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:
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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/1ZmeL3C2avBqAUV2PCoRmoPTQiEvv0t1lJ02Fdwj7Ybl2vTJDgXvZRgBXc2Z4ikgPwki8Luj-r9RQlimWSwlyJGa6DEDNRTOkQlnhELtrTSR7kANd5NsYt_iad4BYqk5lAsg1ER_m9jj-3yhf2eqmLDco56xEfPlQ6o_sIfJDYGvg84DDjAdO3AE4Qb8THxPtAzK8E6LQXqeLY00HkJZApOdvGgsTXf9AmukyFpoai6D-UyTbE5nYMojvGNg_kvxs6_-dsqkLqiB7yd3uWAZrjW5PRbPCcutI_mtGEnw6YH3g1aijywN1piEDrLwNbl9c/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg
Thank you,
David
Message: 3
Date: Mon, 26 Sep 2022 22:14:37 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than
cross-sectional
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: <34a07418-b022-160b-bfac-39c493226f28@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
AMC disclaimer : www.amc.nl/disclaimer
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Message: 4
Date: Tue, 27 Sep 2022 03:45:29 +0000
From: Emily Iannazzi <eiann@uw.edu mailto:eiann@uw.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates
To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<PH0PR08MB80141C3C693A17E429423C4ECF559@PH0PR08MB8014.namprd08.prod.outlook.com mailto:PH0PR08MB80141C3C693A17E429423C4ECF559@PH0PR08MB8014.namprd08.prod.outlook.com>
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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@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu<freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu>
Sent: Friday, September 23, 2022 6:58 AM
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu<freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Digest, Vol 223, Issue 39
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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@contbay.com mailto:fsbuild@contbay.com>
Subject: Re: [Freesurfer] Running v7 with recon-all v6 files
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Cc: brouillard.alexandra@gmail.com mailto:brouillard.alexandra@gmail.com
Message-ID: <9bf58e7024ed99c7c06379a6876dda10@trashmail.com mailto:9bf58e7024ed99c7c06379a6876dda10@trashmail.com>
Content-Type: text/plain; charset="utf-8"
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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-web... https://secure-web.cisco.com/17zDxbZj38d7X1lAF2NHcEOvXvsOg7gjmyjfLHsbG026mHJlz2zUwU7aFCWXuy9hZ6V1WcgUWVXaVEE9zMAhXrWNQLY_rOjdE9K9wKODy4Far1JadIzUBRnXIHk85Ug2JUspAbo7pZbofu5dvxp_qhaRfWfoXkA6tXQ3q7KhwCNeWF_ykXfB_llmy-Bocy-65J4z2KKPRIb9Rn_c7815S1Wprr2TLehdzObHWp5IIUm5Kr0IV4OIvPmYc2sh-M4LyzmV7FvKhHkrkYTy5c_rSunLa_HRWvUhEicNZy-UMyMYnwbrFJ9HqXehrOq8nEli4/https%3A%2F%2Feur04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1h8voqUHNsdhi9ys-CwoL0SIgr1DmXws2WTt1cB7SmS2bkt2hpxLPCdDnHgZCi1mh1d2triLjxmboiQ3F3XNO6FzhNgC795r4rndOzrG1VLKV7o4fOEg29COaDn0z6Di1m3pZIXXjIjEmPdxu7gOmlIN0lqS1NceG3xpveW32qRvY7q9eP7vnMOZeEpse77jSr-W6LpPxkVHEMWLpLosjU5csPupoiwfd1ReYTdnQDF-nulu1lycNrdB_HfuRVmgxeUpHu8W-1L0eBHWmrW4dGBntqj6isGBFty0P9vBQ1NMcQp13Ft8iFVkP5qlBWHMP%252Fhttps%25253A%25252F%25252Furldefense.com%25252Fv3%25252F__https%25253A%25252F%25252Fsecure-web.cisco.com%25252F1bbOhG1CjL59gEStW3FxyyS6evApjdBtrtnRNMXkTQqF0f3Y2vNJ3fv6xor1cZOFSNyNQR0fTSr3j3W0w9GElQ-JpDU_UJ_hnre3ioM3GTWCOo_LMVo6dJjN4zZGXndw0iMY4mdOlClFiKqUo5SqSeGEuePDdXeo6g1M7fk-I4Vi-keRLxbymtvJ0PlfiiA1bEuehH2vdOanpD27tszBo3PsOVVy9jGPzgFHpr9YOL61Mp4_YF_4ju2qkf3w8bHgKy7KPn6Gq2zLFmJt7v-nXB4r50aGl0pD013qN4YvG2i1Quti06FCypcmW4RB0a8jU%25252Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh..harvard.edu%2A2Ffswiki%2A2Frel7downloads__%253BJSUlJSU%21%21K-Hz7m0Vt54%21hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2%26amp%3Bdata%3D05%257C01%257Cd.vannederpelt%2540amsterdamumc.nl%257Cb9a955ae58594184127408daa03b826b%257C68dfab1a11bb4cc6beb528d756984fb6%257C0%257C0%257C637998475380121879%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26amp%3Bsdata%3DKSpgm%252Btpl35VxUdubIGgEfUvWtjrjTdw8Zoo7WcobjM%253D%26amp%3Breserved%3D0
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@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
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Message: 2
Date: Fri, 23 Sep 2022 11:34:25 +0530
From: Ahmad Khan <110ahmadkhan@gmail.com mailto:110ahmadkhan@gmail.com>
Subject: [Freesurfer] Fwd: Error
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAPNe=2f_e1woMTMoimoxZ8hvPWPbqrNLS2NMVTgugPsBQsRjwA@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
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Message: 3
Date: Fri, 23 Sep 2022 08:34:28 +0200
From: fsbuild <fsbuild@contbay.com mailto:fsbuild@contbay.com>
Subject: Re: [Freesurfer] Error
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Cc: 110ahmadkhan@gmail.com mailto:110ahmadkhan@gmail.com
Message-ID: <3ba2f92436c570f01d2b49ccc0305947@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-web... https://secure-web.cisco.com/1QhkkAfZYZRIGuigV_t1vwkpqZkmjAHasLRrfesN3yn0RdiBCtPpxodvzQngzsNdn9fvL93OzmkwzH2sw8yCyejgq4QV52zmxK69BcZiJYuN6vyYbf_aoHHSDS0oQ1_9haNDrQXz8xxhhuV6dOTHE_JKqRofkWKU0A-jTFJXIUxlHzB7BGh9yQfg-AwnTuR3ua1wDn0m11pf7lT2lQDCBWwgPY6cKzB_HAzSnE_DumVQrdpLioz2WNrB_7-f1bxEQweAM9nrtpvgvRvf6cfjku-ANZQxkKR1Y_UrMhONHkI4pTZA4o_0GtJLR7IVC1IaJ/https%3A%2F%2Feur04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1B2iDU13Zj8Tu5lJ9OJGCLNPLemmBMb1PbQWYbi-KHCteIsSirpO19JkPtPYGVztgYPjGMFnNkHXco1I4g1h9jDqtL0pXeXkzWotjVxkvlqbOVKKe9BtLe3ou6WNB4EhriEUmbrYjNg4WJ2zGHiFsMSnpxS9YeLiX6LM3eVq4pPGfPveVO3-dp2lw0fnaGDvIxZgzthlyhDI8p9Wl9ZWfH0cROzKNi-BHKmTihLSRhltSWgfiO0mdtl3UfdmsgGMD3MuVSodlZIJRI7c4BXTYdOYvNt0_r-IX-4GzoO2CdgvTJaWbOothDunNq8mqAhka%252Fhttps%25253A%25252F%25252Furldefense.com%25252Fv3%25252F__https%25253A%25252F%25252Fsecure-web.cisco.com%25252F1X7NA_6gOlCGu2ju8c-dGWtwYTkO0F2UyQn6LX3rWhDeWjyF0xKYDEMTG9JloMqwXl2TmqreXsJ64l2sn7uK0LnqYNE9uNR_dvpDVxEH389iV4Iic737MilGFa0RULauzaKJf91cSFfXFO_BoIRAXLQ6jyffj7yMXaaim_uxrlzcLdDBT59Q9pIM_GfgpQyjvufE6PeHhd0A47VyeX7mj3z6RVJGXHoYeqBE8qduJOn-HjpuoTMdXW2oMLCaXA_wbYwAMv55krtwONpw1IXGKFuOxbRGjkNj268o6U-MT32euGCcrOXopfxxVVSv-fRUkstH-kFL6sCvrc11fd4ey9g%25252Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Fpub%2A2Fdist%2A2Ffreesurfer%2A2F7.3.2%2A2Ffreesurfer_ubuntu%26amp%3Bdata%3D05%257C01%257Cd.vannederpelt%2540amsterdamumc.nl%257Cb9a955ae58594184127408daa03b826b%257C68dfab1a11bb4cc6beb528d756984fb6%257C0%257C0%257C637998475380278045%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26amp%3Bsdata%3DjkO7EVINjwvqYglrVoyjRb%252FS8j3ZKSNaEWxFrsro2iA%253D%26amp%3Breserved%3D0
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-web... https://secure-web.cisco.com/14j0m631KdUh_XriselHzTqvzw8n0r0g0qe02gTiyySUtVMgItZ4UxCPEWU6iLRnCH_BsEqsib9frLF1q65eKvJekizOvrhNetNIucAiWhS9hs60Tycm9plFVO9Mfk3AzaELN3GRLB3DnBq6S_Dm30Uz8NXFQfHE28oT0GA9gXuqnQFByvSRaZRtgSKrBw1pPxm711Moz_LM_E7zQkYm7rArJGQJ626Ux0Tey7jK7WrWoNkSKiyix1LRyC9nP37mjHevFOOc4euA2WMfnUxS9vCHgMyhvGMV8ALAPseWJOSPCbdsk60b9P9jb6rJ8av5R/https%3A%2F%2Feur04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1riJUxznDcg7__oB4XKhVcxjiuYlkXM3V0Jv4Kyvr_09WoD6t7bB8N6Yv1n_fS3ZjlZq7x221CZWBrMpCmMGNuhMrZhzV9M6crD4LOlT1dsyx6jnIl2KvI6wUbOCXRa-B0uEj3LgcrRfknBHiigNcLklDVenVrgG1V1FUTCe9ugmQGnOxSBQRPJn6YDeur4oNM6RyZwFS97aAO6aVRAiuH8E5Tm2q8ftG4IjJmKhAmIf6gPd5vEEUzRgD5FOFAxRMBTlqJxYAib_7jRrr2iFG9rldI-iYvL2L6qhgx_VBJmMHyrbOB8YkCcQW4AFM7B_s%252Fhttps%25253A%25252F%25252Furldefense.com%25252Fv3%25252F__https%25253A%25252F%25252Fsecure-web.cisco.com%25252F1UYiwKeazHITmgtErAJKToWU57RsDIl-czevJWE_lnANvBZa1W3VWoB0k8W51Ul0OYReT2eKxt7a-0YZf9ZkL8BktHWQAxKGtGaB9XsriNUt91b_gM0FOob7qKZT4XLrJo8tgo14qYKhbC3HCoAVelnrXTN__boC5i-5tAdyu1efkyiYepkCM69ost5vOy1_EJQfR2HWbCX2PaOIeyDT0LKjNauRdiGRp20CH0SqutxMy3KV4hkqJVIXGkMFpyl8yd3qLwOJvEenJqQ3t5wwRNG0c4le8IC40RaC9CIdPUYbmOHjYe7Vtw0h6WloK8JYsB_kg4__%253B%21%21K-Hz7m0Vt54%21hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJc%26amp%3Bdata%3D05%257C01%257Cd.vannederpelt%2540amsterdamumc.nl%257Cb9a955ae58594184127408daa03b826b%257C68dfab1a11bb4cc6beb528d756984fb6%257C0%257C0%257C637998475380278045%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26amp%3Bsdata%3DYiIqaJeNV0rcja8PwBMTY7afaDBGy9cBq4RxpABcpmg%253D%26amp%3Breserved%3D0
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@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.m... 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
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Message: 4
Date: Fri, 23 Sep 2022 13:26:43 +0000
From: "O'Dor, Sarah,PHD" <SODOR@mgh.harvard.edu mailto:SODOR@mgh.harvard.edu>
Subject: [Freesurfer] dcmunpack
