Freesurfer September 2022

freesurfer@nmr.mgh.harvard.edu

92 participants
129 discussions

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

Freesurfer: fs_install_mcr: Unzip command not found
by You Na Lee 30 Sep '22

30 Sep '22

5 21

tissue type not set in mri_compute_volume_fractions
by Bauer, Martin 29 Sep '22

29 Sep '22

External Email - Use Caution Dear Freesurfer experts, I’m trying to get a 5TT output from freesurfer data as FSL would provide it using MRtrix wrapper 5ttgen fsl. mri_compute_volume_fractions looks like doing the job, but I can’t wrap my head around some tissue type that seemed to be missing. For clarification, its infant data but it comes from a freesurfer based processing pipeline. If I’m using it like this: mri_compute_volume_fractions --o test --regheader 2035 /Users/path/to/data/2035/mri/norm.mgz I’ll get this error: $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Darwin hostname xxx.charite.de<http://secure-web.cisco.com/1duNm437197YxIoR1NUN7k5zEN8kZoKQenYNRSG9UrqckbQ…> machine x86_64 user martinbauer setenv SUBJECTS_DIR /Users/martinbauer/Daten/MRI/FS_corrected cd /Users/martinbauer mri_compute_volume_fractions --o test --regheader 2035 /Users/martinbauer/Daten/MRI/FS_corrected/2035/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz wsurf white psurf pial TempVolFile (null) USF 2 Reading in aseg and surfs from /Users/martinbauer/Daten/MRI/FS_corrected/2035 Loading /Users/martinbauer/Daten/MRI/FS_corrected/2035/mri/aseg.mgz Changing type of seg from UCHAR to INT Filling empty voxels with extracerebral CSF (if not there already), nDil=3 Computing registration from header 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; t = 4.53563 Computing PVF (USF=2, resmm=0.500000) MRIhiresSeg(): filling unknowns with 257 ERROR: MRIseg2TTypeMap() tissue type for seg 172 Vermis not set Fair enough, so I force it using finer parcellations doing: mri_compute_volume_fractions --o test --regheader 2035 /Users/path/to/data/2035/mri/norm.mgz --seg aparc.a2009s+aseg.mgz Vermis is now part of the game but: $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Darwin hostname xxx.charite.de<http://secure-web.cisco.com/1duNm437197YxIoR1NUN7k5zEN8kZoKQenYNRSG9UrqckbQ…> machine x86_64 user martinbauer setenv SUBJECTS_DIR /Users/martinbauer/Daten/MRI/FS_corrected cd /Users/martinbauer mri_compute_volume_fractions --o test --regheader 2035 /Users/martinbauer/Daten/MRI/FS_corrected/2035/mri/norm.mgz --seg aparc.a2009s+aseg.mgz outstem test regfile (null) regtype 0 segfile aparc.a2009s+aseg.mgz wsurf white psurf pial TempVolFile (null) USF 2 Reading in aseg and surfs from /Users/martinbauer/Daten/MRI/FS_corrected/2035 Loading /Users/martinbauer/Daten/MRI/FS_corrected/2035/mri/aparc.a2009s+aseg.mgz Filling empty voxels with extracerebral CSF (if not there already), nDil=3 Computing registration from header 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; t = 4.40752 Computing PVF (USF=2, resmm=0.500000) MRIhiresSeg(): filling unknowns with 257 ERROR: MRIseg2TTypeMap() tissue type for seg 12104 ctx_rh_G_and_S_subcentral not set What files are exactly read and can those files be adjusted? In FreeSurferColorLUT.txt Vermis and 12104 are included, I tried to add 12104 to the parcellation stats LUT but it didn’t solve the problem. I’m also open to go another way. Thank you so much in advance for pointing me towards the right direction! All the best, Martin

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Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than cross-sectional
by Douglas N. Greve 29 Sep '22

29 Sep '22

I was not able to replicate this on one of my data sets. I tihnk Stefano may be looking into it. On 9/28/2022 7:07 AM, Nederpelt, D.R. van (David) wrote: > > External Email - Use Caution > > Hi Douglas, > > Maybe my reply didn’t reach you: > > Thank you for the response. > > I've attached the log files for each cross sectional analysis > separately and the longitudinal as one log file. > > Cross-sectional commandline: > > run_samseg -I sub-001_tp1_T1.nii.gz --threads 4 -o result_sub-001 > > longitudinal commandline: > > mri_robust_template --mov sub-001_tp1_T1.nii.gz sub-001_tp2_T1.nii.gz > sub-001_tp3_T1.nii.gz --template mean_sub-001.mgz --satit --mapmov > sub-001_tp0_T1.mgz sub-001_tp1_T1.mgz sub-001_tp2_T1.mgz > > run_samseg_long --timepoint sub-001_tp0_T1.mgz --timepoint > sub-001_tp1_T1.mgz --timepoint sub-001_tp2_T1.mgz --threads 4 -o > result_sub-001_long > > I believe this was the command line suggested by > https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg > <https://secure-web.cisco.com/1ZmeL3C2avBqAUV2PCoRmoPTQiEvv0t1lJ02Fdwj7Ybl2v…> > > Thank you, > > David > > Message: 3 > > Date: Mon, 26 Sep 2022 22:14:37 -0400 > > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > Subject: Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than > > cross-sectional > > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Message-ID: <34a07418-b022-160b-bfac-39c493226f28(a)mgh.harvard.edu > <mailto:34a07418-b022-160b-bfac-39c493226f28@mgh.harvard.edu>> > > Content-Type: text/plain; charset="utf-8" > > Can you send your command line and log file? In particular, how did you > > register the time points? > > On 9/26/2022 6:46 AM, Nederpelt, D.R. van (David) wrote: > > > > > > ????????External Email - Use Caution > > > > > > Dear SAMSEG developers, > > > > > > We have a dataset with 55 subjects (MS patients and controls) scanned > > > on three timepoints with yearly intervals. > > > > > > When we ran the (SAMSEG) longitudinal pipeline we noticed that the > > > sbTIV always had an increased volume (between 0.5 and 3.5% larger) > > > compared to the sbTIV computed cross-sectionally. Do you have any idea > > > how and why we may see these effects? > > > > > > Thank you in advance! > > > > > > Best regards, > > > > > > David van Nederpelt | Amsterdam UMC > > > > > > ______________________________________________________ > > > VUmc disclaimer : www.vumc.nl/disclaimer > <http://secure-web.cisco.com/1FNOpgRHBdY_PkpgrNeL_lnAJjCpQVjIQ3OuIpCtbwI5psU…> > > > AMC disclaimer : www.amc.nl/disclaimer > <http://secure-web.cisco.com/1ZkZ0-hp5VX8NyydNH-arlyVc_s5B0KnEYnYBQGpbeWNpVK…> > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… > <https://secure-web.cisco.com/1vSA8-35xEaoZUdoOw3CKdc0O2aOIdtbh-VPYbByJVt7bC…> > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.nmr.m… > <https://secure-web.cisco.com/1gE1fZ-jHZQJOUA93sSGdwDW70vnjip15HgB48wKh6MlC0…> > > ------------------------------ > > Message: 4 > > Date: Tue, 27 Sep 2022 03:45:29 +0000 > > From: Emily Iannazzi <eiann(a)uw.edu <mailto:eiann@uw.edu>> > > Subject: Re: [Freesurfer] FSFAST first level covariates > > To: "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Message-ID: > > > <PH0PR08MB80141C3C693A17E429423C4ECF559(a)PH0PR08MB8014.namprd08.prod.outlook.com > <mailto:PH0PR08MB80141C3C693A17E429423C4ECF559@PH0PR08MB8014.namprd08.prod.outlook.com>> > > Content-Type: text/plain; charset="us-ascii" > > 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 > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu><freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of > freesurfer-request(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu><freesurfer-request(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu>> > > Sent: Friday, September 23, 2022 6:58 AM > > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu><freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Subject: Freesurfer Digest, Vol 223, Issue 39 > > Send Freesurfer mailing list submissions to > > freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > To subscribe or unsubscribe via the World Wide Web, visit > > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1_qouscVTT371XOKGSSa3bhjnWzQgV4qJnWFw3JWxpu7H8…> > > or, via email, send a message with subject or body 'help' to > > freesurfer-request(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu> > > You can reach the person managing the list at > > freesurfer-owner(a)nmr.mgh.harvard.edu > <mailto:freesurfer-owner@nmr.mgh.harvard.edu> > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. 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 <mailto:fsbuild@contbay.com>> > > Subject: Re: [Freesurfer] Running v7 with recon-all v6 files > > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Cc: brouillard.alexandra(a)gmail.com <mailto:brouillard.alexandra@gmail.com> > > Message-ID: <9bf58e7024ed99c7c06379a6876dda10(a)trashmail.com > <mailto:9bf58e7024ed99c7c06379a6876dda10@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, > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/17zDxbZj38d7X1lAF2NHcEOvXvsOg7gjmyjfLHsbG026mH…> > > pUC4zyOTmLw$ , 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 > <mailto:brouillard.alexandra@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 ?$FREESURFER_HOME? (but have the permissions/sudo). I > > also can?t open Freeview: by double clicking on the app, the GUI > > crashes, or by typing ?freeview? in the terminal > > I get a PETSC error.  > > According > > to some previous forum threads, I?m thinking of downloading the v7 but > > would like to validate that it?s OK when using recon-all v6 > > files. > >   > > Thank you for your support, > >   > > Alexandra > >   > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1hbZ2Vzerz2Owdq5AvTQCVqMt0WAjRiT1pAcqfmvbAOFI5…> > > The information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in error > and the e-mail contains patient information, please contact the Mass > General Brigham Compliance HelpLine at > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1RcFCCish5qhvU0B9oI6R6GKXIVK4kpO_7jh3XeDX-Z5AF…> > > IXFkWjbgRYSOUocM2siQ%2Fhttps*3A*2F*2Fwww.massgeneralbrigham.org*2Fcomplianceline__;JSUlJQ!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC75vM4BSw$ > <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-web.cisco.com%2F1ODrGbxxaKclPvtjL5GjXY28DLLx66WIe0MpKi9TvUrgA8yMpuw9Az1UEiKz3ZEmzQpPFJG0aY3eyRv4dPWc9saAi1lUcF95WyDKOpsHv_Y8Xk3G7-ZOxKTawTeRD9-VR4KByLwX7H2kRY-ZnveKcN0X7_NUJXbbOL2AaWNT4ARXvFJvMfxxYfgsRWeJ9MdfSesCBSrK7h5QUfeznYTFoHltKLZz4if2ZnSC2xBb1GTu_3fl0kQDPF6AU2VXE5eh6_E8-ewZouLRn3aliC42pz78wQbC_8zqvqd3RGg5eoZvN5w1DRhsO6s85wf870GKj%2Fhttps%253A%252F%252Furldefense.com%252Fv3%252F__https%253A%252F%252Fsecure-web.cisco.com%252F1QEu65hJzFz0Qlr-f85ovtCCFPcEQTuVjkATuX8Dzuz3-aNImRz08NXygo1pKr2Wbp8Y7ERP6XX_QXuwwA7OQtL95Jy8KMvQkj8V15v6C3snSGsuYEymHIorCwk50lasrKb8M0DVESSb7lpsfhGW7Z8XrutrhY2vETqwYjoknqZ2L7coJdB9m0JwsRPxH88FkJaPyuapnujCIKZ0QiH7JLW_PxPUN1xjG8C0rI2ClwPd8PHXFdDo4ft_5ujxHY0YquA5UdKOwf3hc1himt1m2KKha9Xl8__%3B!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIX&data=05%7C01%7Cd.vannederpelt%40amsterdamumc.nl%7Cb9a955ae58594184127408daa03b826b%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637998475380278045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=my84DR7poSiO8DsKM6Bxy8To0F%2FTR36V6%2B6MM5it9HU%3D&reserved=0 > > olLfsm45BoW1QBeS9mtry47EyJ2pUC7hKRKUCg$ > > 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. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1ZkmiJKJUYwHqVpLoLAbCIN9QR_dX2rtjzIfrKtt9ZmeLw…> > > ------------------------------ > > Message: 2 > > Date: Fri, 23 Sep 2022 11:34:25 +0530 > > From: Ahmad Khan <110ahmadkhan(a)gmail.com <mailto:110ahmadkhan@gmail.com>> > > Subject: [Freesurfer] Fwd: Error > > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Message-ID: > > > <CAPNe=2f_e1woMTMoimoxZ8hvPWPbqrNLS2NMVTgugPsBQsRjwA(a)mail.gmail.com > <mailto:CAPNe=2f_e1woMTMoimoxZ8hvPWPbqrNLS2NMVTgugPsBQsRjwA@mail.gmail.com>> > > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear Free Surfer Development Team. > > I am using the recon -all command to compute the volume of different > > regions of the brain. I am running the free surfer version > > freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 installed on > > a virtual box. I am getting the following errors and the log file is also > > attached with this email. > > *ERROR: mri_ca_register with non-zero status 137* > > Your timely response would be highly appreciated. > > Best Regards > > Dr. Ahmad Raza Khan > > (Ramalingaswami Fellow) > > Center of Bio-Medical Research (CBMR) > > SGPGI Campus, Raibareli Road > > Lucknow-226014, UP, INDIA > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1QdPOdrZZIats_smnzv6Z2eoD8CnoU7X8vIu-sHC3LVj08…> > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: recon-all.log > > Type: application/octet-stream > > Size: 118057 bytes > > Desc: not available > > Url : > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1_GFv-uRNTzx0GuSf1xcGItcnQBuxAZ1sRTbiHGuIXAxTx…> > > ------------------------------ > > Message: 3 > > Date: Fri, 23 Sep 2022 08:34:28 +0200 > > From: fsbuild <fsbuild(a)contbay.com <mailto:fsbuild@contbay.com>> > > Subject: Re: [Freesurfer] Error > > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Cc: 110ahmadkhan(a)gmail.com <mailto:110ahmadkhan@gmail.com> > > Message-ID: <3ba2f92436c570f01d2b49ccc0305947(a)trashmail.com > <mailto:3ba2f92436c570f01d2b49ccc0305947@trashmail.com>> > > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello Ahmed, > > Command terminated by signal 9 can mean you ran out of memory.  I > would try allocating more memory to the VM.  But you may still > run out of memory depending upon what is available on your machine. > > If you do not have to use 7.1.1 and can switch to using the newer > 7.3.2 release, then for Ubuntu 20, we have a .deb file installer > (https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1QhkkAfZYZRIGuigV_t1vwkpqZkmjAHasLRrfesN3yn0Rd…> > > 20-7.3.2_amd64.deb) __;JSUlJSUlJSU!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC4bEtEHOA$ > or a tar archive > (https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/14j0m631KdUh_XriselHzTqvzw8n0r0g0qe02gTiyySUtV…> > > jBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC5u3fJlpg$ > > Y_oK--864Et-ISjWw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer-linux-ubuntu20_amd64-7.3.2.tar.gz) > which you try.  I would uninstall 7.1.1 if you are going to use > 7.3.2 though.  Again, that may not help if available memory is > the issue. > > - R. > > On Sep 23, 2022, at 02:04, Ahmad Khan <110ahmadkhan(a)gmail.com> > wrote:        External Email - > Use Caution         Dear > Free Surfer Development Team.I am using the recon -all command to > compute the volume of different regions of the brain. I am running the > free surfer version freesurfer-linux-centos7_x86_64-7.1.1-20200723 on > Ubuntu 20.4 installed on a virtual box. I am getting the following > errors and the log file is also attached with this email. ERROR: > mri_ca_register with non-zero status 137Your timely response would be > highly appreciated.Best Regards Dr. Ahmad Raza > Khan(Ramalingaswami Fellow)Center of Bio-Medical Research (CBMR)SGPGI > Campus, Raibareli RoadLucknow-226014, UP, > INDIA<recon-all.log>_______________________________________________Freesurfer > mailing > listFreesurfer@nmr.mgh.harvard.eduhttps://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=05%7C01%7Cd.vannederpelt%40amsterdamumc.nl%7Cb9a955ae58594184127408daa03b826b%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637998475380278045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wCcNDIRQuONMX79Hcj7NsN7V2wLey82DJTGiBr7aL6Y%3D&reserved=0 > <mailto:listFreesurfer@nmr.mgh.harvard.eduhttps://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=05%7C01%7Cd.vannederpelt%40amsterdamumc.nl%7Cb9a955ae58594184127408daa03b826b%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637998475380278045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wCcNDIRQuONMX79Hcj7NsN7V2wLey82DJTGiBr7aL6Y%3D&reserved=0> > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1YkPEnLJ1kcMY37GvegIoKFZLtsYF5fiJnCsYRmVQEOaN7…> > > ------------------------------ > > Message: 4 > > Date: Fri, 23 Sep 2022 13:26:43 +0000 > > From: "O'Dor, Sarah,PHD" <SODOR(a)mgh.harvard.edu > <mailto:SODOR@mgh.harvard.edu>> > > Subject: [Freesurfer] dcmunpack > > To: "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Message-ID: > > > <BL0PR04MB65325927F567249B3A514F71F34E9(a)BL0PR04MB6532.namprd04.prod.outlook.com > <mailto:BL0PR04MB65325927F567249B3A514F71F34E9@BL0PR04MB6532.namprd04.prod.outlook.com>> > > Content-Type: text/plain; charset="windows-1252" > > Good afternoon, > > Quick question about unpacking: > > The instructions I have from a previous staff member said to do this: > > In folder where files are going, type: unpacksdcmdir -src <location of > scans> -targ . -scanonly scanout.txt > > So what I submit is: > > unpacksdcmdir -src > /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 > -targ . -scanonly scanout.txt > > When I do that, it just makes the files: > > dicomdir.sumfile scanout.txt unpack.log > > I?m trying to use the dcmunpack command instead. From following the > template on the website, I?ve been trying the following commands: > > [pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src > /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 > -index-out dcm.index.dat > > {lots of other content here, so let?s skip to?.} > > dcmunpack done > > [pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src > /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 > -index-in dcm.index.dat -targ . > > ERROR: need input runs > > How should I specify input runs? > > Thanks, > > Sarah > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1h9Ms3n5Z4uUynv96HcjaVRXkMuQ9B_3awOkuikWoanGCo…> > > ------------------------------ > > Message: 5 > > Date: Fri, 23 Sep 2022 09:50:25 -0400 > > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > Subject: Re: [Freesurfer] Fwd: Error > > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Message-ID: <271c230a-538a-d7ae-d3b5-1c3025c3ed2e(a)mgh.harvard.edu > <mailto:271c230a-538a-d7ae-d3b5-1c3025c3ed2e@mgh.harvard.edu>> > > Content-Type: text/plain; charset="utf-8" > > not sure what is going on. It received a kill signal (the 9 mentioned at > > the end). This often means that it was killed externally. Does this > > happen repeatedly? Does this happen on other subjects? How much memory > > did you allocate to your virtual box? > > On 9/23/2022 1:04 AM, Ahmad Khan wrote: > > > > > > ????????External Email - Use Caution > > > > > > > > > Dear Free Surfer Development Team. > > > > > > I am using the recon -all command to compute the volume of different > > > regions of the brain. I am running the free surfer version > > > freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 > > > installed on a virtual box. I am getting the following errors and the > > > log file is also attached with this email. > > > *ERROR: mri_ca_register with non-zero status 137* > > > Your timely response would be highly appreciated. > > > > > > Best Regards > > > ?Dr. Ahmad Raza Khan > > > (Ramalingaswami Fellow) > > > Center of Bio-Medical Research (CBMR) > > > SGPGI Campus, Raibareli Road > > > Lucknow-226014, UP, INDIA > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1xGGEKaBx5MDRI4oBQr0aNTNMJu2r3EFZG70Dd14wKXbK0…> > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1tMqxm8TOfrHNZf40slCeMfNSkolM35lj6rngG_XCHBznW…> > > ------------------------------ > > Message: 6 > > Date: Fri, 23 Sep 2022 09:54:22 -0400 > > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > Subject: Re: [Freesurfer] dcmunpack > > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Message-ID: <df1177a3-a59c-223e-c766-09d726abdf15(a)mgh.harvard.edu > <mailto:df1177a3-a59c-223e-c766-09d726abdf15@mgh.harvard.edu>> > > Content-Type: text/plain; charset="utf-8" > > Sam way as with unpacksdcmdir, ie, by specifying? -run run subdir format > > stemname > > Another way it to use the -auto-runseq format , eg -auto-runseq mgz > > this will output all the runs preprending the run number and protocol name > > If you are using 7.3.X, then you can also add --dcm2niix which will > > speed things up a lot > > On 9/23/2022 8:26 AM, O'Dor, Sarah,PHD wrote: > > > > > > Good afternoon, > > > > > > Quick question about unpacking: > > > > > > The instructions I have from a previous staff member said to do this: > > > > > > In folder where files are going, type: unpacksdcmdir -src <location of > > > scans> -targ . -scanonly scanout.txt > > > > > > So what I submit is: > > > > > > unpacksdcmdir -src > > > /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 > > > -targ . -scanonly scanout.txt > > > > > > When I do that, it just makes the files: > > > > > > dicomdir.sumfile scanout.txt? unpack.log > > > > > > I?m trying to use the dcmunpack command instead. From following the > > > template on the website, I?ve been trying the following commands: > > > > > > [pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src > > > /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 > > > -index-out dcm.index.dat > > > > > > {lots of other content here, so let?s skip to?.} > > > > > > dcmunpack done > > > > > > [pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src > > > /cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 > > > -index-in dcm.index.dat -targ . > > > > > > ERROR: need input runs > > > > > > How should I specify input runs? > > > > > > Thanks, > > > > > > Sarah > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1xGGEKaBx5MDRI4oBQr0aNTNMJu2r3EFZG70Dd14wKXbK0…> > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/16mP6Xxy2hzpFZdVoVc4B0Y2kZRGsISXsaWACTHjewa_kf…> > > ------------------------------ > > Message: 7 > > Date: Fri, 23 Sep 2022 09:57:33 -0400 > > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > Subject: Re: [Freesurfer] FSFAST first level covariates > > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Message-ID: <6f7768e7-47de-9da1-a919-2d68f46a400b(a)mgh.harvard.edu > <mailto:6f7768e7-47de-9da1-a919-2d68f46a400b@mgh.harvard.edu>> > > Content-Type: text/plain; charset="utf-8" > > I'm not sure what you mean by selfrelevance-alone? and valence-alone. I? > > thought they were two aspects of the same stimulus (ie, they cannot > > appear alone). selfrelevance is an offset and valence is a slope -- not > > sure how you'd commpare them > > On 9/22/2022 4:49 PM, Emily Iannazzi wrote: > > > > > > ????????External Email - Use Caution > > > > > > Hi Doug, > > > > > > Just following up on this to see whether there?s a way to test for > > > both self-relevance and valence of stimuli separately from each other > > > as well as their interaction within the same paradigm file. > > > > > > Our current setup is as follows: > > > > > > 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 > > > > > > We first had 7 for ?Other? and ?Case? conditions but ran into a > > > ?design is ill-conditioned? error which we thought might be due to how > > > many conditions we had coded. We?re still getting the same error with > > > the current design and are receiving it after our ?XCond=? line, which > > > is being calculated to be 5.45e16. > > > > > > Do you have any insight on the best way to set this up within > > > Freesurfer? Essentially, we want to test the equation [y = > > > selfrelevance + valence + selfrelevance*valence], where > > > [selfrelevance] is a binary 1/0 variable and [valence] ranges from -4 > > > to 4, and both are individualized ratings for each word presented in > > > the scanner. > > > > > > At the end, we want to be able to test the effect of selfrelevance > > > alone, valence alone, and their interaction. > > > > > > Thanks for all your help on this, it is much appreciated! > > > > > > *From: *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>> on behalf of > > > freesurfer-request(a)nmr.mgh.harvard.edu > > > <freesurfer-request(a)nmr.mgh.harvard.edu> > > > *Date: *Wednesday, August 31, 2022 at 9:22 PM > > > *To: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:*freesurfer@nmr.mgh.harvard.edu><freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > *Subject: *Freesurfer Digest, Vol 223, Issue 1 > > > > > > Send Freesurfer mailing list submissions to > > > freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > *MailScanner has detected a possible fraud attempt from > > > "secure-web.cisco.com" claiming to be* > > > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/1Ruhae50y6bg2zQvpmq9zPeM7YmO1pfu11egj6X7D_jEMi…> > > > <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > > SUlJSUlJSUl!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC4ffDWqlw$ > > > > > > > > or, via email, send a message with subject or body 'help' to > > > freesurfer-request(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu> > > > > > > You can reach the person managing the list at > > > freesurfer-owner(a)nmr.mgh.harvard.edu > <mailto:freesurfer-owner@nmr.mgh.harvard.edu> > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > Today's Topics: > > > > > > ?? 1. Re: FSFAST first level covariates (Angela Fang) > > > ?? 2. Bus error using VM (#@# Nu Intensity Correction) > > > ????? (daedalus39(a)aol.com <mailto:daedalus39@aol.com>) > > > ?? 3. Re: Bus error using VM (#@# Nu Intensity Correction) (fsbuild) > > > ?? 4. Re: sclimbic sometimes does not detect left basal forebrain > > > ????? (Douglas N. Greve) > > > ?? 5. Re: FSFAST first level covariates (Douglas N. Greve) > > > ?? 6. Re: FSFAST first level covariates (Angela Fang) > > > ?? 7. Re: Thalamic nuclei exited with ERRORS (Yann Quid?) > > > ?? 8. Re: Thalamic nuclei exited with ERRORS (fsbuild) > > > ?? 9. Re: Unable to run trac-all -prep? : cannot file??????????? > > > bvals??? bvecs > > > ????? file (Ashwati Vipin (Dr)) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Wed, 31 Aug 2022 16:39:37 +0000 > > > From: Angela Fang <angfang(a)uw.edu <mailto:angfang@uw.edu>> > > > Subject: Re: [Freesurfer] FSFAST first level covariates > > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Message-ID: <2A2F422F-279C-4736-885A-C609F488C21E(a)uw.edu > <mailto:2A2F422F-279C-4736-885A-C609F488C21E@uw.edu>> > > > Content-Type: text/plain; charset="utf-8" > > > > > > ??????? External Email - Use Caution > > > > > > That makes sense! And if we wanted to identify brain regions > > > associated with valence (across self/non-self) that is unique from > > > condition 2, can we add a 5th condition? Maybe we can code self as 2 > > > and non-self as 1 so that condition 2 (self*valence) would be > > > different from condition 5 (valence ratings only)? > > > > > > Incredibly helpful, Doug- thank you so much! > > > > > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Douglas > > > N. Greve" <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> > > > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Date: Tuesday, August 30, 2022 at 7:38 AM > > > To: "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Subject: Re: [Freesurfer] FSFAST first level covariates > > > > > > Oh, I think I see now. In realty, each trial is either self or not > > > self and then