Hi Tapsya, I've verified the problem and am working on a fix. doug tap...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > It seems that there are still problems related to using -per-session. > Preproc-sess now finishes apparently fine (correct file names are > generated, i.e., fmc.*) but the analyses again defaults to using -per-run > at mkanalysis-sess. > > Specifically, mkanalysis-sess creates an analysis.info file (attached) > where the parameters mcstem and nuisreg still point to -per-run (mcstem > fmcpr and nuisreg mcprextreg 3). Consequently the rest of the analysis > fails. I have attached the analysis.info file in the email > > Thank you for your help again! > > -Tapsya > > Details: > > Machine: adapt > nmr-dev-env (vs 5.1) > > preproc-sess -s avml07 -surface faverage lhrh -mni305 -per-session -so > siemens -fsd bold -fwhm 5 > > set ana_BASIC_lh = ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat_lh > > mkanalysis-sess -analysis $ana_BASIC_lh -surface fsaverage lh -fwhm 5 -TR > 1.15 -paradigm AVML_BRERT_ISIXTR_001_18cat.par -event-related -nconditions > 18 -fir 2.3 18.4 -mcextreg -polyfit 5 -runlistfile rlf_ISIXTR_BERT.txt > -stc siemens -force -fsd bold -tpef tpef.txt > > --------------------------------------------------------------------------- > >>> I just ran this co >>> >> mmand and it completed successfully >> >>> preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm >>> >> 5 >> >>> Is this what you ran? I'm also running it to generate the surfaces now, >>> >> but it does not seem to be complaining. >> >>> doug >>> >>> Douglas N Greve wrote: >>> >>>> I'm currently running >>>> preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm >>>> 5 >>>> and it seems to be going ok, I won't know until tomorrow whether this >>>> >> is really working or not >> >>>> doug >>>> r...@nmr.mgh.harvard.edu wrote: >>>> >>>>> Still no luck. mc-sess is stubbornly using -per-run despite that the >>>>> >> preproc-sess requests per-sess. This may be where things get on the >> wrong >> >>>>> track. -Tommi >>>>> >>>>>> Sorry, what I meant was for you to change the name and then run the >>>>>> >> stream as usual. >> >>>>>> doug >>>>>> r...@nmr.mgh.harvard.edu wrote: >>>>>> >>>>>>> Done. I also made a backup of the registration. The entire >>>>>>> directory at >>>>>>> /space/adapt/1/users/raij/AVISI_FSFAST5.1/ >>>>>>> is a copy of the actual data residing elsewhere (apart from the >>>>>>> >> Freesurfer >> >>>>>>> recons) so feel free to change anything you need. -Tommi >>>>>>> >>>>>>>> I think I've found the problem, but it's going to be a bit >>>>>>>> difficult to >>>>>>>> fix. Can you change the name of your registration file to >>>>>>>> register.dof6.dat and remove write permissions so that it does not >>>>>>>> get >>>>>>>> overwritten? >>>>>>>> doug >>>>>>>> r...@nmr.mgh.harvard.edu wrote: >>>>>>>> >>>>>>>>> Yes we have. It exits with the same error as below. -Tommi >>>>>>>>> >>>>>>>>>> Have you tried specifying your regfile with -regfile? >>>>>>>>>> doug >>>>>>>>>> r...@nmr.mgh.harvard.edu wrote: >>>>>>>>>> >>>>>>>>>>> Hi Doug, >>>>>>>>>>> Thank you for your help today! I tried running preproc-sess >>>>>>>>>>> >> again >> >>>>>>>>>>> but >>>>>>>>>>> it >>>>>>>>>>> again exits with per-session related errors. However, the errors >>>>>>>>>>> >> are >> >>>>>>>>>>> different than before so I think the changes you made were a >>>>>>>>>>> >> step to >> >>>>>>>>>>> the >>>>>>>>>>> right direction. This time >>>>>>>>>>> preproc-sess \ >>>>>>>>>>> -sf subjectname \ >>>>>>>>>>> -df sessdir \ >>>>>>>>>>> -mni305 \ >>>>>>>>>>> -per-session \ >>>>>>>>>>> -sliceorder siemens \ >>>>>>>>>>> -fsd bold \ >>>>>>>>>>> -fwhm 5 \ >>>>>>>>>>> -surface $SUBJECT lhrh \ >>>>>>>>>>> -noreg \ # I want to use my manually adjusted >>>>>>>>>>> bold/register.dof6.dat >>>>>>>>>>> file >>>>>>>>>>> (1) mc-sess output is still saved with the per-run stem (pr) >>>>>>>>>>> >> despite >> >>>>>>>>>>> that >>>>>>>>>>> we defined -per-session. >>>>>>>>>>> (2) stc-sess output is still saved with the per-run stem (pr) >>>>>>>>>>> >> despite >> >>>>>>>>>>> that >>>>>>>>>>> we defined -per-session. >>>>>>>>>>> (3) rawfunc2surf-sess defaults to -per-run and then expects to >>>>>>>>>>> find >>>>>>>>>>> instem >>>>>>>>>>> fmcpr.siemens >>>>>>>>>>> (4) ERROR: cannot find >>>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/register.dof6.dat. >>>>>>>>>>> >> Apparently the script looks for the registration file inside the >> run >> >>>>>>>>>>> directory (as it should for per-run analysis) instead of the fsd >>>>>>>>>>> >> <bold> >> >>>>>>>>>>> where it should reside for a -per-session analysis. This forces >>>>>>>>>>> the >>>>>>>>>>> script >>>>>>>>>>> to exit. >>>>>>>>>>> I changed permissions so that you can write in the study >>>>>>>>>>> directory. >>>>>>>>>>> For details please see below. >>>>>>>>>>> Thanks! >>>>>>>>>>> -Tommi & Tapsya >>>>>>>>>>> on machine avml >>>>>>>>>>> nmr-dev-env (vs 5.1) >>>>>>>>>>> cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 >>>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs >>>>>>>>>>> >> setenv SUBJECT avml07 >> >>>>>>>>>>> logs in /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07/log >>>>>>>>>>> >> preproc-sess log file >> >>>>>>>>>>> $Id: preproc-sess,v 1.48 2011/11/14 17:41:35 greve Exp $ raij >>>>>>>>>>> setenv FREESURFER_HOME /usr/local/freesurfer/dev >>>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs >>>>>>>>>>> >> Linux avml 2.6.32-131.12.1.el6.x86_64 #1 SMP Mon Sep 26 >> >>>>>>>>>>> 10:13:43 BST >>>>>>>>>>> 2011 >>>>>>>>>>> x86_64 x86_64 x86_64 GNU/Linux >>>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07 >>>>>>>>>>> >> /usr/local/freesurfer/dev/fsfast/bin/preproc-sess >> >>>>>>>>>>> -sf subjectname -df sessdir -mni305 -per-session -sliceorder >>>>>>>>>>> >> siemens >> >>>>>>>>>>> -fsd >>>>>>>>>>> bold -fwhm 5 -surface avml07 lhrh -noreg >>>>>>>>>>> Mon Nov 14 20:07:57 EST 2011 >>>>>>>>>>> instem f >>>>>>>>>>> mc 1 f fmcpr >>>>>>>>>>> stc 1 fmcpr fmcpr.siemens >>>>>>>>>>> sm 0 >>>>>>>>>>> mask 1 brain >>>>>>>>>>> ---------------------------- Original Message >>>>>>>>>>> ---------------------------- >>>>>>>>>>> Subject: [FreeSurfer]: preproc-sess error >>>>>>>>>>> From: tap...@nmr.mgh.harvard.edu >>>>>>>>>>> Date: Thu, November 10, 2011 1:41 pm >>>>>>>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> Cc: r...@nmr.mgh.harvard.edu >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> >> Dear Doug, >> >>>>>>>>>>> We have encountered errors running preproc-sess (FSFAST v5.1) >>>>>>>>>>> >> command >> >>>>>>>>>>> with >>>>>>>>>>> the flag "-per-session". The command line is >>>>>>>>>>> on machine adapt (same result on machine avml) >>>>>>>>>>> cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 >>>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs >>>>>>>>>>> >> setenv SUBJECT avml07 >> >>>>>>>>>>> nmr-std-env (=FS 5.1) >>>>>>>>>>> preproc-sess \ >>>>>>>>>>> -sf subjectname >>>>>>>>>>> -df sessdir \ >>>>>>>>>>> -mni305 \ >>>>>>>>>>> -per-session \ >>>>>>>>>>> -sliceorder siemens \ >>>>>>>>>>> -fsd bold \ >>>>>>>>>>> -fwhm 5 \ >>>>>>>>>>> The error message: >>>>>>>>>>> ... >>>>>>>>>>> stc-sess Done >>>>>>>>>>> avml07 To MNI305 ---------------- >>>>>>>>>>> rawfunc2tal-sess -fwhm 5 -s avml07 -d >>>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1 -fsd bold >>>>>>>>>>> >> -stc >> >>>>>>>>>>> siemens -update -subcort-mask >>>>>>>>>>> ---------------- >>>>>>>>>>> 1/1 avml07 >>>>>>>>>>> 1/1 avml07 002 ---------------- >>>>>>>>>>> "ERROR: could not determine file for >>>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/fmcpr.siemens" >>>>>>>>>>> >> Hence it looks like rawfunc2tal-sess is searching for -per-run >> files (stem fmcpr*) rather than -per-session files (stem fmc*). >> We tried to take control over the stems and added the following >> lines: >> >>>>>>>>>>> -mcin f \ >>>>>>>>>>> -mcout fmc \ >>>>>>>>>>> -stcin fmc \ >>>>>>>>>>> -stcout fmcstc \ >>>>>>>>>>> -smin fmcstc \ >>>>>>>>>>> -smout fmcstcsm5 \ >>>>>>>>>>> OR (modern naming conventions): >>>>>>>>>>> -mcin f >>>>>>>>>>> -mcout fmc >>>>>>>>>>> -stcin fmc >>>>>>>>>>> -stcout fmc.siemens \ >>>>>>>>>>> -smin fmc.siemens \ >>>>>>>>>>> -smout fmc.siemens.sm5.mni305.2mm \ >>>>>>>>>>> However, these resulted in the same error. >>>>>>>>>>> We also tried this on a more recent data set and received the >>>>>>>>>>> same >>>>>>>>>>> error. >>>>>>>>>>> In summary, it appears that rawfunc2tal-sess (and in fact also >>>>>>>>>>> >> rawfunc2surf-sess) expect the stem fmcpr even when we use >> per-session >> >>>>>>>>>>> (where they should expect the stem fmc). >>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>> Best regards, >>>>>>>>>>> Tapsya >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> gr...@nmr.mgh.harvard.edu >>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> gr...@nmr.mgh.harvard.edu >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> gr...@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> >> > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
