You can try running mri_glmfit to run a fixed effects analysis
fist, concatenate all the ces.nii.gz files (mri_concat */ces.nii.gz --o
all.ces.nii.gz)
second, do the same for the cesvar.nii.gz files
third, compute total dof (see the dof.dat files in each run folder)
4th, mri_glmfit --y all.ces.nii.gz --yffxvar all.cesvar.nii.gz --ffxdof
DOFtotal --osgm --glmdir glmdiroutput
If you want to do a higher level analysis, then you will have to do it
by hand (ie, not using isxconcat-sess)
On 6/25/2022 4:57 PM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi Doug,
thanks for the advice! I can compute the GLM and contrasts per run.
But selxavg3 does not compute contrasts across the runs with per-run.
Could you give me some advice on how to concatenate the per run
contrasts - can I just append them and add the df degrees of freedom?
Thanks, Caspar
Am Fr., 24. Juni 2022 um 16:36 Uhr schrieb Douglas N. Greve
<dgr...@mgh.harvard.edu>:
*Caution: External email*
Sorry, I thought I sent an email responding to this. Try running
it with -run-wise. This will analyze each run separately. I can't
remember whether it generates a final combined average (been a
long time since I used this option), but run it and see what it does.
On 6/23/2022 2:00 PM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi!
Any advice on this issue?
The error message is:
Starting contrasts
UrInv J=1 -------------
Out of memory. Type "help memory" for your options.
Error in fast_glm_pcc (line 39)
yhatd = Rd*(X*beta);
Error in fast_fratiow (line 136)
if(nargout == 6) pccbin =
fast_glm_pcc(beta(:,indbin),Xbin,C,rvarbin);
end
Error in fast_selxavg3b (line 1148)
fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));
>> ------------------------------------------
ERROR: fast_selxavg3() failed\n
Thank you,
Caspar
Am Mo., 20. Juni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik
<cschwie...@rockefeller.edu>:
Hi!
I am running large single subject GLMs with selxavg3-sess and
I run into a Matlab "out of memory" error. I was wondering
whether you had any advice on how to get around that.
I have 40-50 runs per subject, and the analyses are whole brain.
The GLM per subject runs through fine, but the error occurs
once selxavg3-sess starts computing contrasts.
The problem occurs with v5.3 and v7.2.
This is a Centos 7 system with 320 GB of memory, and 7 GB of
swap memory.
Any advice would be appreciated!
Caspar
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/12PGxx2RHC_XQgDCPYf9ta8K6tYfyxHwARW_ny-jud1x-Fz3jj_ynNiFiqwK2q5Cq8UWQOxsKhi59xLMujR6pxvZJRfbtdeWmSRceOnc89HPyk07ySALKuhmO72di-e4V2Gsm4BWEFzlAmP5GSggiwBmvF_ajTv0qki1rRDiXFyZCmz5989lH85WYUmK2QKvW57ntAirzVtBosOhDubj2Laa__nShkfgyg2bzGryIgNM-7cKf9hEkiTod4Empr2k5PRsswWkRzVTok4rG1DFCj5SPlxQ9IG8-Bb9_schkkArXUsENhHdM-HC_hyGNUnN0/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwMDaQ%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3DH95LjesGbfsNCtW_mKrgRUqGdfVYeVTJIFrxf_eIeKpXWikHEq-96bCVL-LHC4b_%26s%3Dc-fyD_s-Txw2LzO2td1pE1hjL17pGlRRag6lvmoEZfo%26e%3D>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=H95LjesGbfsNCtW_mKrgRUqGdfVYeVTJIFrxf_eIeKpXWikHEq-96bCVL-LHC4b_&s=c-fyD_s-Txw2LzO2td1pE1hjL17pGlRRag6lvmoEZfo&e=
