZIXhWSQ59arE0CmdqxLsfd5NoPQjZUu… and you may email Dr. Jing Jiang (jing-jiang(a)uiowa.edu) please attach (1) cover letter and (2) your CV. Applications will be reviewed on a rolling basis until the position is filled. Start date is flexible depending on candidate availability. Thank you very much for your attention! Jing Jiang, PhD Assistant Professor (she/her/hers) Departments of Pediatrics and Psychiatry | Iowa Neuroscience Institute | Iowa's Hawkeye Intellectual and Developmental Disabilities Research Center (Hawk-IDDRC) W270 GH, 200 Hawkins Dr, Iowa City, Iowa 52242 Twitter<https://secure-web.cisco.com/1koMaJk-i1w7PMVqaqY0nTka_w8nZK-juZUlmjWSW1zhsP…> Lab Website<https://secure-web.cisco.com/1kOcSJkyo1xCVO1eLJX_lrVfYy2-aYQoxsJT_jedzPuGSI…> [1658344624806]

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 223, Issue 60
by Emily Iannazzi 30 Sep '22

30 Sep '22

External Email - Use Caution Yes of course! Attached is the first run for the first subject (in txt format). ------------------------------ Message: 2 Date: Fri, 30 Sep 2022 10:29:26 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <bc8d956f-8990-0cc9-e47a-3dcd8f70c3df(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" can you send the par file? On 9/29/2022 6:45 PM, Emily Iannazzi wrote: > > ????????External Email - Use Caution > > Here is the error again in plain text rather than an attachment > (running selxavg3): > > cd /autofs/cluster/manoach/angela/FSFAST > > /usr/local/freesurfer/stable6_0_0/fsfast/bin/selxavg3-sess > > parfiles condition id list:? 1? 2? 3? 4? 5? 6 > > Found 149955/163842 (91.5) voxels in mask 1 > > Creating Design Matrix > > ... creation time =? 0.011 sec > > DoMCFit = 1 > > ntptot = 507, nX = 15, DOF = 492 > > XCond = 5.45236e+16 (normalized) > > ERROR: design is ill-conditioned > > Many thanks again! > > *From: *Emily Iannazzi <eiann(a)uw.edu> > *Date: *Thursday, September 29, 2022 at 12:29 PM > *To: *freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *Re: FSFAST first level covariates > > Apologies, that was a bad example! Yes, like you said we want to have > two variables (one binary & one continuous) that represent different > aspects of the same stimulus. > > We?re wondering if we can rescale the values to incorporate both > responses ? do you know whether Freesurfer allows negative modulation > values in the par files? We would essentially make negative values > represent the valence ratings of stimuli with ?no? responses and > positive values represent those with ?yes? responses. > > Additionally, do you have any advice for debugging the ?design is > ill-conditioned? error we received before? We still don?t know why our > XCond was calculated to be so high at 5.45e16. > > Here was our setup: > > 1 SelfRelevant (=1, included only for trials rated as self-relevant) > 2 ValenceOffset (=1, included only for trials rated as self-relevant) > 3 ValenceSlope (=valence rating) > 4 SelfIrrelevant (=1, included only for trials rated as self-IRrelevant) > 5 ValenceOffset (=1, included only for trials rated as self-IRrelevant) > 6 ValenceSlope (=valence rating) > 0 Other > 0 Case > 0 Fixation > > Thank you very much for your continued help! > > ------------------------------ > > Message: 2 > Date: Tue, 27 Sep 2022 09:51:58 -0400 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] FSFAST first level covariates > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <d4a6ad9a-6463-6e7e-1c19-e951622915e7(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > See *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1FPAjTGQthCNC6V_0uEo5zizB2LlMeFgMn4ET7ianGVFHq…<https://secure-web.cisco.com/141Bug0GGUy2NNMeC5nvt17kJ0C2GapTNkQ4JDTydTgyxC…> > <https://secure-web.cisco.com/19oqDqWOwB11ZwEnN4pHhVW1JDyTYZhEvKoCKx0hw2aFkc… > > where group1=female, group2=male, and variable=age > > On 9/26/2022 10:45 PM, Emily Iannazzi wrote: > > > > ????????