you have a separate valence measure, so your coding > > > should be > > > 1. Self-offset > > > 2. SelfValence > > > 3. NoSelf-offset > > > 4. NoSelfValence > > > > > > Where 1+2 are used for a self event and 3+4 are used for a noself > > > event. If you want to test for the difference between self and noself > > > valence slope, then you would just use -a 2 -c 4 > > > > > > On 8/29/2022 12:08 PM, Angela Fang wrote: > > > > > > ??????? External Email - Use Caution > > > Great, thanks so much Doug- this setup makes sense to me. However, > > > isn?t it a problem that the brain regions associated with the contrast > > > for -a 3 and the contrast for -a 4 would be the same for trials that > > > subjects rate as 1 (self-relevant) vs 0 (not self-relevant)? Could we > > > code it as 2 (self-relevant) and 1 (not self-relevant)? > > > > > > Many thanks!! > > > > > > From: > > > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>><mailto:freesurfer-bounces@nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> > > > on behalf of "Douglas N. Greve" > > > <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>><mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > > Reply-To: Freesurfer support list > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>><mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Date: Sunday, August 28, 2022 at 1:07 PM > > > To: > > > "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>"<mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>><mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Subject: Re: [Freesurfer] FSFAST first level covariates > > > > > > I was under the impression that Self and Valence were ratings from the > > > same event (in that mail archive, they were different events and so > > > needed different offsets). If Self and Valence are from the same > > > event, then you would have something like > > > 1. Offset > > > 2. Self > > > 3. Valence > > > 4. Self*Valence > > > I've never tried the interaction (self*valence). You might have to > > > demean before computing the product > > > On 8/14/2022 4:58 PM, Angela Fang wrote: > > > > > > ??????? External Email - Use Caution > > > The two coding schemes are different because the second one does > > > include the self*valence variable you?re talking about, whereas the > > > first one doesn?t. I only included the 2nd offset because you > > > suggested to someone else to include it (see 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://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > <https://secure-web.cisco.com/16GZN1BVBGZxz9rNMepIm0LgmJFUn9c1CmpTXJQZuQ6jqP…> > > > <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > > Fw4S9sp6o7il_xApboosWIOBOJb1zh7hBwMks3eFrd04OkImYWLahgGjjS7Zs4BjsQy1dYPiBCXK_vv2cHadYnHraA451p-pjerGjuvaFs9cp4jm03dcia0ilLlFFYK5n74UApp-Da_ShPd4EN_o7az4F96Vwm7OtA1A2eemJw*2Fhttps*2A3A*2A2F*2A2Fwww.mail-archive.com*2A2Ffreesurfer*2A40nmr.mgh.harvard.edu*2A2Fmsg19957.html__*3BJSUlJSUl*21*21K-Hz7m0Vt54*21l_I7fXsMJ4M3cIew2iE5P2t1jYRmoaXBQ9rD7yLr2JjjCmZ3MBR-uMd5aDdELUdkSvaoOF4O9CTeXmCRrZD4XjPjqd-rlIA1__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC6hTQPyZw$ > > kw%24> > > > > <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > > > > > > > ?hRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>). > > > If we don?t need it, would it just be 2 conditions, as follows? > > > > > > > > > ? 1.? SelfOffset > > > ? 2.? Self*ValenceSlope > > > > > > But then I?m not clear how to get the main effect of valence (brain > > > regions that scale with increasing emotion valence, while holding > > > self-relevance constant)? > > > > > > From: > > > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>><mailto:freesurfer-bounces@nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> > > > on behalf of "Douglas N. Greve" > > > <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>><mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > > Reply-To: Freesurfer support list > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>><mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Date: Sunday, August 14, 2022 at 1:37 PM > > > To: > > > "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>"<mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>><mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Subject: Re: [Freesurfer] FSFAST first level covariates > > > > > > Those look like they are the same coding scheme. What is different? > > > You can only have one offset. The Self vs Valence -a 2 -a 4 is not > > > testing for an interaction. If you want an interaction you have to > > > create a new variable which is SelfRating*ValenceRating. > > > > > > On 8/10/2022 2:38 PM, Angela Fang wrote: > > > > > > ??????? External Email - Use Caution > > > Hello, > > > > > > Just re-sending my question below. If I have a variable with 2 levels > > > (yes/no) and another variable that is continuous, based on this post > > > (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://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > > > <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > > Fw4S9sp6o7il_xApboosWIOBOJb1zh7hBwMks3eFrd04OkImYWLahgGjjS7Zs4BjsQy1dYPiBCXK_vv2cHadYnHraA451p-pjerGjuvaFs9cp4jm03dcia0ilLlFFYK5n74UApp-Da_ShPd4EN_o7az4F96Vwm7OtA1A2eemJw*2Fhttps*2A3A*2A2F*2A2Fwww.mail-archive.com*2A2Ffreesurfer*2A40nmr.mgh.harvard.edu*2A2Fmsg19957.html__*3BJSUlJSUl*21*21K-Hz7m0Vt54*21l_I7fXsMJ4M3cIew2iE5P2t1jYRmoaXBQ9rD7yLr2JjjCmZ3MBR-uMd5aDdELUdkSvaoOF4O9CTeXmCRrZD4XjPjqd-rlIA1__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC6hTQPyZw$ > > kw%24> > > > > <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-we… > > > > > > > ?4mWO1Xyd_7RwNbKkVMPeDwG6K9W59gzBf_t0G-AzmUhxGC8zfKM0bxA9hhZv4GR2BQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>), > > > it sounds like I should code as follows:<o: >

1 0

White matter normalization of FLAIR images
by James Brown 29 Sep '22

29 Sep '22

External Email - Use Caution Dear Freesurfer experts, In order to normalize white matter intensity of T1 images and correct for bias field. We do the following steps: mri_convert T1.nii.gz T1.mgz mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 mri_normalize -g 1 T1_N3.mgzT1_norm.mgz mri_convert T1_norm.mgz T1_norm.nii.gz We would like to apply bias field correction on FLAIR images then normalize white matter intensity. We tried N4biasfieldcorrection from ANTS but it didn't work as expected. Reviewing documents about N4biasfieldcorrection we realize that the algorithm has been developed to correct bias field correction in T1 not clear if it works on FLAIR images. Are the steps above valid for normalizing FLAIR images or can it only be applied on T1 images? I would like to send a "recon-all.log" file that includes the processing steps of FLAIR. Is there any link I can use to upload the file. It gets rejected every time I send it due to size limitations. We appreciate any feedback about the proper way to correct FLAIR images for bias fields and normalize white matter intensity in FLAIR images. Thank you JamesB

3 9

Ask for password to open .7z file
by Gracian Garcia Marti 29 Sep '22

29 Sep '22

External Email - Use Caution Dear all, I kindly ask for the needed password to open the virtual machine FS_7_2_0_ubuntu_18_04_06.ova.7z Best regards. [firma_r2_c1] Gracián García Martí Ingeniero Área de Imagen Médica Cuantitativa [firma_r4_c2] [firma_r2_c1] [firma_r1_c3] Avenida Blasco Ibáñez, 14. 46010 Valencia (España) [firma_r3_c3]+34 96 369 06 00 Ext: 21260 http://secure-web.cisco.com/1qK3N9UUeWonL3fc5ilPcjDq5iPBSjZBWBkH3KMdGGjE-yM…<https://secure-web.cisco.com/1XvU2S3ssNi0947Ik1BcMxeKDnu7ri2F6oIsPCaXW2uRB5…> [cid:image006.jpg@01D83DCC.EEFC1430][cid:image007.jpg@01D83DCC.EEFC1430][cid:image008.jpg@01D83DCC.EEFC1430][cid:image009.jpg@01D83DCC.EEFC1430][cid:image010.jpg@01D83DCC.EEFC1430][cid:image011.jpg@01D83DCC.EEFC1430][cid:image012.jpg@01D83DCC.EEFC1430] Cuidemos el Medio Ambiente, por favor, no imprima este correo electrónico si no es necesario. Advertencia Este correo electrónico contiene información privada y estrictamente confidencial. Si usted no es el destinatario, no está autorizado a leerlo, retenerlo o difundirlo. Si ha recibido este mensaje por error, le rogamos lo notifique a su emisor y borre los documentos adjuntos.

1 0

MRI & PET positions available - BBRC Barcelona
by Juan Domingo Gispert López 29 Sep '22

