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Yes of course! Attached is the first run for the first subject (in txt format).
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Message: 2 Date: Fri, 30 Sep 2022 10:29:26 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates To: freesurfer@nmr.mgh.harvard.edu Message-ID: bc8d956f-8990-0cc9-e47a-3dcd8f70c3df@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
can you send the par file?
On 9/29/2022 6:45 PM, Emily Iannazzi wrote:
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Here is the error again in plain text rather than an attachment (running selxavg3):
cd /autofs/cluster/manoach/angela/FSFAST
/usr/local/freesurfer/stable6_0_0/fsfast/bin/selxavg3-sess
parfiles condition id list:? 1? 2? 3? 4? 5? 6
Found 149955/163842 (91.5) voxels in mask 1
Creating Design Matrix
... creation time =? 0.011 sec
DoMCFit = 1
ntptot = 507, nX = 15, DOF = 492
XCond = 5.45236e+16 (normalized)
ERROR: design is ill-conditioned
Many thanks again!
*From: *Emily Iannazzi eiann@uw.edu *Date: *Thursday, September 29, 2022 at 12:29 PM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: FSFAST first level covariates
Apologies, that was a bad example! Yes, like you said we want to have two variables (one binary & one continuous) that represent different aspects of the same stimulus.
We?re wondering if we can rescale the values to incorporate both responses ? do you know whether Freesurfer allows negative modulation values in the par files? We would essentially make negative values represent the valence ratings of stimuli with ?no? responses and positive values represent those with ?yes? responses.
Additionally, do you have any advice for debugging the ?design is ill-conditioned? error we received before? We still don?t know why our XCond was calculated to be so high at 5.45e16.
Here was our setup:
1 SelfRelevant (=1, included only for trials rated as self-relevant) 2 ValenceOffset (=1, included only for trials rated as self-relevant) 3 ValenceSlope (=valence rating) 4 SelfIrrelevant (=1, included only for trials rated as self-IRrelevant) 5 ValenceOffset (=1, included only for trials rated as self-IRrelevant) 6 ValenceSlope (=valence rating) 0 Other 0 Case 0 Fixation
Thank you very much for your continued help!
Message: 2 Date: Tue, 27 Sep 2022 09:51:58 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST first level covariates To: freesurfer@nmr.mgh.harvard.edu Message-ID: d4a6ad9a-6463-6e7e-1c19-e951622915e7@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
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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?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu *Sent:* Friday, September 23, 2022 6:58 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Freesurfer Digest, Vol 223, Issue 39 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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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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- 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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