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 > > *MailScanner has detected a possible fraud attempt from > > "secure-web.cisco.com" claiming to be* > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1Q7MW-UcNnQncExRUwZFHqRK20GQNaWTQw_JwGrZ0B8Gpp…<https://secure-web.cisco.com/1qs7pJisBSkSWGudX_y52QMySNTKFuDtZOqAB0AYxZ-0rE…> > <https://secure-web.cisco.com/1HrrFpinAIfgRX2hQvESidOHFogT-wyFU6AXiE-6UWgFtN… > > > > <https://secure-web.cisco.com/1jkx4MmTLVS1SItZfU_TMaCUk5SL6XOaWgCp1FDZAqf8IO… > > > > > > 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, > > *MailScanner has detected a possible fraud attempt from > > "secure-web.cisco.com" claiming to be* > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1i_s2-zqBL3pfKrLid-WdLzDvn1MOgyVMD_liyWw3-IQRJ…<https://secure-web.cisco.com/1hImmhpse1YPlmdwSUEc_OsIJEQPktrXbkXy1sm35Y-ivZ…> > <https://secure-web.cisco.com/15WNGmgur49yw6YvNa5JsR-vaxrGkot9nVglfWZga66KLo… > > > > <https://secure-web.cisco.com/1noPxPcBJ4oToDG1HP_rFIaYo_PojttqM_dEQo7z_qZpge… SUlJSUlJSUlJSUlJSUlJSU!!K-Hz7m0Vt54!jGvrRR9VM6xcBPp92dAa2oSAppkbjQf0teSfufDA1bklSHGqCo2593CJwOCE5klGCHXwWYW15gzZQC3H8mojamSgpVshN0UNIA$ > > > > , 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 ?$FREESURFER_HOME? (but have the permissions/sudo). I > > ?also can?t open Freeview: by double clicking on the app, the GUI > > crashes, or by typing ?freeview? in the terminal > > ?I get a PETSC error.  > > According > > ?to some previous forum threads, I?m thinking of downloading the v7 but > > would like to validate that it?s OK when using recon-all v6 > > ?files. > >   > > Thank you for your support, > >   > > Alexandra > >   > > > > > > > > > > > > > > > > > > ? _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > *MailScanner has detected a possible fraud attempt from > > "secure-web.cisco.com" claiming to be* > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1xMFiWXiQLLVHmnywyrqn3k2_AKG27Vx-zBQqyxEMI4NB5…<https://secure-web.cisco.com/1sWidY6q1uT3jKhShf2FbR036mqwxpuf-R9Ble8Oa6U-2o…> > <https://secure-web.cisco.com/1ssgFgu2T4mjXGETqYl-_Rmzgdfc0A1JXutNZa8tGPFZWK… > > > > <https://secure-web.cisco.com/1A6LDYH2FJs-bMuKHAN_uZcD0S01r0MdkjRBaqRo91tZYw… try47EyJ2pUC7SoYKoGw*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!K-Hz7m0Vt54!jGvrRR9VM6xcBPp92dAa2oSAppkbjQf0teSfufDA1bklSHGqCo2593CJwOCE5klGCHXwWYW15gzZQC3H8mojamSgpVthb_5oDw$ > > > > > > 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 *MailScanner has detected a > > possible fraud attempt from "secure-web.cisco.com" claiming to be* > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1ST69clnGxPoTencEMKUd7CxuPCv2MFNtCmkZcNuh93_ug…<https://secure-web.cisco.com/1BZQPb3G7o7YGInEOYrC5pyppfGtF_vXT6L9sr1P8HeBZW…> > <https://secure-web.cisco.com/1kiPe_XBi9wjbRZdVoNCAIPyC_QbXoHwex6XSseQzD3aQq… > > > > <https://secure-web.cisco.com/1WwBOtEdOIs0XzxZJ9h1noGFuRF2SKeO-d-s6tOyY3jAAg… 24__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!K-Hz7m0Vt54!jGvrRR9VM6xcBPp92dAa2oSAppkbjQf0teSfufDA1bklSHGqCo2593CJwOCE5klGCHXwWYW15gzZQC3H8mojamSgpVsRsAK6QQ$ > > > > > <https://secure-web.cisco.com/1dvYi94asFBeMBoECp_DZEI1i0RR1mRwrw8XZXLznqhF9NDYjGrK_-DEERRLdZIL7fLDN6O0GU432TpzfnkCrzwBB-LNNS5RyVK2UAkBzp9pMCRUWZ1Fou1E5cdlvXB6QHcIkf9olyMhUXYPonbxMDj3xupdYAAHvlCXBd4TDHGIfH9AeFTNApfDVGSo-LwTvjxnZc0CVdVwc74PYHxF-JG-h74X5e9F4JUe4dRxt9nxf2UtvSNPYmKROx4Skp-AB3Kdm9tRvVPjJUjcfFKMJ_AjUrh180RuG1oQoQmeStAn33NcmjBnQpjiCJlve2UV0/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. > > > > > > > >