To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
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<BL0PR04MB65325927F567249B3A514F71F34E9@BL0PR04MB6532.namprd04.prod.outlook.com mailto:BL0PR04MB65325927F567249B3A514F71F34E9@BL0PR04MB6532.namprd04.prod.outlook.com>
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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
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Message: 5
Date: Fri, 23 Sep 2022 09:50:25 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: Error
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: <271c230a-538a-d7ae-d3b5-1c3025c3ed2e@mgh.harvard.edu mailto:271c230a-538a-d7ae-d3b5-1c3025c3ed2e@mgh.harvard.edu>
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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
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Message: 6
Date: Fri, 23 Sep 2022 09:54:22 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] dcmunpack
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: <df1177a3-a59c-223e-c766-09d726abdf15@mgh.harvard.edu mailto:df1177a3-a59c-223e-c766-09d726abdf15@mgh.harvard.edu>
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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
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Message: 7
Date: Fri, 23 Sep 2022 09:57:33 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: <6f7768e7-47de-9da1-a919-2d68f46a400b@mgh.harvard.edu mailto:6f7768e7-47de-9da1-a919-2d68f46a400b@mgh.harvard.edu>
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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@nmr.mgh.harvard.edu
mailto:*freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
freesurfer-request@nmr.mgh.harvard.edu
*Date: *Wednesday, August 31, 2022 at 9:22 PM
*To: *freesurfer@nmr.mgh.harvard.edu
mailto:*freesurfer@nmr.mgh.harvard.edu<freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Freesurfer Digest, Vol 223, Issue 1
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Today's Topics:
?? 1. Re: FSFAST first level covariates (Angela Fang)
?? 2. Bus error using VM (#@# Nu Intensity Correction)
????? (daedalus39@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@uw.edu mailto:angfang@uw.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2A2F422F-279C-4736-885A-C609F488C21E@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@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas
N. Greve" <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, August 30, 2022 at 7:38 AM
To: "freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@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
- Self-offset
- SelfValence
- NoSelf-offset
- 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:
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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@nmr.mgh.harvard.edu
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on behalf of "Douglas N. Greve"
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<freesurfer@nmr.mgh.harvard.edu
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Date: Sunday, August 28, 2022 at 1:07 PM
To:
"freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu
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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
- Offset
- Self
- Valence
- 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:
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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
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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$
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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@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"
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Date: Sunday, August 14, 2022 at 1:37 PM
To:
"freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu
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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:
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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
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?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:
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve