See https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V where group1=female, group2=male, and variable=age
On 9/26/2022 10:45 PM, Emily Iannazzi wrote:
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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?
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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 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"
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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, *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://secure-web.cisco.com/1bbOhG1CjL59gEStW3F... https://secure-web.cisco.com/1A5BkoCrIN0knv5vfaP5n1FvULf1tBYPAo9hYPfUnB3nmsnf81oKebApA4bnNt8MZk3AUNsuR_Zn547LcByh9Qc5EeI_kiqhVK5ET24ZjM8g1Zd_xpOIUW8WSVnYTNOCnUxLd_iwqzGLON9IoS1DDiYiXADTjWumEDyR4244PlA-W-1rwhmue_Ps6ojOlmCZaVA2G4NngPbcd7tM13KyBL_S6TjVudcqubN0JeeaClgC_HsRLqmiipMGOvB8ALSJi2q_umUDujoOevofF2IvMZxEar-XmpR-Uo9_OqCKuIuadfK40k8qfbXLQinxYthJW/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1bbOhG1CjL59gEStW3FxyyS6evApjdBtrtnRNMXkTQqF0f3Y2vNJ3fv6xor1cZOFSNyNQR0fTSr3j3W0w9GElQ-JpDU_UJ_hnre3ioM3GTWCOo_LMVo6dJjN4zZGXndw0iMY4mdOlClFiKqUo5SqSeGEuePDdXeo6g1M7fk-I4Vi-keRLxbymtvJ0PlfiiA1bEuehH2vdOanpD27tszBo3PsOVVy9jGPzgFHpr9YOL61Mp4_YF_4ju2qkf3w8bHgKy7KPn6Gq2zLFmJt7v-nXB4r50aGl0pD013qN4YvG2i1Quti06FCypcmW4RB0a8jU%2Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh..harvard.edu%2A2Ffswiki%2A2Frel7downloads__%3BJSUlJSU%21%21K-Hz7m0Vt54%21hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC4zyOTmLw%24 , 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:
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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 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"
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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: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__http://mail.nmr.mgh.harvard.edu/pipermail/freesu... https://secure-web.cisco.com/1NJhbznBojJrwbPGW6repdRpWahjDQpUCG714SwacChxCc7Wa9ZhG96Je74kTpS8n3Xq_QkTGgxe_xvXUVumO5eIBcQZYz0DilJvHkoQoQJsp0ypQffl2iP69S8-f2eOgBdv_gqGGd_bN9macOfNcadGuP8ouDzyXHU-GaXHuVmkD5NoAtvkhDaiWJkxLj-Fy3Bmh0MCBVaOwX4SctaSjZZfQ1fH6xZf3ldsHyp0fHGZ6jN1Q-FROw67kawpL-yGTA6YRJG-rlq78dg-Baq_-ouPlJxht4qlQxPnqNaB0cOouLXDIATf_MWKX-Ac3ZoPU/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20220923%2Ff39dc96f%2Fattachment-0001.html__%3B%21%21K-Hz7m0Vt54%21hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC6iz3zjRQ%24
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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"
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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://urldefense.com/v3/__https://secure-web.cisco.com/1X7NA_6gOlCGu2ju8c-... https://secure-web.cisco.com/1iU4zT9EHg-wn3UcpgReQ4W2D_KyIYtOT25VjBGs6KEq8j7Ex64Kfb996zTaQjKx-zAd2e_x2jSYh6RUtRwjeZDukzh54EIUgydIP8g58eLJ4sEtG6rlDHsFPVZKYTmTYdR4XPt_FgfSbkaOFJqy-KsmgyXuLG8FpF95HPkBY-yjYuKV6RhEXcMGVBfe46wJ4o8tdsMFW87EQRL1mD5_PD6ebYFTbI2yy-_7ExwQHzNbgi1xjuC-GROLkk63b3mS10UwDIY__8ogBexzPspsEcsySgaAeG1-YRbegkgtGBGSEb2KRTH45XIpPGGyimVB9/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1X7NA_6gOlCGu2ju8c-dGWtwYTkO0F2UyQn6LX3rWhDeWjyF0xKYDEMTG9JloMqwXl2TmqreXsJ64l2sn7uK0LnqYNE9uNR_dvpDVxEH389iV4Iic737MilGFa0RULauzaKJf91cSFfXFO_BoIRAXLQ6jyffj7yMXaaim_uxrlzcLdDBT59Q9pIM_GfgpQyjvufE6PeHhd0A47VyeX7mj3z6RVJGXHoYeqBE8qduJOn-HjpuoTMdXW2oMLCaXA_wbYwAMv55krtwONpw1IXGKFuOxbRGjkNj268o6U-MT32euGCcrOXopfxxVVSv-fRUkstH-kFL6sCvrc11fd4ey9g%2Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Fpub%2A2Fdist%2A2Ffreesurfer%2A2F7.3.2%2A2Ffreesurfer_ubuntu20-7.3.2_amd64.deb) __;JSUlJSUlJSU!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC4bEtEHOA$ or a tar archive (https://urldefense.com/v3/__https://secure-web.cisco.com/1UYiwKeazHITmgtErAJ...
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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__http://mail.nmr.mgh.harvard.edu/pipermail/freesu... https://secure-web.cisco.com/14lLS99BBF5AhM5MVMyLdLogtQG36JidKFqQKj36Q1sSIccCcGa20vWxWtJYrynUOKAuC3z9FulVZKljBWjsL3JGoBQYYig4fAcsowF7PZgolkg5Aln-KkAYqfoXODMKXs4eU12F1FaGb0XB8K264QRJBe6FJqhyffaXtqOmBF-VV5j3l6oMflc9840AN2EN71-wbriPQwQNNye1rAPUKT_2J9EaYSPLhjzz5h8OHpwEgomZ5_rKnZsAk-fVrvIVX3C1H5TZXp7CFbDSzOCzEvrKugMFUAV13Xj2vToYTyhCev6szL9ATmNWhfvprx4En/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20220923%2F2c5491c1%2Fattachment-0001.html__%3B%21%21K-Hz7m0Vt54%21hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC7SkgtEXw%24
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:
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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 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
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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
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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
- 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:
??????? 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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
- 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:
??????? 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* *MailScanner has detected a possible fraud attempt from
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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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* *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://secure-web.cisco.com/1axFb8Uk3EidN7RU3Px... https://secure-web.cisco.com/1E9II9dA9vX8C4O6Z2l1djmVVR4tL3LkIftYrdBI86CdaysrIGUiQveJEHdMNfQJ7VwOvTnKUWM9LUpy7suRu7FBB9RD_nq-GFDTDxyKS5wT4FDKBYcFlTU5X-2sITtEHkFTqvOwNgHkJx32XqpHwqHl5VNLWjnZBGMbhCcKJeZuy7XL9tfFeSmz5BteoxMDoUgBqT0diVjB4Y1KSD1wPdDmPlQl_d3k0iPwaQK592jUQivftaCjSsL0GwrCGBlQ5ZL_J7WXx-09munjIHNfFK_Z2MqrUP3QKgAfQCuaz77Ry6rnY3VzVCZp1BLntOIT_/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1axFb8Uk3EidN7RU3PxCMFcOtbS8C3cmNULxUDXhNgudqc2v-5LUyAYUUUC6m-FcwrPwdVKy2Y7n8DAVcyRmfV5k4NWvno0aemc07RzaIinRQ8-6_FFiXeiHdOzhbARiwJyY4xdCGKBBbKJGuolxWhUQ5ZaDv2NtX0TJ7BmyhFTGOFw4S9sp6o7il_xApboosWIOBOJb1zh7hBwMks3eFrd04OkImYWLahgGjjS7Zs4BjsQy1dYPiBCXK_vv2cHadYnHraA451p-pjerGjuvaFs9cp4jm03dcia0ilLlFFYK5n74UApp-Da_ShPd4EN_o7az4F96Vwm7OtA1A2eemJw/https*3A*2F*2Fwww.mail-archive.com*2Ffreesurfer*40nmr.mgh.harvard.edu*2Fmsg19957.html__;JSUlJSUl!!K-Hz7m0Vt54!l_I7fXsMJ4M3cIew2iE5P2t1jYRmoaXBQ9rD7yLr2JjjCmZ3MBR-uMd5aDdELUdkSvaoOF4O9CTeXmCRrZD4XjPjqd-rlIA1kw$
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it sounds like I should code as follows:
? 1.? SelfOffset ? 2.? Self-ValenceSlope (would the weight in the 4th column reflect the value of self multiplied by the value of valence for this participant?) ? 3.? NonSelfOffset ? 4.? NonSelf-ValenceSlope
If the other way of modifying the paradigm file is also acceptable to test the interaction (as I describe below), that would also be helpful to know.
Thanks! Angela
From:
freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of Angela Fang angfang@uw.edumailto:angfang@uw.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, August 1, 2022 at 4:35 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates
??????? External Email - Use Caution Hi Doug,
Nevermind to my first question! I read 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* *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://secure-web.cisco.com/1x486JnVcuVKZFlKc9l... https://secure-web.cisco.com/1hyojp1atPpmAlnXottMRCK1slgWsODWEgkz9b-7actYicKt0EsFxC0Cffl9ivACQcegOIoS91e_Y5k-4VA5vEFwlQwtuMJSDNXz8wcUSmAnY7_QA6AWOeTcNXBAmzwLdynia_BLjp_ntMpw6KK2E1haV1Kls78g5S7oqo4XDieCojTGUbOVxjqU-m2js-WlTc-mhhNX0kS08cEXCOtlXpVMMuuATmb3qWlF56Utk6BPdaRv1lG7oqLJpmCgCeBbg0slR3nMvDcnpvp0pUD6w84hF_RkoPqyaMoLDEtWZaoLSO7Y-LdiX3RKtZpD9tiDc/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1x486JnVcuVKZFlKc9lnM17mkutiyvGdWJ7I2FV8fwW_DW3coauzdEYjTthPWCuUI49R8eR7JdFGVDEm-PGd9Gp03GX15R1fQSmiF_Oa0GSUysb9oU2BILoHtXNRTr2wYopYLEgZzR0uHoS42fJD6Y6OgxNPab4zkRakvC9SczCpOmDIjix_3coBjxNyEGBZxGeQ43psRUWNXcOqObLo5i75Sk5As8_8hlVX0lY3Nhlg6GpZxPNxznyC2k4HTCODw-faGH-b0xy25IwE7YN7YmWgVADwyzJ3Ra2p48FjTCCD90Yn7ggECXgkApxbdwYhEozkxSvgygst9PXkZBXgH3g%2Fhttps%2A3A%2A2F%2A2Fwww.mail-archive.com%2A2Ffreesurfer%2A40nmr.mgh.harvard.edu%2A2Fmsg32235.html__%3BJSUlJSUl%21%21K-Hz7m0Vt54%21l_I7fXsMJ4M3cIew2iE5P2t1jYRmoaXBQ9rD7yLr2JjjCmZ3MBR-uMd5aDdELUdkSvaoOF4O9CTeXmCRrZD4XjPjqd_Wb_lRvQ%24
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?archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html>) and realized that we always include a subject-specific par file in each run for first-level analyses.
However, I?m still confused about how to modify my paradigm file. I also need to model the trials of non-interest, so would it be as
follows?
0???????????? 1????????????? 2.5????????? 1.0 SelfOffset 0????????????? 2????????????? 2.5????????? 1.0 SelfSlope (equal to subject?s rating of self-relevance) 0????????????? 3????????????? 2.5????????? 1.0 ValenceOffset 0????????????? 4????????????? 2.5????????? 3.0 ValenceSlope (equal to subject?s rating of valence)
2.5????????? 0????????????? 2.5????????? 1.0 FIXATION
5.0????????? 1????????????? 2.5????????? 1.0 SelfOffset 5.0????????? 2????????????? 2.5????????? 0 SelfSlope (equal to subject?s rating of self-relevance, in this case subject responded 0, or non-relevant) 5.0????????? 3????????????? 2.5????????? 1.0 ValenceOffset 5.0????????? 4????????????? 2.5????????? 2.0 ValenceSlope (equal to subject?s rating of valence)
7.5????????? 5????????????? 2.5????????? 1.0 OTHER
Do these contrasts look correct to you? Self vs Fixation -a 1 -c 0 (main effect of self) Valence vs Fixation -a 3 -c 0 (main effect of valence) Self vs Valence -a 2 -a 4 (interaction between self x valence)
Thank you so much for your help! Angela
From:
freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of Angela Fang angfang@uw.edumailto:angfang@uw.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 28, 2022 at 1:02 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates
Thanks Doug. This wiki page is extremely helpful. However, my question is about individual subject responses. I could see how you could include a summary (e.g., average) value of the parametric variable across subjects in your ?weight? column but it?s not clear to me how you could integrate individual subject responses to each word in the parametric modulation paradigm file? I?m imagining something like the FSGD file where a value is given for each subject, but for first-level analysis.
We have a similar design as someone else who posted a similar question (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* *MailScanner has detected a possible fraud attempt from
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?ttps%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>).
We have an event-related experiment presenting trait adjectives in terms of whether they describe themselves (SELF condition) or someone else (OTHER condition). We are interested in testing a 2x2 ANOVA to examine an interaction between self-relevance x emotional valence. Assuming you can?t integrate individual subject responses to each word in the paradigm file, would we set it up as follows?
?Usual? paradigm file: 0????????????? 1????????????? 2.5????????? 1.0 SELF 2.5????????? 0????????????? 2.5????????? 1.0 FIXATION 5.0????????? 1????????????? 2.5????????? 1.0????????? SELF 7.5????????? 2????????????? 2.5????????? 1.0 OTHER
Parametric modulation paradigm file: 0????????????? 1????????????? 2.5????????? 1.0 SELFoffset 0????????????? 2????????????? 2.5????????? 0.8 SELFslope 0????????????? 3????????????? 2.5????????? 1.0 VALENCEoffset 0????????????? 4????????????? 2.5????????? 2.0 VALENCEslope
(where 0.8 reflects the percentage of time the word was endorsed as self-relevant and 2.0 is the average valence rating given for that word)
And then create a contrast of 2 vs 4 to test the interaction? Would testing contrast 1 vs 0 be a test of the main effect of self-relevance and contrast 3 vs 0 the main effect of valence?
Thanks so much for your help! Angela
From:
freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 28, 2022 at 10:25 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates
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<https://urldefense.com/v3/__https://secure-web.cisco.com/1vlnv3wLgT6AWyuomHX...
?ulation> On 7/25/2022 6:56 PM, Angela Fang wrote:
??????? External Email - Use Caution Hi Freesurfer community, I have run participants through an event-related fMRI task in which subjects rate whether trait adjectives are descriptive of themselves or not, and afterwards asked them to rate each trait word on emotional valence. Is it possible to include these individual level subjective ratings of emotional valence as covariates in the first level contrast in FSFAST? If so, how? Thanks, Angela
Angela Fang, Ph.D. Assistant Professor Department of Psychology University of Washington Lab website: 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* *MailScanner has detected a possible fraud attempt from
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Pronouns: she, her, hers
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Message: 2 Date: Wed, 31 Aug 2022 22:32:39 +0000 (UTC) From: daedalus39@aol.com Subject: [Freesurfer] Bus error using VM (#@# Nu Intensity Correction) To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 819256121.2629465.1661985159026@mail.yahoo.com Content-Type: text/plain; charset="utf-8"
??????? External Email - Use Caution
Hello FreeSurfer Developers, In an effort to relieve strain on my local C:/ drive, I was testing "export" to an existing shared folder on my SSD drive (D:/) Guidance came
from:https://urldefense.com/v3/__https://secure-web.cisco.com/1YO7E9aNxbSzoJwOfWq...
export SUBJECTS_DIR=/media/sf_0007_Subjects-FS/subjects
I had tested the FS-7.2 VM on this same image leaving the?SUBJECTS_DIR environment variable as default and this MRI was processed and ran to completion without error.? While certain early portions for FS ran without issue for this 2nd test (shared folder in the VM set up upon installation), the recon-all run exited with errors at the Nu Intensity Correction step.? Bus error?Command exited with non-zero status 1?
I don't understand how "mri_binarize" could crash and I'm hoping you can provide some guidance.?? Did I need to use a variation of the command:mkdir -p /home/developer/guest_shared/sf_0007_Subjects-FS/subjects(?) I am running all this on the VM FS_Ubuntu_18_04_06. Thanks in advance for any insight. -Randy PS. I only know enough Linux to get into trouble
-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME? ?/usr/local/freesurfer/7.2.0FSFAST_HOME? ? ? ?/usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR? ? ? /usr/local/freesurfer/7.2.0/subjectsMNI_DIR? ? ? ? ? ?/usr/local/freesurfer/7.2.0/mni
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx from recon-all.log xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx #@# Nu Intensity Correction Wed Aug 31 14:19:28 EDT 2022 ?mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4?
/usr/bin/bc/media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mri/usr/local/freesurfer/7.2.0/bin/mri_nu_correct.mni--i
orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4nIters 2mri_nu_correct.mni 7.2.0Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxWed Aug 31 14:19:28 EDT 2022tmpdir is ./tmp.mri_nu_correct.mni.6181cd
/media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mriAntsN4BiasFieldCorrectionFs
-i orig.mgz -o ./tmp.mri_nu_correct.mni.6181/nu0.mgz --dtype ucharAntsN4BiasFieldCorrectionFs donemri_binarize --i ./tmp.mri_nu_correct.mni.6181/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.6181/ones.mgzBus error?Command exited with non-zero status 1@#@FSTIME? 2022:08:31:14:19:28 mri_nu_correct.mni N 9 e 139.45 S 1.50 U 137.65 P 99% M 508172 F 1 R 155334 W 0 c 291 w 1359 I 720 O 0 L 0.91 0.50 0.26@#@FSLOADPOST 2022:08:31:14:21:48 mri_nu_correct.mni N 9 2.37 1.22 0.56Linux developer-VirtualBox ? 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s WBI-FES_S_0862x exited with ERRORS at Wed Aug 31 14:21:48 EDT 2022 To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from
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Message: 3 Date: Thu, 01 Sep 2022 04:19:21 +0200 From: fsbuild fsbuild@contbay.com Subject: Re: [Freesurfer] Bus error using VM (#@# Nu Intensity ??????? Correction) To: freesurfer@nmr.mgh.harvard.edu Cc: daedalus39@aol.com Message-ID: 09c5d2e524982669c629f02a40af7538@trashmail.com Content-Type: text/plain; charset="utf-8"
??????? External Email - Use Caution
Hard to look at the error w/o a core dump file, but I suspect ?bus error? is from the VM and not from commands in the recon-all acting differently during your 2nd run. It reads like you created a shared folder for the VM to use, and set SUBJECTS_DIR to it so the recon-all will write files to the D: drive which I assume has a windows file system (NTFS) and not a linux file system (ext4). Bus error could be from the VM not being able to do something on the D drive when it needed to. It?s not going to work by default for something running in the linux VM to create a soft link on a Windows file system. There are some postings about how to enable this, but it?s a
pain, https://urldefense.com/v3/__https://secure-web.cisco.com/1o9_6RQMC4nKOlu3EcH...
I would avoid pointing SUBJECTS_DIR to a windows file system for the linux VM to write to. If you want disk space usage on your C drive, consider locating the VM on your external D drive (which should also help the VM run faster since it won?t be running from the boot drive).. You can take your existing VM on the C drive and clone it to a new folder/destination on your D drive using the VirtualBox application. Then you should have 2 instances of the VM. Test bringing up the one on the D drive and then delete the one on the C drive including all its files.
- R.
On Aug 31, 2022, at 18:32, daedalus39@aol.com wrote: External Email - Use Caution Hello FreeSurfer Developers,In an effort to relieve strain on my local C:/ drive, I was testing "export" to an existing shared folder on my SSD drive (D:/)Guidance came
from:https://urldefense.com/v3/__https://secure-web.cisco.com/1QmDaWnb5IenddSg9gr...
SUBJECTS_DIR=/media/sf_0007_Subjects-FS/subjectsI had tested the FS-7.2 VM on this same image leaving the SUBJECTS_DIR environment variable as default and this MRI was processed ? and ran to completion without error. While certain early portions for FS ran without issue for this 2nd test (shared folder in the VM set up upon installation), the recon-all run exited with errors at the Nu Intensity Correction step. Bus error Command exited with non-zero status 1 I don't understand how "mri_binarize" could crash and I'm hoping you can provide some guidance. Did I need to use a variation of the command:mkdir -p /home/developer/guest_shared/sf_0007_Subjects-FS/subjects(?)I am running all this on the VM FS_Ubuntu_18_04_06.Thanks in advance for any insight.-RandyPS. I only know enough Linux to get into trouble-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /usr/local/freesurfer/7.2.0FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /usr/local/freesurfer ?/7.2.0/subjectsMNI_DIR &! ?nbsp; &n bsp;
/usr/local/freesurfer/7.2.0/mnixxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
from recon-all.log xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx#@# Nu Intensity Correction Wed Aug 31 14:19:28 EDT 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
--ants-n4 /usr/bin/bc/media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mri/usr/local/freesurfer/7.2.0/bin/mri_nu_correct.mni--i
orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4nIters 2mri_nu_correct.mni 7.2.0Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxWed Aug 31 14:19:28 EDT 2022tmpdir is ./tmp.mri_nu_correct.mni.6181cd
/media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mriAntsN4BiasFieldCorrectionFs
-i orig.mgz -o ./tmp.mri_nu_correct.mni.6181/nu0.mgz --dtype ucharAntsN4BiasFieldCorrectionFs donemri_binarize --i ./tmp.mri_nu_correct.mni.6181/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.6181/ones.mgzB ?us error Command exited with non-zero status 1@#@FSTIME 2022:08:31:14:19:28 mri_nu_correct.mni N 9 e 139.45 S 1.50 U 137.65 P 99% M 508172 F 1 R 155334 W 0 c 291 w 1359 I 720 O 0 L 0.91 0.50 0.26@#@FSLOADPOST 2022:08:31:14:21:48 mri_nu_correct.mni N 9 2.37 1.22 0.56Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s WBI-FES_S_0862x exited with ERRORS at Wed Aug 31 14:21:48 EDT 2022To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from
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Message: 4 Date: Wed, 31 Aug 2022 23:06:15 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] sclimbic sometimes does not detect left ??????? basal forebrain To: freesurfer@nmr.mgh.harvard.edu Message-ID: 2c416d3a-e9d3-b8f3-30ff-f1e64a639b80@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
I'm not sure but I have a guess. EAch stage of the unet has an intensity normalization step where the intensity of all voxels are spread uniformly over a range. I suspect that the bright, meaningless voxels are causing the meaningful voxels to be forced into too small of a range causing information loss.
On 8/31/2022 11:19 AM, Miriam Taza wrote:
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thank you! One last?question hopefully on this matter. I dont fully understand still why the percentile flag would affect the subcortical regions? the bias field was only in the front and back of the brain.
Thanks, Miriam
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Sunday, August 28, 2022 4:13 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain
On 8/11/2022 6:02 PM, Miriam Taza wrote:
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Hi again,
I have a few questions regarding this.
indeed it does appear that there is a bias field in all of these scans, but this is not specific to those that fail sclimbic.
? 1. why do you think it is consistently *only* the *left* side that ???? fails??My question here is if whether it is mainly the left due ???? to the way sclimbic does its magic or if this might be due to the ???? actual data (i,e smaller left volumes might have an impact).
I have no idea. That's the problem with the machine learning stuff, it just gives you an answer without a reason.
2.?I would really appreciate if someone could explain what --percentile 99.9 is doing a bit more as my results differ a lot depending if this flag is used or not. Im asking because Im not sure what is the best input to use for sclimbic anymore....
The --percentile 99.9 tells it to sort all the voxels by intensity. One of those voxels will rank the 99.9% in intensity. All voxels that are brighter than this intensity are then set to this intensity ("clipping"). This represents more closely how ScLimbic was trained. I will make --percentile 99.9 the default on the next release.
I decided to look at differences(correlation) of volume (.stats) between sclimbic or sclimbic with --percentile 99.9 ran on T1s or on recon all results (I wanted to make confirm the results using recon all subj vs t1s with the percentile flag are similar given that recon all does correct for bias field).? below are the correlation and means. this was on subsample (n=180) and I only looked at one ROI.
?????? left BF? right BF sclimbic x sclimbic99???????? 0.48???? 0.62 sclimbic x recon99??? 0.30???? 0.55 sclimbic x recon????? 0.30???? 0.55 recon99 x recon?????? 0.99???? 0.99 recon99 x sclimbic99? 0.91???? 0.95 recon x sclimbic99??? 0.92???? 0.95
?????? avg left BF????? avg BF mean sclimbic????? 198.77?? 253.96 sclimbic99??? 297.99?? 328.93 recon???????? 312.12?? 340.44 recon99?????? 315.80?? 343.92
(recon = sclimbic ran on recon all outputs; recon99 = sclimbic --percentile 99 ran on recon outputs; sclimbic=ran sclimbic on t1s; sclimbic99=with flag ran on t1s)
*3.so the most important question is what would you judge to provide the "most accurate" result to be used in subsequent group analysis. recon99, recon, sclimbic, or sclimbic99.
*This confirms my suspicions above (ie, the training). The "recon" method will most closely track the training (and the results from the paper).*
Thank you very?much! Miriam
*From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
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*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain
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but this(bright at back and nose) also seems to be the case with participants that sclimbic did work on..
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*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain There was something a little strange about the cases that were failing -- there were very bright values at the back of the head and around the nose. This probably messes up the normalization in the unet. I ran it with --percentile 99.9 (this eliminates the extreme voxels) and the results looked ok after that.
On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them. They?re T1w scans 1x1x1mm3
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*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain Have you looked at the input volume to see if there is anything strange about them? What kind of scans are you passing to it? What is the resolution?
On 7/25/2022 9:03 PM, Miriam Taza wrote:
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Hello, I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked up after running ScLimbic. These are healthy adults and their scans look good. Also, I noticed often when this occurs NAcc is also 0 or other regions. I am concerned if there is a systematic issue with left volumes ending up smaller than they should relative to right.
Thanks, Miriam
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Message: 5 Date: Wed, 31 Aug 2022 23:07:25 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates To: freesurfer@nmr.mgh.harvard.edu Message-ID: 9193e9d3-1d12-a74f-bad1-df438612345a@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
sorry, you lost me there ...
On 8/31/2022 12:39 PM, Angela Fang wrote:
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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 5^th 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
- 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:
???? *????????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
<mailto: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 <mailto: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
<mailto: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
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>>
freesurfer@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 2^nd 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
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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" dgreve@mgh.harvard.edu ???????? <mailto:dgreve@mgh.harvard.edu
<mailto: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
<mailto: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
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>>
freesurfer@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* *MailScanner has detected a possible fraud attempt from
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<https://urldefense.com/v3/__https://secure-web.cisco.com/1S2s08xk6_r2FFsEB5S...
), ???????????? it sounds like I should code as follows:
????????????? 1. SelfOffset ????????????? 2. Self-ValenceSlope (would the weight in the 4^th column ???????????????? reflect the value of self multiplied by the value of ???????????????? valence for this participant?) ????????????? 3. NonSelfOffset ????????????? 4. NonSelf-ValenceSlope
???????????? If the other way of modifying the paradigm file is also ???????????? acceptable to test the interaction (as I describe below), ???????????? that would also be helpful to know.
???????????? Thanks!
???????????? Angela
???????????? *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 Angela Fang angfang@uw.edu <mailto:angfang@uw.edu
<mailto:angfang@uw.edu mailto:angfang@uw.edu>>
???????????? *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu ???????????? <mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>>
???????????? *Date: *Monday, August 1, 2022 at 4:35 PM ???????????? *To: *Freesurfer support list freesurfer@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
???????????? *????????External Email - Use Caution *
???????????? Hi Doug,
???????????? Nevermind to my first question! I read 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* *MailScanner has detected a possible fraud attempt from
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) ???????????? and realized that we always include a subject-specific par ???????????? file in each run for first-level analyses.
???????????? However, I?m still confused about how to modify my ???????????? paradigm file. I also need to model the trials of ???????????? non-interest, so would it be as follows?
???????????? 0 1????????????? 2.5????????? 1.0????????? SelfOffset
???????????? 0 2????????????? 2.5????????? 1.0????????? SelfSlope ???????????? (equal to subject?s rating of self-relevance)
???????????? 0 3????????????? 2.5????????? 1.0????????? ValenceOffset
???????????? 0 4????????????? 2.5????????? 3.0 ValenceSlope?(equal to ???????????? subject?s rating of valence)
???????????? 2.5 0????????????? 2.5????????? 1.0????????? FIXATION
???????????? 5.0 1????????????? 2.5????????? 1.0????????? SelfOffset
???????????? 5.0 2????????????? 2.5????????? 0????????????? SelfSlope ???????????? (equal to subject?s rating of self-relevance, in this case ???????????? subject responded 0, or non-relevant)
???????????? 5.0 3????????????? 2.5????????? 1.0????????? ValenceOffset
???????????? 5.0 4????????????? 2.5????????? 2.0????????? ValenceSlope ???????????? (equal to subject?s rating of valence)
???????????? 7.5 5????????????? 2.5????????? 1.0????????? OTHER
???????????? Do these contrasts look correct to you?
???????????? Self vs Fixation -a 1 -c 0 (main effect of self)
???????????? Valence vs Fixation -a 3 -c 0 (main effect of valence)
???????????? Self vs Valence -a 2 -a 4 (interaction between self x
valence)
???????????? Thank you so much for your help!
???????????? Angela
???????????? *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 Angela Fang angfang@uw.edu <mailto:angfang@uw.edu
<mailto:angfang@uw.edu mailto:angfang@uw.edu>>
???????????? *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu ???????????? <mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>>
???????????? *Date: *Thursday, July 28, 2022 at 1:02 PM ???????????? *To: *Freesurfer support list freesurfer@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
???????????? Thanks Doug. This wiki page is extremely helpful. However, ???????????? my question is about individual subject responses. I could ???????????? see how you could include a summary (e.g., average) value ???????????? of the parametric variable across subjects in your ???????????? ?weight? column but it?s not clear to me how you could ???????????? integrate individual subject responses to each word in the ???????????? parametric modulation paradigm file? I?m imagining ???????????? something like the FSGD file where a value is given for ???????????? each subject, but for first-level analysis.
???????????? We have a similar design as someone else who posted a ???????????? similar question (*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* *MailScanner has detected a possible fraud attempt from
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<https://urldefense.com/v3/__https://secure-web.cisco.com/11nFbIrJYBqRI1W_4wY...
). ???????????? We have an event-related experiment presenting trait ???????????? adjectives in terms of whether they describe themselves ???????????? (SELF condition) or someone else (OTHER condition). We are ???????????? interested in testing a 2x2 ANOVA to examine an ???????????? interaction between self-relevance x emotional valence. ???????????? Assuming you can?t integrate individual subject responses ???????????? to each word in the paradigm file, would we set it up as ???????????? follows?
???????????? ?Usual? paradigm file:
???????????? 0 1????????????? 2.5????????? 1.0????????? SELF
???????????? 2.5 0????????????? 2.5????????? 1.0????????? FIXATION
???????????? 5.0 1????????????? 2.5????????? 1.0????????? SELF
???????????? 7.5 2????????????? 2.5????????? 1.0????????? OTHER
???????????? Parametric modulation paradigm file:
???????????? 0 1????????????? 2.5????????? 1.0????????? SELFoffset
???????????? 0 2????????????? 2.5????????? 0.8????????? SELFslope
???????????? 0 3????????????? 2.5????????? 1.0????????? VALENCEoffset
???????????? 0 4????????????? 2.5????????? 2.0????????? VALENCEslope
???????????? (where 0.8 reflects the percentage of time the word was ???????????? endorsed as self-relevant and 2.0 is the average valence ???????????? rating given for that word)
???????????? And then create a contrast of 2 vs 4 to test the ???????????? interaction? Would testing contrast 1 vs 0 be a test of ???????????? the main effect of self-relevance and contrast 3 vs 0 the ???????????? main effect of valence?
???????????? Thanks so much for your help!
???????????? Angela
???????????? *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" dgreve@mgh.harvard.edu ???????????? <mailto:dgreve@mgh.harvard.edu
<mailto: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
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>>
???????????? *Date: *Thursday, July 28, 2022 at 10:25 AM ???????????? *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 ???????????? <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
???????????? Yes, see *MailScanner has detected a possible fraud ???????????? attempt from "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from
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???????????? On 7/25/2022 6:56 PM, Angela Fang wrote:
???????????????? *????????External Email - Use Caution *
???????????????? Hi Freesurfer community,
???????????????? I have run participants through an event-related fMRI ???????????????? task in which subjects rate whether trait adjectives ???????????????? are descriptive of themselves or not, and afterwards ???????????????? asked them to rate each trait word on emotional ???????????????? valence. Is it possible to include these individual ???????????????? level subjective ratings of emotional valence as ???????????????? covariates in the first level contrast in FSFAST? If ???????????????? so, how?
???????????????? Thanks,
???????????????? Angela
???????????????? ---
???????????????? Angela Fang, Ph.D.
???????????????? Assistant Professor ???????????????? Department of Psychology
???????????????? University of Washington
???????????????? Lab website: *MailScanner has detected a possible ???????????????? fraud attempt from "secure-web.cisco.com" claiming to ???????????????? be* *MailScanner has detected a possible fraud
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Message: 6 Date: Thu, 1 Sep 2022 03:13:38 +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: A8DEED3B-8F8E-43F2-A724-C48115F59D6D@uw.edu Content-Type: text/plain; charset="utf-8"
??????? External Email - Use Caution
Sorry if I was unclear. The analysis we have set up will allow me to test for the difference between self and non self valence slope, but I?m also interested in testing for the slope of valence alone (identifying the brain regions associated with increasing valence ratings). Can I add another condition for valence, and if so, how do we make the weights different from the self*valence condition (because self is always coded 1 so the weights for self*valence and valence only will be identical)?
On Aug 31, 2022, at 8:08 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
?sorry, you lost me there ...
On 8/31/2022 12:39 PM, Angela Fang wrote:
??????? 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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:
??????? 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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
- 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:
??????? 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* *MailScanner has detected a possible fraud attempt from
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[secure-web.cisco.com]<https://urldefense.com/v3/__https://secure-web.cisco.com/1n9NaxxOQGYBn2vf8MJ...
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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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* *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://secure-web.cisco.com/1ibJu9DNCEQ80IS8XnY... https://secure-web.cisco.com/1lDueYjwErxN-uEq7cJbVPurgn09i79YvirIKieORipEpMXnKMFshYI63NFuB8lh0x3ArEQ01GXJZ5wh7ZIub4gcgMLzNX6_Zbc51xA8xLKUF48pcPgvWgMTXrKSulTvX7ybH525FbkvHB1F9oX65i9C3CV4R5-vCt7s9n2fIUlXgTlidIr5naOM3Krew6Lkg9fWWeKQSkco5ajd7gGOynjkNEOaa-B0tM5u-FDnHysOXZxVSJJZRH2wKsUCQWJp1TTpx5bl5X850PhLO2jYadSTegme0TosQmuR2K2Id-LwyQDf6NlYsc-XcBN4qca5E/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1ibJu9DNCEQ80IS8XnYQe64G3qUwBk_mJpSfJiHpiFjdObD9fykxEUJll6wFW1-iyN02rfgtRiXTnU4tJAcadUeslBYPf-5CRhCzFKS5taH5e0tcr9yHQucLQZtMPwSNjLSKr-EMGQl4s3bOljQ7SzM7l6ZQZBC6x74q-pCqkQlgW50Mo8uKIDwwDfPnF04ok_kWyqNSL0h4dA3bGXpjQGWY4qb8REA8F3zJTfPieNKjhTBe92G4KDFXX89v_EwUnQw-1GiIs15MK4BUf5eS1LmzTtShQ99QPfHfFSABruvyX4IXN1a1oyCVeBCtRlgya%2Fhttps%2A3A%2A2F%2A2Fwww.mail-archive.com%2A2Ffreesurfer%2A40nmr.mgh.harvard.edu%2A2Fmsg19957.html__%3BJSUlJSUl%21%21K-Hz7m0Vt54%21l_I7fXsMJ4M3cIew2iE5P2t1jYRmoaXBQ9rD7yLr2JjjCmZ3MBR-uMd5aDdELUdkSvaoOF4O9CTeXmCRrZD4XjPjqd9ugT8qvA%24
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[secure-web.cisco.com]<https://urldefense.com/v3/__https://secure-web.cisco.com/1XE1lL3vmTF46oAiDk9...
?8040MZtmQrZ7fPHU4dpe2yPkC0lGZ_YWgnhGTlJNePPxw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1S2s08xk6_r2FFsEB5S1KdOcfq6G8ToJwyZuNFONdwgOYd87JJkB-uznJW2pelg24KQwX3lweVOmFs99TCKitjbJOqKWgEH_UW7wir5JQ113csODerDntanBrEibOdt6Mxs2QeQ5D7n69Ds6NaOSOJIbLFeMjuoaTXCkNccNydn7jvjmVd0zW2YhEXG9JtLxMNVIYt8q48ZK0sJUt8sjTP6xuCzA1pzB19MUHA078Zgygtns0YVgn1n5Sg41ZbVZ3jWciX5ZF34AejW5nWj1Z4mWO1Xyd_7RwNbKkVMPeDwG6K9W59gzBf_t0G-AzmUhxGC8zfKM0bxA9hhZv4GR2BQ%2Fhttps*3A*2F*2Fwww.mail-archive.com*2Ffreesurfer*40nmr.mgh.harvard.edu*2Fmsg19957.html__;JSUlJSUl!!K-Hz7m0Vt54!ji6For-hJmPcW17cpltXyyzEnXZRMzaxRMDE33CdvLR4Q_kP7EegDZ6_SSQVOXEDDzrFFGPTAepz16TQhQby$>),
it sounds like I should code as follows:
? 1.? SelfOffset ? 2.? Self-ValenceSlope (would the weight in the 4th column reflect the value of self multiplied by the value of valence for this participant?) ? 3.? NonSelfOffset ? 4.? NonSelf-ValenceSlope
If the other way of modifying the paradigm file is also acceptable to test the interaction (as I describe below), that would also be helpful to know.
Thanks! Angela
From:
freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of Angela Fang angfang@uw.edumailto:angfang@uw.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, August 1, 2022 at 4:35 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates
??????? External Email - Use Caution Hi Doug,
Nevermind to my first question! I read 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* *MailScanner has detected a possible fraud attempt from
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<https://urldefense.com/v3/__https://secure-web.cisco.com/1bDSDRjEYX2xBE_8lJQ...
[secure-web.cisco.com]<https://urldefense.com/v3/__https://secure-web.cisco.com/12yTQcAEwE0LLr2bz8J...
?3A%2F%2Fsecure-web.cisco.com%2F1646ymi0_yM9ab72e81bZdCKw_zNbXr9RihxDaiDVPq0_Qd4EXYgDmO56zQdi9l_AyV3uyyiURXHoYWQmiu56CbMuIGdZz8EH0gbsnVrAz9KwunZAwLzh0kh-jzVwHtlbEdd1ExEJYHT7o7JtUWg2GM484JTyL0VZJymRuGRyD0ag1nQ_0BPPjQHxPCqNHEU4Y_seBsq9XsUROgyR-bX-tHVXxhshVUHgneudw6tEB2lIVYfYrL3srRbjy1QN9Bq_e3_WaNCDhkXdixnae24i41HHYwJfn3KwsmNoZ2RxLoh3SMkXXwVntAewl8PeldBY0s3UxoEPiFbDdXXuJLUjlw%2Fhttps*3A*2F*2Fwww.mail-archive.com*2Ffreesurfer*40nmr.mgh.harvard.edu*2Fmsg32235.html__;JSUlJSUl!!K-Hz7m0Vt54!ji6For-hJmPcW17cpltXyyzEnXZRMzaxRMDE33CdvLR4Q_kP7EegDZ6_SSQVOXEDDzrFFGPTAepz1-csL2qz$>)
and realized that we always include a subject-specific par file in each run for first-level analyses.
However, I?m still confused about how to modify my paradigm file. I also need to model the trials of non-interest, so would it be as
follows?
0???????????? 1????????????? 2.5????????? 1.0 SelfOffset 0????????????? 2????????????? 2.5????????? 1.0 SelfSlope (equal to subject?s rating of self-relevance) 0????????????? 3????????????? 2.5????????? 1.0 ValenceOffset 0????????????? 4????????????? 2.5????????? 3.0 ValenceSlope (equal to subject?s rating of valence)
2.5????????? 0????????????? 2.5????????? 1.0 FIXATION
5.0????????? 1????????????? 2.5????????? 1.0 SelfOffset 5.0????????? 2????????????? 2.5????????? 0 SelfSlope (equal to subject?s rating of self-relevance, in this case subject responded 0, or non-relevant) 5.0????????? 3????????????? 2.5????????? 1.0 ValenceOffset 5.0????????? 4????????????? 2.5????????? 2.0 ValenceSlope (equal to subject?s rating of valence)
7.5????????? 5????????????? 2.5????????? 1.0 OTHER
Do these contrasts look correct to you? Self vs Fixation -a 1 -c 0 (main effect of self) Valence vs Fixation -a 3 -c 0 (main effect of valence) Self vs Valence -a 2 -a 4 (interaction between self x valence)
Thank you so much for your help! Angela
From:
freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of Angela Fang angfang@uw.edumailto:angfang@uw.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 28, 2022 at 1:02 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates
Thanks Doug. This wiki page is extremely helpful. However, my question is about individual subject responses. I could see how you could include a summary (e.g., average) value of the parametric variable across subjects in your ?weight? column but it?s not clear to me how you could integrate individual subject responses to each word in the parametric modulation paradigm file? I?m imagining something like the FSGD file where a value is given for each subject, but for first-level analysis.
