Re: [Freesurfer] Group Analysis Covariates - Freesurfer

24 May 2020

      External Email - Use Caution
Thanks for your help with the code!
---
Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
________________________________
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: Saturday, May 23, 2020 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 195, Issue 56
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Today's Topics:
1. missing files in he v6 fsaverage on the Martinos  Center
      network (Douglas N. Greve)
   2. Re: Group Analysis Covariates (Douglas N. Greve)
   3. Re: Freesurfer 7.1 hires error (Douglas N. Greve)
   4. Re: LGI problem (Angela Favaro)
   5. Are my slice-time corrected files being used in
      selxavg3-sess? (Mcnorgan, Christopher)
   6. freeview is RAM greedy in version 7.1.0 (Anton?n ?koch)
   7. Re: freeview is RAM greedy in version 7.1.0 (Ruopeng Wang)
   8. Re: freeview is RAM greedy in version 7.1.0 (fsbuild)
   9. Re: freeview is RAM greedy in version 7.1.0 (Anton?n ?koch)
  10. Command cannot recognise session from sessid file
      (Marco Ninghetto)
  11. Longitudinal processing with freesurfer 7.1.0 (Angela Favaro)
  12. Re: freeview is RAM greedy in version 7.1.0 (Ruopeng Wang)
----------------------------------------------------------------------
Message: 1
Date: Fri, 22 May 2020 12:02:56 -0400
From: "Douglas N. Greve" dgreve@mgh.harvard.edu
Subject: [Freesurfer] missing files in he v6 fsaverage on the Martinos
        Center network
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID: fb258210-bab9-dfe2-2039-4ead9e6a64dc@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"; format=flowed
Sorry, I accidentally deleted some files from the v6 fsaverage located
on the Martinos Center network. They have been restored, but it might
have caused your recon-all process to fail if you had one running last
night.
Have a good weekend
doug
------------------------------
Message: 2
Date: Fri, 22 May 2020 12:14:06 -0400
From: "Douglas N. Greve" dgreve@mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis Covariates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 23e96fb1-f2b5-8e23-112a-2d0cb9ec3d88@mgh.harvard.edu
Content-Type: text/plain; charset="windows-1252"
Sorry, I left out a key ingredient. Use pmf below
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[1 2 3])*beta([1 2 3],:);
e = y - yhat;
pmf = yhat+e;
On 5/22/2020 11:55 AM, Hua, Jessica wrote:
...
????????External Email - Use Caution
I just tried the revised code, and it gave me the adjusted values for
each cluster by group. Is there a way to get covariate adjusted?
values for each participant?

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate?Clinical Psychology
University of Missouri

*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, May 22, 2020 10:09 AM
*To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
*Subject:* Freesurfer Digest, Vol 195, Issue 54
Send Freesurfer mailing list submissions to
??????? freesurfer@nmr.mgh.harvard.edu
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
??????? freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at
??????? freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
?? 1. Re: Freesurfer 7.1 hires error (Douglas N. Greve)
?? 2. Re: question on partial volume correction (Barletta, Valeria)
?? 3. Re: question on partial volume correction (Douglas N. Greve)
?? 4. Re: Group Analysis Covariates (Hua, Jessica)
?? 5. Re: Group Analysis Covariates (Douglas N. Greve)
?? 6. Re: mris_register intermediate results display (Chris Adamson)
?? 7. Open Postdoctoral Scholar Position (Neva M Corrigan)
?? 8. Re: Infant Freesurfer: infant_recon_all error (Hoopes, Andrew)
?? 9. Re: circular/cyclic color map for polar data in freeview
????? {Disarmed} (Caspar M. Schwiedrzik)
? 10. OHBM Brainhack registration is open! (Remi Gau)
? 11. FW: Motion correction files contain 0 0 0 1
????? (Camerino, I.L. (Ileana))

Message: 1
Date: Thu, 21 May 2020 12:11:55 -0400
From: "Douglas N. Greve" dgreve@mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer 7.1 hires error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 9eaf8c24-3b80-eb34-7cd0-09080c152b03@mgh.harvard.edu
Content-Type: text/plain; charset="windows-1252"
I don't know what is wrong. Can you upload the hires run? Instructions
below
?From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log? into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.
On 5/21/2020 9:35 AM, Jones, Richard wrote:
...
????????External Email - Use Caution
I ran freesurfer 7.1 with the following options:-
-i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR
./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T ?mprage
?FLAIRpial ??hires ?parallel ?all
The job failed, the logfile recon-all_hires.log is attached. I then
reran the job with the same datasets but exchanged ?hires with
?conf2hires and used the subject ID TEST_050620c and the job completed
successfully (the logfile for this job, recon-all_conf2hires.log, is
also attached). Any idea what the problem is when using the ?hires
option?
...
Thanks
*Richard*

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