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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg

Thank you,

David

Message: 3

Date: Mon, 26 Sep 2022 22:14:37 -0400

From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>

Subject: Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than

cross-sectional

To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <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

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 : MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.vumc.nl/disclaimer

> AMC disclaimer : MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.amc.nl/disclaimer

> _______________________________________________

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edu

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------------------------------

Message: 4

Date: Tue, 27 Sep 2022 03:45:29 +0000

From: Emily Iannazzi <eiann@uw.edu>

Subject: Re: [Freesurfer] FSFAST first level covariates

To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>

Message-ID:

<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@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>

Sent: Friday, September 23, 2022 6:58 AM

To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>

Subject: Freesurfer Digest, Vol 223, Issue 39

Send Freesurfer mailing list submissions to

freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit

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or, via email, send a message with subject or body 'help' to

freesurfer-request@nmr.mgh.harvard.edu

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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@contbay.com>

Subject: Re: [Freesurfer] Running v7 with recon-all v6 files

To: freesurfer@nmr.mgh.harvard.edu

Cc: brouillard.alexandra@gmail.com

Message-ID: <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, 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-web.cisco.com%2F1h8voqUHNsdhi9ys-CwoL0SIgr1DmXws2WTt1cB7SmS2bkt2hpxLPCdDnHgZCi1mh1d2triLjxmboiQ3F3XNO6FzhNgC795r4rndOzrG1VLKV7o4fOEg29COaDn0z6Di1m3pZIXXjIjEmPdxu7gOmlIN0lqS1NceG3xpveW32qRvY7q9eP7vnMOZeEpse77jSr-W6LpPxkVHEMWLpLosjU5csPupoiwfd1ReYTdnQDF-nulu1lycNrdB_HfuRVmgxeUpHu8W-1L0eBHWmrW4dGBntqj6isGBFty0P9vBQ1NMcQp13Ft8iFVkP5qlBWHMP%2Fhttps%253A%252F%252Furldefense.com%252Fv3%252F__https%253A%252F%252Fsecure-web.cisco.com%252F1bbOhG1CjL59gEStW3FxyyS6evApjdBtrtnRNMXkTQqF0f3Y2vNJ3fv6xor1cZOFSNyNQR0fTSr3j3W0w9GElQ-JpDU_UJ_hnre3ioM3GTWCOo_LMVo6dJjN4zZGXndw0iMY4mdOlClFiKqUo5SqSeGEuePDdXeo6g1M7fk-I4Vi-keRLxbymtvJ0PlfiiA1bEuehH2vdOanpD27tszBo3PsOVVy9jGPzgFHpr9YOL61Mp4_YF_4ju2qkf3w8bHgKy7KPn6Gq2zLFmJt7v-nXB4r50aGl0pD013qN4YvG2i1Quti06FCypcmW4RB0a8jU%252Fhttps*3A*2F*2Fsurfer.nmr.mgh..harvard.edu*2Ffswiki*2Frel7downloads__%3BJSUlJSU!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2&data=05%7C01%7Cd.vannederpelt%40amsterdamumc.nl%7Cb9a955ae58594184127408daa03b826b%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637998475380121879%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KSpgm%2Btpl35VxUdubIGgEfUvWtjrjTdw8Zoo7WcobjM%3D&reserved=0

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) wrote:

        External Email - Use Caution        

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@nmr.mgh.harvard.edu

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------------------------------

Message: 2

Date: Fri, 23 Sep 2022 11:34:25 +0530

From: Ahmad Khan <110ahmadkhan@gmail.com>

Subject: [Freesurfer] Fwd: Error

To: freesurfer@nmr.mgh.harvard.edu

Message-ID:

<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>

Subject: Re: [Freesurfer] Error

To: freesurfer@nmr.mgh.harvard.edu

Cc: 110ahmadkhan@gmail.com

Message-ID: <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 (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-web.cisco.com%2F1B2iDU13Zj8Tu5lJ9OJGCLNPLemmBMb1PbQWYbi-KHCteIsSirpO19JkPtPYGVztgYPjGMFnNkHXco1I4g1h9jDqtL0pXeXkzWotjVxkvlqbOVKKe9BtLe3ou6WNB4EhriEUmbrYjNg4WJ2zGHiFsMSnpxS9YeLiX6LM3eVq4pPGfPveVO3-dp2lw0fnaGDvIxZgzthlyhDI8p9Wl9ZWfH0cROzKNi-BHKmTihLSRhltSWgfiO0mdtl3UfdmsgGMD3MuVSodlZIJRI7c4BXTYdOYvNt0_r-IX-4GzoO2CdgvTJaWbOothDunNq8mqAhka%2Fhttps%253A%252F%252Furldefense.com%252Fv3%252F__https%253A%252F%252Fsecure-web.cisco.com%252F1X7NA_6gOlCGu2ju8c-dGWtwYTkO0F2UyQn6LX3rWhDeWjyF0xKYDEMTG9JloMqwXl2TmqreXsJ64l2sn7uK0LnqYNE9uNR_dvpDVxEH389iV4Iic737MilGFa0RULauzaKJf91cSFfXFO_BoIRAXLQ6jyffj7yMXaaim_uxrlzcLdDBT59Q9pIM_GfgpQyjvufE6PeHhd0A47VyeX7mj3z6RVJGXHoYeqBE8qduJOn-HjpuoTMdXW2oMLCaXA_wbYwAMv55krtwONpw1IXGKFuOxbRGjkNj268o6U-MT32euGCcrOXopfxxVVSv-fRUkstH-kFL6sCvrc11fd4ey9g%252Fhttps*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Fpub*2Fdist*2Ffreesurfer*2F7.3.2*2Ffreesurfer_ubuntu&data=05%7C01%7Cd.vannederpelt%40amsterdamumc.nl%7Cb9a955ae58594184127408daa03b826b%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637998475380278045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jkO7EVINjwvqYglrVoyjRb%2FS8j3ZKSNaEWxFrsro2iA%3D&reserved=0

20-7.3.2_amd64.deb) __;JSUlJSUlJSU!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC4bEtEHOA$ or a tar archive (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-web.cisco.com%2F1riJUxznDcg7__oB4XKhVcxjiuYlkXM3V0Jv4Kyvr_09WoD6t7bB8N6Yv1n_fS3ZjlZq7x221CZWBrMpCmMGNuhMrZhzV9M6crD4LOlT1dsyx6jnIl2KvI6wUbOCXRa-B0uEj3LgcrRfknBHiigNcLklDVenVrgG1V1FUTCe9ugmQGnOxSBQRPJn6YDeur4oNM6RyZwFS97aAO6aVRAiuH8E5Tm2q8ftG4IjJmKhAmIf6gPd5vEEUzRgD5FOFAxRMBTlqJxYAib_7jRrr2iFG9rldI-iYvL2L6qhgx_VBJmMHyrbOB8YkCcQW4AFM7B_s%2Fhttps%253A%252F%252Furldefense.com%252Fv3%252F__https%253A%252F%252Fsecure-web.cisco.com%252F1UYiwKeazHITmgtErAJKToWU57RsDIl-czevJWE_lnANvBZa1W3VWoB0k8W51Ul0OYReT2eKxt7a-0YZf9ZkL8BktHWQAxKGtGaB9XsriNUt91b_gM0FOob7qKZT4XLrJo8tgo14qYKhbC3HCoAVelnrXTN__boC5i-5tAdyu1efkyiYepkCM69ost5vOy1_EJQfR2HWbCX2PaOIeyDT0LKjNauRdiGRp20CH0SqutxMy3KV4hkqJVIXGkMFpyl8yd3qLwOJvEenJqQ3t5wwRNG0c4le8IC40RaC9CIdPUYbmOHjYe7Vtw0h6WloK8JYsB_kg4__%3B!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJc&data=05%7C01%7Cd.vannederpelt%40amsterdamumc.nl%7Cb9a955ae58594184127408daa03b826b%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637998475380278045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=YiIqaJeNV0rcja8PwBMTY7afaDBGy9cBq4RxpABcpmg%3D&reserved=0

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.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>

Subject: [Freesurfer] dcmunpack

To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>

Message-ID:

<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

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Message: 5

Date: Fri, 23 Sep 2022 09:50:25 -0400

From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>

Subject: Re: [Freesurfer] Fwd: Error

To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <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@nmr.mgh.harvard.edu

> 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-web.cisco.com%2F1IzCHemGL_AtVnb1hKsNw_yrWd8f7jBmtqch_lhK5jVhdFnqU5Wsd84MgroGr8DFF8vTQjlqdkKiM-7dr7HAabj4hDJu8Sg2PIjWACBHF0Fpbj2QO_M7vlv3edWoKZh2c7jKfJO4sWU9ZuyjamfaK4DUmtcY5b062tNeKp1jKVjQKpbJXHKieE5MZgKvX3xNKZB3hJ7kxmbdP4xuYAp4l-jIuq0BZ1WVtIZQcVvmcV7R5RlYk2-MOKR9ihDpvaiqY9ibbHt0I3DCdGjLn0-ss0eDEIzO_Itk8VtVD8eodctEtOOr5h2DzAkQtY0dztKDI%2Fhttps%253A%252F%252Furldefense.com%252Fv3%252F__https%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer__%3B!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC5GmNYT6w%24&data=05%7C01%7Cd.vannederpelt%40amsterdamumc.nl%7Cb9a955ae58594184127408daa03b826b%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637998475380278045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=aIDo1isqv%2Fpc%2ByDiwBqKo9TIJB5TZa81CZ7lH8589g8%3D&reserved=0

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Message: 6

Date: Fri, 23 Sep 2022 09:54:22 -0400

From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>

Subject: Re: [Freesurfer] dcmunpack

To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <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@nmr.mgh.harvard.edu

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------------------------------

Message: 7

Date: Fri, 23 Sep 2022 09:57:33 -0400

From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>

Subject: Re: [Freesurfer] FSFAST first level covariates

To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <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@nmr.mgh.harvard.edu

> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of

> freesurfer-request@nmr.mgh.harvard.edu

> <freesurfer-request@nmr.mgh.harvard.edu>

> *Date: *Wednesday, August 31, 2022 at 9:22 PM

> *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>

> *Subject: *Freesurfer Digest, Vol 223, Issue 1

> Send Freesurfer mailing list submissions to

> freesurfer@nmr.mgh.harvard.edu

> To subscribe or unsubscribe via the World Wide Web, visit

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> or, via email, send a message with subject or body 'help' to

> freesurfer-request@nmr.mgh.harvard.edu

> You can reach the person managing the list at

> 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@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>

> Subject: Re: [Freesurfer] FSFAST first level covariates

> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

> Message-ID: <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> on behalf of "Douglas

> N. Greve" <dgreve@mgh.harvard.edu>

> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

> Date: Tuesday, August 30, 2022 at 7:38 AM

> To: "freesurfer@nmr.mgh.harvard.edu" <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@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: Sunday, August 28, 2022 at 1:07 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: 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

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kw%24>

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> ?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@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: Sunday, August 14, 2022 at 1:37 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: 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-web.cisco.com%2F1XAzFzZRGENjZVkmwRArrsIKda0sr3N4PL5pVyWpA354uTQ5rdCO0eWnPlKiOpFVQGBmMAn6-EvFVt_IaWvEi-n3Yno1neKqFtdUZXTItByn-ZdOEldXHwvQqu3yuzMUZS7BrPqPqXZVXbqcIwVgqbI7iXnHzCZvZA-OOqpjo1ulSKrxnthidV6AAz36X_1Tcxk02Pj2b4y6etl0p--XH_6jd_x5bWSdWu8bp5le5nRd73mU3rrRLlVz4oNBptlOyG3fkA0wL6F2ZvnpEHBch7eU8ZN0HkhloA8p1gdA8EmiXwSUo_i0Oef6vRS_Mng2Y%2Fhttps%253A%252F%252Furldefense.com%252Fv3%252F__https%253A%252F%252Fsecure-web.cisco.com%252F1axFb8Uk3EidN7RU3PxCMFcOtbS8C3cmNULxUDXhNgudqc2v-5LUyAYUUUC6m-FcwrPwdVKy2Y7n8DAVcyRmfV5k4NWvno0aemc07RzaIinRQ8-6_FFiXeiHdOzhbARiwJyY4xdCGKBBbKJGuolxWhUQ5ZaDv2NtX0TJ7BmyhFTGOFw4S9sp6o7il_xApboosWIOBOJb1zh7hBwMks3eFrd04OkImYWLahgGjjS7Zs4BjsQy1dYPiBCXK_vv2cHadYnHraA451p-pjerGjuvaFs9cp4jm03dcia0ilLlFFYK5n74UApp-Da_ShPd4EN_o7az4F96Vwm7OtA1A2eemJw%252Fhttps*3A*2F*2Fwww.mail-archive.com*2Ffreesurfer*40nmr.mgh.harvard.edu*2Fmsg19957.html__%3BJSUlJSUl!!K-Hz7m0Vt54!l_I7fXsMJ4M3cIew2iE5P2t1jYRmoaXBQ9rD7yLr2JjjCmZ3MBR-uMd5aDdELUdkSvaoOF4O9CTeXmCRrZD4XjPjqd-rlIA1kw%24&data=05%7C01%7Cd.vannederpelt%40amsterdamumc.nl%7Cb9a955ae58594184127408daa03b826b%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637998475380434259%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mK7GEf2dyTD8nNyQhu0LWTUsAsOLzwL66DapgNbqnSc%3D&reserved=0

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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: