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Re: [Freesurfer] Tracula Question, step 2
by Anastasia Yendiki 10 Nov '11

10 Nov '11

That should be the latest version, so I'm not sure why the file was not saved. I'll have ro refer you to the FSL list for further support with running bedpost. On Thu, 10 Nov 2011, Shannon Buckley wrote: > Hi Anastasia, > > I checked the brain mask and it looks good. We are using > FSLv4.1.4. I take it that we are due for an upgrade? Is there a > minimum version number that we should be using in order for > bedpostx to run smoothly? > > Thanks again, > ~SB > > -----Original Message----- > From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] > Sent: Wednesday, November 09, 2011 4:57 PM > To: Shannon.Buckley(a)radiology.ucsf.edu > Cc: freesurfer(a)nmr.mgh.harvard.edu; Mensch, Henry > Subject: RE: [Freesurfer] Tracula Question, step 2 > > > Hi Shannon - Which version of FSL do you have? Older versions didn't use > to save the mean_dsamples.nii.gz, but that was a while ago. > > How quickly it runs depends on the size of the brain mask, so I'd check > that that's ok too. > > a.y > > On Wed, 9 Nov 2011, Shannon Buckley wrote: > >> Hi Anastasia, >> >> It turns out that I was NOT able to run the original bedpostx on our cluster, so thank you for pointing me in the right direction! In case other users experience a similar problem, this is what we did to get the ball rolling on our grid: >> >> We found the "fsl_sub_seychelles" and "fsl_sub" scripts where the default q-names were identified. We modified the files (changing long and short.q to reflect the naming convention used here) and ran the original bedpostx. The preproc and datacheck functions worked perfectly. The bedpostx function SEEMED to have launched fine, but we hit another snag... >> >> The program finished far too quickly for it to have worked properly (an hour, tops), and when I try to run the next "-prep" step I get the following error, which confirms that suspicion: >> >> _+_+_+_+_+_+_+_+_+_+_ >> "Loading BEDPOST parameter samples from /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX >> niiRead(): error opening file /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz >> ERROR: Could not read /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz >> Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux >> >> trac-paths exited with ERRORS at Wed Nov 9 16:18:53 PST 2011 >> >> Word too long." >> +_+_+_+_+_+_+_+_+_+_+_ >> >> >> I have to confess I'm not familiar with the "word too long" error. In any case, bedpostx seems to fail to produce the requisite files for -prep (mean_dsamples.nii.gz). Since I'm not sure what the inputs would be for creating such a file, I'm including my "ls" output for our dmri.bedpostX path. >> >> _+_+_+_+_+_+_+_+_+_+_+ >> >> "[vhasfcbuckls@paris dmri.bedpostX]$ ls >> bvals dyads2.nii.gz mean_ph2samples.nii.gz merged_ph2samples.nii.gz >> bvecs error.log mean_th1samples.nii.gz merged_th1samples.nii.gz >> cancel logs mean_th2samples.nii.gz merged_th2samples.nii.gz >> commands.txt mean_f1samples.nii.gz merged_f1samples.nii.gz monitor >> dmri.bedpostX.nii.gz mean_f2samples.nii.gz merged_f2samples.nii.gz nodif_brain_mask.nii.gz >> dyads1.nii.gz mean_ph1samples.nii.gz merged_ph1samples.nii.gz xfms >> [vhasfcbuckls@paris dmri.bedpostX]$" >> +_+_+_+_+_+_+_+_+_+_ >> >> >> Do you have any advice for getting passed this step? We are fairly in the dark with this function over here, so any help / hints you can provide would be wonderful. Please let me know if you need more information. >> >> Thanks again for your help and patience, >> >> ~Shannon B. >> -----Original Message----- >> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >> Sent: Thursday, November 03, 2011 7:39 AM >> To: Shannon.Buckley(a)radiology.ucsf.edu >> Cc: freesurfer(a)nmr.mgh.harvard.edu; Mensch, Henry >> Subject: Re: [Freesurfer] Tracula Question, step 2 >> >> >> Hi Shannon - Does the original bedpostx run fine on your cluster? You'd >> probably have to edit that to get it to work, it's not made to work on >> every possible cluster. Bedpostx_seychelles is the modified version that >> tracula calls that I've modified from the original FSL version so that it >> runs on our clusters. >> >> In either case, trac-all is meant to always be