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 > > >
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
tapsya＠nmr.mgh.harvard.edu