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?
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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
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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))
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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*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
To subscribe or unsubscribe via the World Wide Web, visit 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*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Hua, Jessica