Hi Tapsya, I've verified the problem and am working on a fix. doug
tapsya@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 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
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