We have a similar design as someone else who posted a similar question (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* *MailScanner has detected a possible fraud attempt from
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<https://urldefense.com/v3/__https://secure-web.cisco.com/1BSlEtqhqclg05rf53k...
[secure-web.cisco.com]<https://urldefense.com/v3/__https://secure-web.cisco.com/1T3b2JFQFteTd3ZHOhc...
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We have an event-related experiment presenting trait adjectives in terms of whether they describe themselves (SELF condition) or someone else (OTHER condition). We are interested in testing a 2x2 ANOVA to examine an interaction between self-relevance x emotional valence. Assuming you can?t integrate individual subject responses to each word in the paradigm file, would we set it up as follows?
?Usual? paradigm file: 0????????????? 1????????????? 2.5????????? 1.0 SELF 2.5????????? 0????????????? 2.5????????? 1.0 FIXATION 5.0????????? 1????????????? 2.5????????? 1.0????????? SELF 7.5????????? 2????????????? 2.5????????? 1.0 OTHER
Parametric modulation paradigm file: 0????????????? 1????????????? 2.5????????? 1.0 SELFoffset 0????????????? 2????????????? 2.5????????? 0.8 SELFslope 0????????????? 3????????????? 2.5????????? 1.0 VALENCEoffset 0????????????? 4????????????? 2.5????????? 2.0 VALENCEslope
(where 0.8 reflects the percentage of time the word was endorsed as self-relevant and 2.0 is the average valence rating given for that word)
And then create a contrast of 2 vs 4 to test the interaction? Would testing contrast 1 vs 0 be a test of the main effect of self-relevance and contrast 3 vs 0 the main effect of valence?
Thanks so much for your help! Angela
From:
freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 28, 2022 at 10:25 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates
Yes, 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* *MailScanner has detected a possible fraud attempt from
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On 7/25/2022 6:56 PM, Angela Fang wrote:
??????? External Email - Use Caution Hi Freesurfer community, I have run participants through an event-related fMRI task in which subjects rate whether trait adjectives are descriptive of themselves or not, and afterwards asked them to rate each trait word on emotional valence. Is it possible to include these individual level subjective ratings of emotional valence as covariates in the first level contrast in FSFAST? If so, how? Thanks, Angela
Angela Fang, Ph.D. Assistant Professor Department of Psychology University of Washington Lab website: 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* *MailScanner has detected a possible fraud attempt from
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<https://urldefense.com/v3/__https://secure-web.cisco.com/1U7c8iyL5IheayGabq5...
[secure-web.cisco.com]<https://urldefense.com/v3/__https://secure-web.cisco.com/1m6Qv1hdbciF39yOXbp...
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Message: 7 Date: Thu, 1 Sep 2022 13:16:43 +1000 From: Yann Quid? yannquide@gmail.com Subject: Re: [Freesurfer] Thalamic nuclei exited with ERRORS To: fsbuild fsbuild@contbay.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: B1CBE771-22A9-459E-B5F6-4035A01B5482@gmail.com Content-Type: text/plain; charset="utf-8"
??????? External Email - Use Caution
Hi again,
Just wanted to confirm the randomness of the issue? and see if there was any potential explanation for this.
I decided to go back from scratch, using a copy of my scans processed with FS5.3. I re-ran the thalamic nuclei pipeline from FS7.2.0 a first time: 3 subjects only (out of 139) were actually processed for thalamic nuclei. I ran it a second time (did not change any parameter), ?excluding" the 3 scans that were processed in the previous round (deleted from a text file I call to identify my subjects), and got 2 new scans to be processed; these 2 were not processed in the previous round, giving me the segmentation violation error! I am currently running a third round (minus the previous 5 scans), and at least 1 new scan is being processed?. that sent an error at the 2 previous round.
Any idea of what could go wrong?
Thanks for your time.
Yann
On 31 Aug 2022, at 2:12 pm, Yann Quid? yannquide@gmail.com wrote:
This is the error I get when for example, I use MCRv93
sub-BA_IGP001
ERROR: cannot find Matlab 2014b runtime in location:
/Applications/freesurfer/7.2.0/MCRv84
It is looking for either: ?? bin/glnxa64/libmwlaunchermain.so??? (Linux 64b) or ?? bin/maci64/libmwlaunchermain.dylib (Mac 64b)
The hippocampal/amygdala and brainstem modules require the (free)
Matlab runtime.
You will need to download the Matlab Compiler Runtime (MCR) for
Matlab 2014b.
To do so, please run the following command (you might need root
permissions):
fs_install_mcr R2014b
For further details, please visit *MailScanner has detected a
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/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.volumes.txt
/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.mgz
/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
.
Yann
On 31 Aug 2022, at 1:51 pm, fsbuild <fsbuild@contbay.com
<mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com
mailto:fsbuild@contbay.com>>> wrote:
It?s possible something in 7.2.0 still requires MCRv84.? If so, it
is probably not going to work to use a soft link to fake out the name, and using a different version of Matlab run time could explain the crashes. Please send along the output showing MCRv84 is required.
- R.
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Message: 8 Date: Thu, 01 Sep 2022 05:28:23 +0200 From: fsbuild fsbuild@contbay.com Subject: Re: [Freesurfer] Thalamic nuclei exited with ERRORS To: freesurfer@nmr.mgh.harvard.edu Cc: yannquide@gmail.com Message-ID: fbb010a15da7bba394823cef650c0e58@trashmail.com Content-Type: text/plain; charset="utf-8"
??????? External Email - Use Caution
For MacOS, the 7.2.0 release was done on MacOS 10.14.6 and it will check for Matlab runtime MCRv84 which you install with R2014b as the argument to fs_install_mcr
For MacOS, the 7.3.2 release was done on MacOS 10.15.7 and it will check for Matlab runtime MCRv97 which you install with R2019b as the argument to fs_install_mcr
I think we already know your machine running MacOS 10.13 does not match the above but MCRv84 sometimes works for you running the 7.2.0 release. The errors you posted from Matlab could be an issue with MCRv84 w.r.t MacOS 10.13 or your machine. Upgrading your OS to match the above could eliminate the matlab errors.
If you want to experiment with running different versions of Matlab, e.g.., R2017b, then you can go into the file ./freesurfer/bin/checkMCR.sh and comment out the check for the version of matlab by adding pound sign ?#? to the beginning of the lines that do the check. Then you don?t need to try and bypass the check with soft links. But we have not done testing for the above releases on MacOS 10.13.
I don?t know if you have experience with using multiple boot partitions for MacOS (set via Startup Disk in System Prefeernces). One test would be to do a clean install of MacOS 10.14 or 10.15 on an empty (internal) disk partition or external disk drive. Then boot from that partition and install the 7.2.0 or 7.3.2 release with the matching version of Matlab listed above. You would probably want at least a USB3 connection (or equivalent speed) to an external drive for that to not run slowly. A clean install should eliminate any issues with the current state of your machine. Then try running your commands with the matching Freesurfer release in the new/clean version of the OS.
- R.
On 31 Aug 2022, at 2:12 pm, Yann Quid? <yannquide@gmail.com> wrote:This is the error I get when for example, I use MCRv93sub-BA_IGP001 ERROR: cannot find Matlab 2014b runtime in location: /Applications/freesurfer/7.2.0/MCRv84 It is looking for either: bin/glnxa64/libmwlaunchermain.so (Linux 64b) or bin/maci64/libmwlaunchermain.dylib (Mac 64b) The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b.To do so, please run the following command (you might need root permissions): fs_install_mcr R2014b
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Message: 9 Date: Thu, 1 Sep 2022 04:19:43 +0000 From: "Ashwati Vipin (Dr)" ashwati.vipin@ntu.edu.sg Subject: Re: [Freesurfer] Unable to run trac-all -prep? : cannot???????? file ??????? bvals??? bvecs file To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: "Yendiki, Anastasia" AYENDIKI@MGH.HARVARD.EDU, "Cook,???? Philip" cookpa@pennmedicine.upenn.edu Message-ID:
TYZPR01MB4211923CC21767525F1A7EB4C27B9@TYZPR01MB4211.apcprd01.prod.exchangelabs.com
Content-Type: text/plain; charset="windows-1252"
??????? External Email - Use Caution
Sending this again ? please help!
Thank you! I didn?t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:
[cid3189490776*image005.png@01D8B937.AC0099D0]
The subject?s scripts folder still has an IsRunning.trac file. I?ve attached the log files and my configuration file. Not sure what?s going wrong?
Best, Ashwati
-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from
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[signature_2362934844]
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Monday, 29 August 2022 at 10:19 AM To: cookpa@pennmedicine.upenn.edu cookpa@pennmedicine.upenn.edu, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [External] Re: Unable to run trac-all -prep : cannot file bvals bvecs file
??????? External Email - Use Caution Thank you! I didn?t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:
[cid:image005.png@01D8B937.AC0099D0]
The subject?s scripts folder still has an IsRunning.trac file. I?ve attached the log files and my configuration file. Not sure what?s going wrong?
Best, Ashwati
-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from
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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Friday, 26 August 2022 at 10:56 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, cookpa@pennmedicine.upenn.edu cookpa@pennmedicine.upenn.edu Subject: Re: [Freesurfer] [External] Re: Unable to run trac-all -prep : cannot file bvals bvecs file
??????? External Email - Use Caution Thank you! I didn?t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:
[cid:image005.png@01D8B937.AC0099D0]
The subject?s scripts folder still has an IsRunning.trac file. I?ve attached the log files and my configuration file. Not sure what?s going wrong?
Best, Ashwati
-- Ashwati Vipin (PhD) Research Fellow ? Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore 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* *MailScanner has detected a possible fraud attempt from
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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Cook, Philip cookpa@pennmedicine.upenn.edu Date: Wednesday, 24 August 2022 at 9:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, AYENDIKI@MGH.HARVARD.EDU AYENDIKI@MGH.HARVARD.EDU Subject: Re: [Freesurfer] [External] Re: Unable to run trac-all -prep : cannot file bvals bvecs file
??????? External Email - Use Caution Hi,
If you're having trouble building ANTs, you might be interested in the ANTs binaries now available from Github for Mac and Linux.
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<https://urldefense.com/v3/__https://secure-web.cisco.com/1X_uzaIT9kQcox3lwjp...
<https://urldefense.com/v3/__https://secure-web.cisco.com/1RXhqmCs7-WVg_KC9lh...
The zip files will unzip to a folder ants-2.4.1. So you would do (in
bash)
? export ANTSPATH=/path/to/ants-2.4.1/bin/
including the trailing slash, and replacing `/path/to` with wherever you unzipped the archive.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Wednesday, August 24, 2022 at 1:14 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, AYENDIKI@MGH.HARVARD.EDU AYENDIKI@mgh.harvard.edu Subject: [External] Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file
??????? External Email - Use Caution Dear Anastasia,
Thank you so much for your help. So silly of me, the trac-all prep step went off alright after I fixed the config file but it now gives me the error:
ERROR: must set ANTSPATH environment variable to use ANTs
I noticed on a previous thread that another user had a similar issue, so I also decided to install ANTs. As with them, I am also running into a lot of issues installing ANTs and you mentioned in the thread that using ANTs for registration is optional in the new versions of TRACULA. Would you please recommend how to go about the option of not running ANTs? Is it an option I need to set/add to the config file for TRACULA?
Thanks again!
Best, Ashwati
-- Ashwati Vipin (PhD) Research Fellow ? Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore 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* *MailScanner has detected a possible fraud attempt from
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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@MGH.HARVARD.EDU Date: Friday, 19 August 2022 at 2:39 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file Dear Ashwati - Check out the instructions in the example config file: 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* *MailScanner has detected a possible fraud attempt from
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... # Diffusion gradient tables (file names can be relative to dcmroot) ... # Diffusion b-value tables (file names can be relative to dcmroot) ...
Because you defined dcmroot, these filenames should be relative paths (which you did correctly for the DWI nifti file). The error occurs because it prepends dcmroot to the filenames you provided, so there's a replication (check what the error says and you'll see that).
Best, Anastasia.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Sent: Tuesday, August 16, 2022 9:50 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file
??????? External Email - Use Caution
Dear Freesurfer developers,
I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0.? The configuration file seems to be alright but when I start running the -prep step it gives me the error:
writing to
/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...
/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt:
No such file or directory.
Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022
I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I?m not sure why it?s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn?t work.
[cid2203429043*image001.png@01D8B09D.94718010]
I have run tracula before with no issues so I?m really lost here. Could you please help?
Thank you so much!
Best,
Ashwati
--
Ashwati Vipin (PhD)
Research Fellow - Dementia Research Centre (Singapore)
Lee Kong Chian School of Medicine
Nanyang Technological University, Singapore
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[signature_3677307404]
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Monday, 15 August 2022 at 11:59 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file
??????? External Email - Use Caution
Dear Freesurfer developers,
I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0.? The configuration file seems to be alright but when I start running the -prep step it gives me the error:
writing to
/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...
/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt:
No such file or directory.
Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022
I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I?m not sure why it?s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn?t work.
[cid:image001.png@01D8B09D.94718010]
I have run tracula before with no issues so I?m really lost here. Could you please help?
Thank you so much!
Best,
Ashwati
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End of Freesurfer Digest, Vol 223, Issue 1
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End of Freesurfer Digest, Vol 223, Issue 39
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