Re: [Freesurfer] [FreeSurfer]: mkanalysis-sess
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
Re: [Freesurfer] [FreeSurfer]: mkanalysis-sess
OK, I think I've fixed it. I've checked the fix into dev which should be live tomorrow. When you make the analysis, add -per-session to the cmd line. doug Douglas N Greve wrote: 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
[Freesurfer] [FreeSurfer]: mkanalysis-sess
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 1fmcpr 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
