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 raij@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 raij@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 > raij@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 >>> raij@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: tapsya@nmr.mgh.harvard.edu >>>>>>>>> Date: Thu, November 10, 2011 1:41 pm >>>>>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>>>>> Cc: raij@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 >>>>>>>> greve@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 >>>>>> greve@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 >>>> greve@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 > greve@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 > > >