29 Sep '22

External Email - Use Caution The Barcelonabeta Brain Research Center is welcoming applications for two neuroimaging analyst positions (MRI & PET) to help analyze longitudinal MRI and PET imaging data collected in the ALFA+ project ( https://secure-web.cisco.com/1coUA_P7zLcvpSWy46GKmA2yvwLEoJYpiS0zLXCA4l9TLy… ). *Main Responsibilities (MRI analyst):* - Developing analytical pipelines for advanced MRI sequences (ASL, QSM, DWI, MRS, etc…) using MatLab, Python, R and standard neuroimaging software suits (SPM, FSL, Freesurfer, etc…) - Analyzing and communicating results on participants of BBRC studies. - Help drafting research manuscripts and presentations. For full details, see: https://secure-web.cisco.com/10GKtYKBIwjBZRk1NMBlk9mUklU4l0eJOEWJAMHdK-1Zox… *Main Responsibilities (PET analyst):* - Applying and developing analytical pipelines for amyloid-β and tau PET scans (e.g. Centiloid, Regional Staging Methods, etc…) - Analyzing and communicating resulting data in the context of the main variables of participants in BBRC studies - Help drafting research manuscripts and presentations For full details, see: https://secure-web.cisco.com/1Qqx7_PEX7aTpY5kysR44EjvUQRcscoR49vSbfpkFFncOW… *Application Process:* To apply, please submit a single PDF file containing the following: 1. Cover letter describing research interests and relevant background; 2. CV 3. All files or inquiries should be submitted electronically to: talent(a)barcelonabeta.org Subject: MRI/PET Analyst *Deadline for submission of the applications: 31-10-2022* -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://secure-web.cisco.com/1LONTOII43IQoHTFWDGJVJbNbDz1Nc4NR4E_ZCAjRF3Ijk…> 08005 Barcelona <https://secure-web.cisco.com/1LONTOII43IQoHTFWDGJVJbNbDz1Nc4NR4E_ZCAjRF3Ijk…> http://secure-web.cisco.com/1jX-sWITlQvzslceNR1DXJ55pPyTHjDmeugdspvflx_NW5X… http://secure-web.cisco.com/12M_5iytgF96hiLf7bqDfbPxsfZMZ0w9zeScn_H6NlBW1zx… ------------------------------ Confidencialitat correu electrònic BBRC <https://secure-web.cisco.com/1JA18Ulsrw2-jVOA6_lK3VqBxnTWw0eYzK0ZyxY3JaVgY7…>. Confidencialidad correo electrónico BBRC <https://secure-web.cisco.com/1-dlln3AKC95HIyf2YbhVDn_DF3bE7g39UHeLOR0SYAt4W…>. E-mail confidentiality BBRC <https://secure-web.cisco.com/1OOHMIedhba4ZLayKXYRDCLubVKFG9OjE9W4fGqGdA4put…>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

1 0

How to verify that cortical surface orientation volume w/ respect to b0 is accurate?
by Bansal, Krishan Chandra 28 Sep '22

28 Sep '22

External Email - Use Caution I have created a volume which is supposed to have the cortical surface orientation with respect to b0 at each voxel. To do this I got the 6 frame overlay file from mris_convert. Then I isolated the first 3 values from each row in Matlab to create an Nx3 matrix, then from this I calculated the angle between each row vector and the b0 vector (which was just [0 1 0]) using the usual angle between two vectors formula. The result was an Nx1 matrix.I then saved it as an .mgh surface file (using save_mgh) and projected it back onto the original volume using surf2vol. I believe that I did this correctly, however the professor that I am developing this method for told me he wants me to verify that the results are correct. He was not very specific in how to do this, all he told me was that I could use volumes of the individual scanner x,y,z angles to help me figure out if my b0 results are right. What I assume he meant is: since the b0 axis goes vertically down the middle of the brain when in coronal view I can tell if the b0 angles are correct by seeing where the cortical surface is with respect to the z scanner direction and seeing if the b0 angle at the corresponding location makes sense. My problem is that I can’t tell if my results make sense. In theory I believe that at the locations where the cortex appears to be orthogonal to the B0 (z scanner) axis, the overall B0 angle of the cortical surface should be closer to 90 degrees. I still don’t understand what pattern I should be seeing in the values of the z scanner volume compared to the b0 angles volume. Comparing my z scanner volume results to the B0 angle volume the only pattern I can see is that the cortical surface with respect to B0 is closer to 90 degrees when the z scanner volume is closer to 0 degrees. No B0 angle I got is actually greater than 89 though. I can’t tell if this is the right pattern or enough to verify the results in the way the professor I’m working for wants. Any help here would be GREATLY appreciated. So far I have been able to get pretty far in teaching myself Freesurfer, but the some of the underlying mathematics about how to verify my results are unclear. I can send pictures of my results if someone wants to look at them.

1 0

Assistant Professor in Cognitive Neuroscience at UW-Milwaukee
by Caitlin R Bowman 28 Sep '22

28 Sep '22

External Email - Use Caution The University of Wisconsin-Milwaukee (UWM) is seeking applicants for a tenure-track faculty position in Cognitive Neuroscience. UWM is a Carnegie “Research 1” institution located in Wisconsin’s cultural and economic center. We are interested in recruiting outstanding scientists that will build directly on the current strengths of our program (http://secure-web.cisco.com/1k866Hj6O0LlrfeDn8tfH4EdKsnTmoH6F2ktOgucr0s8Ck9…) We expect to make an appointment at the Assistant Professor level. Responsibilities include developing an independent extramurally funded research program and teaching graduate and undergraduate courses in the neurosciences and experimental psychology. Successful applicants will have access to two research-dedicated MRI scanners maintained by the Center for Imaging Research (https://secure-web.cisco.com/13spGP24aK2sb8fPfNu2ykeT0PNJZJAabHc-QLtSPpbbMD…) and should be actively conducting novel, theory-based research in the domain of cognitive neuroscience. Outstanding individuals who use cutting-edge neuroimaging and/or computational methods to address questions about perception, attention, memory, aging, emotion, decision-making, or any combination of these cognitive domains are encouraged to apply. Individuals from minoritized, underrepresented communities are particularly encouraged to apply. See full job posting: https://secure-web.cisco.com/1cPlunNEn-50PO-A_IKfS2IE4eWAFUpiXPigrsu7QTG1F9… Contact Caitlin Bowman (bowman2(a)uwm.edu<mailto:bowman2@uwm.edu>) with questions. -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee

1 0

How can I get a code to unzip the image for Freesurfer?
by Marisa Smith 27 Sep '22

27 Sep '22

External Email - Use Caution

1 0

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Freesurfer September 2022