run from the command line, >> whether you're on a personal computer (where is runs jobs serially) or a >> cluster (where it submits them as jobs using qsub). But probably some >> editing will be needed as I said. >> >> Hope this helps, >> a.y >> >> On Wed, 2 Nov 2011, Shannon Buckley wrote: >> >>> >>> Hi Anastasia, >>> >>> >>> >>> I am trying to run Tracula for the first time in our lab and >>> I’m getting errors during step 2 that seem to involve how the program wants >>> to be launched via grid. I’ve attached the configuration file I’m using and >>> the error message is below... >>> >>> >>> ____________________________________________________________________________ >>> >>> >>> $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh >>> >>> Using Freesurfer version 5.1. >>> >>> >>> >>> Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/ >>> >>> Sessions Directory is /home/vhasfcbuckls/sessions >>> >>> >>> >>> INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects >>> >>> INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula >>> >>> Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1 >>> >>> ln -sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_ >>> mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n >>> ii.gz >>> >>> ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz >>> /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz >>> >>> WARN: Running FSL's bedbost locally - this might take a while >>> >>> WARN: It is recommended to run this step on a cluster >>> >>> bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri >>> >>> subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri >>> >>> Making bedpostx directory structure >>> >>> Queuing preprocessing stages >>> >>> Unable to run job: Job was rejected because job requests unknown queue >>> "short.q". >>> >>> Exiting. >>> >>> Queuing parallel processing stage >>> >>> Unable to run job: Job was rejected because job requests unknown queue >>> "long.q". >>> >>> Exiting. >>> >>> Queuing post processing stage >>> >>> Unable to run job: denied: "60" is not a valid object name (cannot start >>> with a digit) >>> >>> Job was rejected because job requests unknown queue "long.q". >>> >>> Exiting. >>> >>> >>> ____________________________________________________________________________ >>> >>> >>> >>> >>> >>> >>> Although we DO have a grid, I am trying to test the program for feasibility >>> purposes, just on my own system’s terminal, since we aren’t sure how results >>> will look with our specific data set (3.0 Tesla Siemens, 64 directional DWI >>> @ b=1000, with 1 b0 image). We are very interested in performing >>> tractography in T1-space… I am open to running this over the grid, if that’s >>> really the best way to do it, but the problem is that I don’t see anywhere >>> to specify the name of the queue that should be used for launching the >>> program. >>> >>> >>> >>> Can you please tell me how to launch this without using the so-called long.q >>> and short.q? We typically launch jobs to our grid using our “bash.linux.q”, >>> but I haven’t been able to locate a place in the configuration file, or any >>> switches to use in the cmd line, to specify that this queue should be used. >>> I tried specifically launching Tracula’s step 2 onto our bash.linux.q via >>> the cmd line using “qsub”, but received the same old error I had been >>> getting. I checked the data independently using “bedpostx_preproc.sh”, and >>> it appears that all the required data are set up properly. As far as I can >>> tell, the only issue we have is this inability to use the long.q and >>> short.q… >>> >>> >>> >>> What do you think? >>> >>> >>> >>> I’ve cc’d our IT specialist, Henry Mensch, who oversees our grid system in >>> case you need someone to chime-in with any specific information about how >>> our Linux systems are set-up. >>> >>> >>> >>> Thanks very much for your time, >>> >>> >>> >>> Shannon T. Buckley >>> SRA III - Supervisor >>> CIND, UCSF >>> 4150 Clement St. (114M) >>> San Francisco, CA 94121 >>> Phone: (415) 221-4810 x4251 >>> Fax: (415) 386-3954 >>> >>> >>> >>> >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. >> >> >> >> > > > >

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Re: [Freesurfer] Tracula Question, step 2
by Anastasia Yendiki 10 Nov '11