<https://secure-web.cisco.com/1ffOlZrUhOL9Sifed362mg7dvEfAzelsOQoArlSMbt9LHU02h7pqGX3WjFZs94ebNWGwUXOCuC1cQoqf9Wz2muCRCop4DovnbTzpjyerk5MTy-4mf48clQ0DwMi8xhStHAYWWYywPOyfX6ygg9pPihODah4GygXV73alJDB4W3E2mHTnYz0KQT5AOeC45vuXma6ccltMhgH0ylGHcovdW-WWe5zQ5mLBzQ1sI0AGH0HTNS0_rTCcG0yyEMtPQj_ggYpUgtAD9oY67BKcoCWKUIJuWKF48EE4V_4i7tmaoRmM4Zo0RwSuzqfdLUvfVa-sF/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwIBAg%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3DH95LjesGbfsNCtW_mKrgRUqGdfVYeVTJIFrxf_eIeKpXWikHEq-96bCVL-LHC4b_%26s%3Dc-fyD_s-Txw2LzO2td1pE1hjL17pGlRRag6lvmoEZfo%26e%3D>
The information in this e-mail is intended only for the person to
whom it is addressed. If you believe this e-mail was sent to you
in error and the e-mail contains patient information, please
contact the Mass General Brigham Compliance HelpLine at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.massgeneralbrigham.org_complianceline&d=DwIBAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=H95LjesGbfsNCtW_mKrgRUqGdfVYeVTJIFrxf_eIeKpXWikHEq-96bCVL-LHC4b_&s=t2noSB1h9UB2B-gZBSg70fkX1jzjILfwci4Zm2hLbzk&e=
<https://secure-web.cisco.com/1hGpHfbnuNaJILQeLH4_N8jloWwOdWuJ2ij15XPFYypay59YdfLb24ZFwlDuUolU4PdROKcJG-Wz7ilzPDLXxwdI_xu0mU31l8L-uMPMtiRI4RUKFukqlbTHF6gUapoqncKUFHlofTvA069D3w_aq31VRg7genRFe-4cVa2TgMp97PkEIuQ75crVCJhZzhBUxXyE6gi1fWkcqoY8XGa2TKufXBZysHsPV-Ffv1ASEr7DwAVW2W2lGgosknKS0PLUler606Y5BToEtC2KMcPOekJLas1PvWBuz6XGzX_OoazsGZiR9naA3fQRgbtPcMbNF/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.massgeneralbrigham.org_complianceline%26d%3DDwIBAg%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3DH95LjesGbfsNCtW_mKrgRUqGdfVYeVTJIFrxf_eIeKpXWikHEq-96bCVL-LHC4b_%26s%3Dt2noSB1h9UB2B-gZBSg70fkX1jzjILfwci4Zm2hLbzk%26e%3D>
<*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.massgeneralbrigham.org_complianceline&d=DwIBAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=H95LjesGbfsNCtW_mKrgRUqGdfVYeVTJIFrxf_eIeKpXWikHEq-96bCVL-LHC4b_&s=t2noSB1h9UB2B-gZBSg70fkX1jzjILfwci4Zm2hLbzk&e=
<https://secure-web.cisco.com/1hGpHfbnuNaJILQeLH4_N8jloWwOdWuJ2ij15XPFYypay59YdfLb24ZFwlDuUolU4PdROKcJG-Wz7ilzPDLXxwdI_xu0mU31l8L-uMPMtiRI4RUKFukqlbTHF6gUapoqncKUFHlofTvA069D3w_aq31VRg7genRFe-4cVa2TgMp97PkEIuQ75crVCJhZzhBUxXyE6gi1fWkcqoY8XGa2TKufXBZysHsPV-Ffv1ASEr7DwAVW2W2lGgosknKS0PLUler606Y5BToEtC2KMcPOekJLas1PvWBuz6XGzX_OoazsGZiR9naA3fQRgbtPcMbNF/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.massgeneralbrigham.org_complianceline%26d%3DDwIBAg%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3DH95LjesGbfsNCtW_mKrgRUqGdfVYeVTJIFrxf_eIeKpXWikHEq-96bCVL-LHC4b_%26s%3Dt2noSB1h9UB2B-gZBSg70fkX1jzjILfwci4Zm2hLbzk%26e%3D>
> .
Please note that this e-mail is not secure (encrypted). If you do
not wish to continue communication over unencrypted e-mail, please
notify the sender of this message immediately. Continuing to send
or respond to e-mail after receiving this message means you
understand and accept this risk and wish to continue to
communicate over unencrypted e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
