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 >> >> >> > >
analysis.info
Description: Binary data
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