1 0

7.3.2 skips careg with synthstrip
by Warrington, Oliver 30 Sep '22

30 Sep '22

External Email - Use Caution Hello FreeSurfer Developers, I’m attempting to run recon-all with synthstrip on v7.3.2. I get the following error each time: reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform I’ve tried several variations of the command below, all of which failed at the same point: export FREESURFER_HOME=/usr/local/freesurfer/7.3.2 source $FREESURFER_HOME/SetUpFreeSurfer.sh export FS_ALLOW_DEEP=1 recon-all -all -s freesurfer -i T1.nii -sd . -synthstrip -hires -openmp 20 -parallel It seems that -careg is being skipped for some reason. The command progresses from -canorm to -calabel which then crashes. The status file does not show careg being called at all: status file for recon-all Fri Sep 30 16:19:18 BST 2022 #@# MotionCor Fri Sep 30 16:19:23 BST 2022 #@# Talairach Fri Sep 30 16:20:13 BST 2022 #@# Talairach Failure Detection Fri Sep 30 16:26:43 BST 2022 #@# Nu Intensity Correction Fri Sep 30 16:26:44 BST 2022 #@# Intensity Normalization Fri Sep 30 16:33:05 BST 2022 recon-all -s cluster finished without error at Fri Sep 30 16:37:38 BST 2022 #New# invocation of recon-all status file for recon-all Fri Sep 30 16:38:58 BST 2022 #@# EM Registration Fri Sep 30 16:38:58 BST 2022 #@# CA Normalize Fri Sep 30 16:42:24 BST 2022 #@# SubCort Seg Fri Sep 30 16:44:14 BST 2022 Linux chumbawumba 4.4.0-19041-Microsoft #1237-Microsoft Sat Sep 11 14:32:00 PST 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s cluster exited with ERRORS at Fri Sep 30 16:44:29 BST 2022 I have got it to run by explicitly using the -careg flag: recon-all -all -s freesurfer -i T1.nii -sd . -synthstrip -careg -hires -openmp 24 -parallel I also do not get this error if I omit -synthstrip. Is there anything I’m missing here, a flag I should have specified etc.? Or is this just an unfortunate bug? Thanks in advance! Oliver 1. FreeSurfer versions: * freesurfer-linux-ubuntu20_x86_64-7.3.2 * freesurfer-linux-centos7_x86_64-7.3.2 * freesurfer-darwin-macos-7.3.2 2. Platforms: * WSL ubuntu 20.04 * HPC centos 7 * M1 Macos Montery 12.4 3. recon-all.log: see attached

1 0

Password for virtual disk image
by Carmen Jiménez Mesa 30 Sep '22

30 Sep '22

External Email - Use Caution Dear Admins, Would be possible to obtain the password to open the Ubuntu image FS_7_2_0_Ubuntu_18_04_06.ova.7z? Kind regards, -- Carmen Jiménez Mesa PhD Student Universidad de Granada (UGR)

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer