Freesurfer September 2022

freesurfer@nmr.mgh.harvard.edu

92 participants
129 discussions

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.

4 11

How is cache.th40.pos.sig.voxel.mgh computed, exactly?
by Mark Ebden 04 Aug '23

04 Aug '23

External Email - Use Caution Hi, I was wondering if anyone knows how the numbers in cache.th40.pos.sig.voxel.mgh are computed, or where I'd look to learn this. There is a one-liner in the documentation<https://secure-web.cisco.com/1R2vQZUhHj-zAreoIH8kMlOuUPh5jYx8TyPmfmDzbM1Dl-…> but I'd like the mathematical details of the correction etc. so I can determine what the final numbers (from 0 to 1) represent. I've noticed from browsing the plot in FreeView that significant areas have values close to 1, which is puzzling. Thanks if you could point me in the right direction. Kind regards, Mark Mar [cid:b7c6e65e-f85e-4206-aaa0-1ec00aa2fde2] Mark Ebden, D.Phil (Pronouns: He/Him) Research Analyst The Hospital for Sick Children 555 University Ave, Toronto ON M5G 1X8 P 416.888.0841 [cid:3b077a75-32bb-46ed-b1d2-b74379e6a8d1]<https://secure-web.cisco.com/17-WtJwO2uIWyZ7umzDRCiH0I5Q1NZ-tfYcx_zx9tznEDb…> ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

2 6

Fwd: mri_robust_template - MyMatrix::RotationMean Error
by Andrew Beaudin 07 Feb '23

07 Feb '23

2 8

Tracula - Preproc
by Alan Francis 18 Oct '22

18 Oct '22

External Email - Use Caution Hi Anastasia, King Wei: I did as you suggested with the config file and the preprocessing ran for a bit but then an error occurred. I have attached the run script. It says BET not found. Is this the Brain Extraction tool? Could you please shed some light on this? thanks so much, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

4 4

Thalamic nucleus segmentation 3D export
by Paulk, Angelique C.,PHD 10 Oct '22

10 Oct '22

Hello, I apologize if this has been answered before though I could not find this specific information in the archives. We are hoping to export the Thalamic nuclei segmentations to 3D volumes outside of Freeview/Freesurfer (e.g. .stl or other options) to perform a number of calculations in python or Matlab or visualize in Blender. I have been able to use 3DSlicer and get segmentation and 3D renders by importing the "aparc.DKTatlas+aseg.mgz" file and export .stl files in 3DSlicer, but, when I import the "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz" file, it is only showing the entire thalamus as a mask in 3DSlicer though the nuclei are segmented in Freeview. Is there another type of export from FreeSurfer that would allow this type of saved volume/surface export? Thank you for all your help, Angelique

2 3

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.

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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. > > > >

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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).? 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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

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Freesurfer September 2022