10 Nov '11

Hi Shannon - Which version of FSL do you have? Older versions didn't use to save the mean_dsamples.nii.gz, but that was a while ago. How quickly it runs depends on the size of the brain mask, so I'd check that that's ok too. a.y On Wed, 9 Nov 2011, Shannon Buckley wrote: > Hi Anastasia, > > It turns out that I was NOT able to run the original bedpostx on our cluster, so thank you for pointing me in the right direction! In case other users experience a similar problem, this is what we did to get the ball rolling on our grid: > > We found the "fsl_sub_seychelles" and "fsl_sub" scripts where the default q-names were identified. We modified the files (changing long and short.q to reflect the naming convention used here) and ran the original bedpostx. The preproc and datacheck functions worked perfectly. The bedpostx function SEEMED to have launched fine, but we hit another snag... > > The program finished far too quickly for it to have worked properly (an hour, tops), and when I try to run the next "-prep" step I get the following error, which confirms that suspicion: > > _+_+_+_+_+_+_+_+_+_+_ > "Loading BEDPOST parameter samples from /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX > niiRead(): error opening file /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz > ERROR: Could not read /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz > Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux > > trac-paths exited with ERRORS at Wed Nov 9 16:18:53 PST 2011 > > Word too long." > +_+_+_+_+_+_+_+_+_+_+_ > > > I have to confess I'm not familiar with the "word too long" error. In any case, bedpostx seems to fail to produce the requisite files for -prep (mean_dsamples.nii.gz). Since I'm not sure what the inputs would be for creating such a file, I'm including my "ls" output for our dmri.bedpostX path. > > _+_+_+_+_+_+_+_+_+_+_+ > > "[vhasfcbuckls@paris dmri.bedpostX]$ ls > bvals dyads2.nii.gz mean_ph2samples.nii.gz merged_ph2samples.nii.gz > bvecs error.log mean_th1samples.nii.gz merged_th1samples.nii.gz > cancel logs mean_th2samples.nii.gz merged_th2samples.nii.gz > commands.txt mean_f1samples.nii.gz merged_f1samples.nii.gz monitor > dmri.bedpostX.nii.gz mean_f2samples.nii.gz merged_f2samples.nii.gz nodif_brain_mask.nii.gz > dyads1.nii.gz mean_ph1samples.nii.gz merged_ph1samples.nii.gz xfms > [vhasfcbuckls@paris dmri.bedpostX]$" > +_+_+_+_+_+_+_+_+_+_ > > > Do you have any advice for getting passed this step? We are fairly in the dark with this function over here, so any help / hints you can provide would be wonderful. Please let me know if you need more information. > > Thanks again for your help and patience, > > ~Shannon B. > -----Original Message----- > From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] > Sent: Thursday, November 03, 2011 7:39 AM > To: Shannon.Buckley(a)radiology.ucsf.edu > Cc: freesurfer(a)nmr.mgh.harvard.edu; Mensch, Henry > Subject: Re: [Freesurfer] Tracula Question, step 2 > > > Hi Shannon - Does the original bedpostx run fine on your cluster? You'd > probably have to edit that to get it to work, it's not made to work on > every possible cluster. Bedpostx_seychelles is the modified version that > tracula calls that I've modified from the original FSL version so that it > runs on our clusters. > > In either case, trac-all is meant to always be run from the command line, > whether you're on a personal computer (where is runs jobs serially) or a > cluster (where it submits them as jobs using qsub). But probably some > editing will be needed as I said. > > Hope this helps, > a.y > > On Wed, 2 Nov 2011, Shannon Buckley wrote: > >> >> Hi Anastasia, >> >> >> >> I am trying to run Tracula for the first time in our lab and >> I’m getting errors during step 2 that seem to involve how the program wants >> to be launched via grid. I’ve attached the configuration file I’m using and >> the error message is below... >> >> >> ____________________________________________________________________________ >> >> >> $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh >> >> Using Freesurfer version 5.1. >> >> >> >> Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/ >> >> Sessions Directory is /home/vhasfcbuckls/sessions >> >> >> >> INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects >> >> INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula >> >> Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1 >> >> ln -sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_ >> mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n >> ii.gz >> >> ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz >> /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz >> >> WARN: Running FSL's bedbost locally - this might take a while >> >> WARN: It is recommended to run this step on a cluster >> >> bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri >> >> subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri >> >> Making bedpostx directory structure >> >> Queuing preprocessing stages >> >> Unable to run job: Job was rejected because job requests unknown queue >> "short.q". >> >> Exiting. >> >> Queuing parallel processing stage >> >> Unable to run job: Job was rejected because job requests unknown queue >> "long.q". >> >> Exiting. >> >> Queuing post processing stage >> >> Unable to run job: denied: "60" is not a valid object name (cannot start >> with a digit) >> >> Job was rejected because job requests unknown queue "long.q". >> >> Exiting. >> >> >> ____________________________________________________________________________ >> >> >> >> >> >> >> Although we DO have a grid, I am trying to test the program for feasibility >> purposes, just on my own system’s terminal, since we aren’t sure how results >> will look with our specific data set (3.0 Tesla Siemens, 64 directional DWI >> @ b=1000, with 1 b0 image). We are very interested in performing >> tractography in T1-space… I am open to running this over the grid, if that’s >> really the best way to do it, but the problem is that I don’t see anywhere >> to specify the name of the queue that should be used for launching the >> program. >> >> >> >> Can you please tell me how to launch this without using the so-called long.q >> and short.q? We typically launch jobs to our grid using our “bash.linux.q”, >> but I haven’t been able to locate a place in the configuration file, or any >> switches to use in the cmd line, to specify that this queue should be used. >> I tried specifically launching Tracula’s step 2 onto our bash.linux.q via >> the cmd line using “qsub”, but received the same old error I had been >> getting. I checked the data independently using “bedpostx_preproc.sh”, and >> it appears that all the required data are set up properly. As far as I can >> tell, the only issue we have is this inability to use the long.q and >> short.q… >> >> >> >> What do you think? >> >> >> >> I’ve cc’d our IT specialist, Henry Mensch, who oversees our grid system in >> case you need someone to chime-in with any specific information about how >> our Linux systems are set-up. >> >> >> >> Thanks very much for your time, >> >> >> >> Shannon T. Buckley >> SRA III - Supervisor >> CIND, UCSF >> 4150 Clement St. (114M) >> San Francisco, CA 94121 >> Phone: (415) 221-4810 x4251 >> Fax: (415) 386-3954 >> >> >> >> >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >

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[FreeSurfer]: preproc-sess error
by tapsya＠nmr.mgh.harvard.edu 10 Nov '11

10 Nov '11

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

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Re: [Freesurfer] error mri_glmfit
by Douglas N Greve 10 Nov '11

10 Nov '11

What is your command line? It should be something like "--subject fsaverage lh", assuming that you are using fsaverage as your standard space and the left hemisphere. doug bbruijn(a)bidmc.harvard.edu wrote: > Ok, good, thanks! > > And for my error-message, I was wondering whether you tell me where I need to include my subject and hemi information. I've already tried the words 'subject1pair' and the actual subject code+'pair' but I keep getting the same message. > > > ________________________________________ > From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Thursday, November 10, 2011 11:09 AM > To: Bruijn,Bente (BIDMC - Neurology); freesurfer > Subject: Re: [Freesurfer] error mri_glmfit > > Yes, the --osgm is the right thing to use there. If you run mri_glmfit > with --help, it will tell you how to use the --surf option. There are > also examples on the wiki. > doug > > bbruijn(a)bidmc.harvard.edu wrote: > >> Hi Doug, >> >> Thanks for the fast response! Sorry, I should have included the command line, it's: >> >> mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --osgm >> >> >> So, my first question would be; is it correct to use the flag --osgm because I just want to to a paired T-test without regressors? >> And second; I need to include these (subject names and hemi) in my fsgd file or in my command? >> >> Thanks again, >> >> Bente >> >> ________________________________________ >> From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Sent: Thursday, November 10, 2011 10:39 AM >> To: Bruijn,Bente (BIDMC - Neurology) >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] error mri_glmfit >> >> Hi Bente, it's hard to say without seeing the command line (always a >> good thing to include when posting a question), but it looks like you >> need to include '--surface subject hemi' where subject is the name of >> the subject whose surface the analysis is being performed on and hemi is >> the name of the hemisphere (lh or rh). This information is needed to >> compute the spatial smoothness. >> >> doug >> >> >> >> >> >> >> bbruijn(a)bidmc.harvard.edu wrote: >> >> >>> Dear FS experts, >>> >>> I came across an error-message that I can't figure out, hopefully you can help me. I want to do a paired T-test (first without regressors) and I am following the steps on the Freesurfer website. Preprocessing and smoothing all went OK and I've just created the second fsgd file; >>> >>> GroupDescriptorFile 1 >>> Class Main >>> Input subject1pair Main >>> Input subject2pair Main >>> Input subject3pair Main >>> Input subject4pair Main >>> Input subject5pair Main >>> Input subject6pair Main >>> Input subject7pair Main >>> Input subject8pair Main >>> >>> Because I don't want to include any regressors I put in the flag --osgm (is this right?) and didn't include the contrasts. >>> >>> This is the error message I receive after putting in the mri_glmfit command: >>> >>> ERROR: you must use '--surface subject hemi' with surface data >>> >>> Did I do everything correct or did I forget a step? >>> >>> Thank you so much in advance, >>> >>> Bente >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)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 >> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. >> >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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(a)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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Re: [Freesurfer] error mri_glmfit
by Douglas N Greve 10 Nov '11

10 Nov '11

Yes, the --osgm is the right thing to use there. If you run mri_glmfit with --help, it will tell you how to use the --surf option. There are also examples on the wiki. doug bbruijn(a)bidmc.harvard.edu wrote: > Hi Doug, > > Thanks for the fast response! Sorry, I should have included the command line, it's: > > mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --osgm > > > So, my first question would be; is it correct to use the flag --osgm because I just want to to a paired T-test without regressors? > And second; I need to include these (subject names and hemi) in my fsgd file or in my command? > > Thanks again, > > Bente > > ________________________________________ > From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Thursday, November 10, 2011 10:39 AM > To: Bruijn,Bente (BIDMC - Neurology) > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] error mri_glmfit > > Hi Bente, it's hard to say without seeing the command line (always a > good thing to include when posting a question), but it looks like you > need to include '--surface subject hemi' where subject is the name of > the subject whose surface the analysis is being performed on and hemi is > the name of the hemisphere (lh or rh). This information is needed to > compute the spatial smoothness. > > doug > > > > > > > bbruijn(a)bidmc.harvard.edu wrote: > >> Dear FS experts, >> >> I came across an error-message that I can't figure out, hopefully you can help me. I want to do a paired T-test (first without regressors) and I am following the steps on the Freesurfer website. Preprocessing and smoothing all went OK and I've just created the second fsgd file; >> >> GroupDescriptorFile 1 >> Class Main >> Input subject1pair Main >> Input subject2pair Main >> Input subject3pair Main >> Input subject4pair Main >> Input subject5pair Main >> Input subject6pair Main >> Input subject7pair Main >> Input subject8pair Main >> >> Because I don't want to include any regressors I put in the flag --osgm (is this right?) and didn't include the contrasts. >> >> This is the error message I receive after putting in the mri_glmfit command: >> >> ERROR: you must use '--surface subject hemi' with surface data >> >> Did I do everything correct or did I forget a step? >> >> Thank you so much in advance, >> >> Bente >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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 > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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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error mri_glmfit
by bbruijn＠bidmc.harvard.edu 10 Nov '11

10 Nov '11

Dear FS experts, I came across an error-message that I can't figure out, hopefully you can help me. I want to do a paired T-test (first without regressors) and I am following the steps on the Freesurfer website. Preprocessing and smoothing all went OK and I've just created the second fsgd file; GroupDescriptorFile 1 Class Main Input subject1pair Main Input subject2pair Main Input subject3pair Main Input subject4pair Main Input subject5pair Main Input subject6pair Main Input subject7pair Main Input subject8pair Main Because I don't want to include any regressors I put in the flag --osgm (is this right?) and didn't include the contrasts. This is the error message I receive after putting in the mri_glmfit command: ERROR: you must use '--surface subject hemi' with surface data Did I do everything correct or did I forget a step? Thank you so much in advance, Bente

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Question about tkmedit
by nooshin n.zade 10 Nov '11

10 Nov '11

Dear Freesurfer Expers I have installed FS on the new mini Mac today, it can open bert with tkmedit and tksurfer. Using tkmedit for seeing my subject in /Users/nzadeh/freesurfer/subjects, it says "cannot find subject N3237c in /Users/nzadeh/freesurfer/subjects or it is not readable by you" but when I get "ls", I see my subject in that directory, and with my old Mac I can see that via tkmedit and tksurfer. I think there are still problems for installation Can you please advise me. Thank you very much. -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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Re: [Freesurfer] Tracula Question, step 2
by Anastasia Yendiki 09 Nov '11

09 Nov '11

Hi Shannon - Does the original bedpostx run fine on your cluster? You'd probably have to edit that to get it to work, it's not made to work on every possible cluster. Bedpostx_seychelles is the modified version that tracula calls that I've modified from the original FSL version so that it runs on our clusters. In either case, trac-all is meant to always be run from the command line, whether you're on a personal computer (where is runs jobs serially) or a cluster (where it submits them as jobs using qsub). But probably some editing will be needed as I said. Hope this helps, a.y On Wed, 2 Nov 2011, Shannon Buckley wrote: > > Hi Anastasia, > > > > I am trying to run Tracula for the first time in our lab and > I’m getting errors during step 2 that seem to involve how the program wants > to be launched via grid. I’ve attached the configuration file I’m using and > the error message is below... > > > ____________________________________________________________________________ > > > $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh > > Using Freesurfer version 5.1. > > > > Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/ > > Sessions Directory is /home/vhasfcbuckls/sessions > > > > INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects > > INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula > > Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1 > > ln -sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_ > mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n > ii.gz > > ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz > /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz > > WARN: Running FSL's bedbost locally - this might take a while > > WARN: It is recommended to run this step on a cluster > > bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri > > subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri > > Making bedpostx directory structure > > Queuing preprocessing stages > > Unable to run job: Job was rejected because job requests unknown queue > "short.q". > > Exiting. > > Queuing parallel processing stage > > Unable to run job: Job was rejected because job requests unknown queue > "long.q". > > Exiting. > > Queuing post processing stage > > Unable to run job: denied: "60" is not a valid object name (cannot start > with a digit) > > Job was rejected because job requests unknown queue "long.q". > > Exiting. > > > ____________________________________________________________________________ > > > > > > > Although we DO have a grid, I am trying to test the program for feasibility > purposes, just on my own system’s terminal, since we aren’t sure how results > will look with our specific data set (3.0 Tesla Siemens, 64 directional DWI > @ b=1000, with 1 b0 image). We are very interested in performing > tractography in T1-space… I am open to running this over the grid, if that’s > really the best way to do it, but the problem is that I don’t see anywhere > to specify the name of the queue that should be used for launching the > program. > > > > Can you please tell me how to launch this without using the so-called long.q > and short.q? We typically launch jobs to our grid using our “bash.linux.q”, > but I haven’t been able to locate a place in the configuration file, or any > switches to use in the cmd line, to specify that this queue should be used. > I tried specifically launching Tracula’s step 2 onto our bash.linux.q via > the cmd line using “qsub”, but received the same old error I had been > getting. I checked the data independently using “bedpostx_preproc.sh”, and > it appears that all the required data are set up properly. As far as I can > tell, the only issue we have is this inability to use the long.q and > short.q… > > > > What do you think? > > > > I’ve cc’d our IT specialist, Henry Mensch, who oversees our grid system in > case you need someone to chime-in with any specific information about how > our Linux systems are set-up. > > > > Thanks very much for your time, > > > > Shannon T. Buckley > SRA III - Supervisor > CIND, UCSF > 4150 Clement St. (114M) > San Francisco, CA 94121 > Phone: (415) 221-4810 x4251 > Fax: (415) 386-3954 > > > > > > >

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Re: [Freesurfer] Sub-cortical structure
by Douglas N Greve 09 Nov '11

09 Nov '11

yes, that has the subcortical segmentation based on the automatic algorithm and any changes that you might have made manually. The "auto" is only the result from the automatic method. doug Jie Shi wrote: > Thanks a lot. Will try. Basically, is aseg.mgz the resulting file > which contains the results of FreeSurfer subcortical segmentation? > What role is the aseg.auto.mgz? > > Jie > > > On Wed, Nov 9, 2011 at 5:15 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > cd $SUBJECTS_DIR/subject/surf > mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this generates > a surface with jagged edges > mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # > smooths surface 10 smoothing steps is just a guess > > # Visusalize the surface > tksurfer subject lh hippocampus.sm10 > # See the surface overlaid on the volume > tkmedit subject orig.mgz lh.hippocampus.sm10 -aseg > > Not that when you run the tkmedit/tksurfer commands, they will > complain that the surface does not match. This is not a problem > for this application. > > doug > > > Jie Shi wrote: > > Hi, thank you very much. Actually we do want to know how to > get the surfaces in order to compare with ours. > > Jie > > > On Wed, Nov 9, 2011 at 4:59 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > You can extract a binary mask for any structure with > mri_binarize --i aseg.mgz --match XX --o yourmask.mgh > where XX is a number from > $FREESURFER_HOME/FreeSurferColorLUT.txt > (eg, 17 = left hippo) > It is possible to generate hippo surfaces, but we cannot > guarantee > accuracy. Let me know if you want to know how. > doug > > Jie Shi wrote: > > Hi, experts. We need to use FreeSurfer to process some > analyze > image data. More specifically, we want to extract the > hippocampus surfaces. We know that FreeSurfer has done > subcortical segmentation during -autorecon2 stage in > recon-all. We have checked the resulting aseg.mgz file and > found that it contains all substructures. So we wonder if > there is a way to get the separated .mgz files for each > substructure or could FreeSurfer generate the subcortical > surfaces? Thanks a lot. > > Best, > Jie > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > The information in this e-mail is intended only for the > person to > whom it is > addressed. If you believe this e-mail was sent to you in > error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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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Re: [Freesurfer] Sub-cortical structure
by Douglas N Greve 09 Nov '11

09 Nov '11

cd $SUBJECTS_DIR/subject/surf mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this generates a surface with jagged edges mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # smooths surface 10 smoothing steps is just a guess # Visusalize the surface tksurfer subject lh hippocampus.sm10 # See the surface overlaid on the volume tkmedit subject orig.mgz lh.hippocampus.sm10 -aseg Not that when you run the tkmedit/tksurfer commands, they will complain that the surface does not match. This is not a problem for this application. doug Jie Shi wrote: > Hi, thank you very much. Actually we do want to know how to get the > surfaces in order to compare with ours. > > Jie > > > On Wed, Nov 9, 2011 at 4:59 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > You can extract a binary mask for any structure with > mri_binarize --i aseg.mgz --match XX --o yourmask.mgh > where XX is a number from $FREESURFER_HOME/FreeSurferColorLUT.txt > (eg, 17 = left hippo) > It is possible to generate hippo surfaces, but we cannot guarantee > accuracy. Let me know if you want to know how. > doug > > Jie Shi wrote: > > Hi, experts. We need to use FreeSurfer to process some analyze > image data. More specifically, we want to extract the > hippocampus surfaces. We know that FreeSurfer has done > subcortical segmentation during -autorecon2 stage in > recon-all. We have checked the resulting aseg.mgz file and > found that it contains all substructures. So we wonder if > there is a way to get the separated .mgz files for each > substructure or could FreeSurfer generate the subcortical > surfaces? Thanks a lot. > > Best, > Jie > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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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