Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

error with mri_glmfit and question about registering rh to lh
by kelsi 14 Nov '11

14 Nov '11

Hi all, I receive the error: ERROR: MRISread: cannot read surface data from file ./long/surf/lh.thickness.fsaverage.S1-S3.mgh! when I run mri_glmfit with the command: mri_glmfit --glmdir long/g1v0 --surf long lh thickness.fsaverage.S1-S3.mgh --fsgd long/S1-S3.fsgd --osgm I am working on mri_glmfit for a one sample ttest of the thickness of multiple patients, all qcached to fsaverage. I ran the reconstruction and then ran -qcache for each subject. I then used mri_calc to find the difference in thicknesses of Session 1 and 3 for each patient (in fsaverage) and concatenated with mri_concat for the glm. But when I run the glm, it gives me the above error. How would I fix this? Also, I am wondering if there is a way to register the right hemisphere to the left hemisphere, since we are working with stroke patients and would like to compare all the contralesional hemispheres. Thank you! Kelsi

1 0

reconstruction stop
by LAOUCHEDI MAKHLOUF 14 Nov '11

14 Nov '11

hi i am new in freesurfer (even if i used it many times doing reonstructions using the script reconn-all in the past and on another machine), i launched a reconstruction of one patient using the reconn-all script and i gave before this the path to the SUBJECTS_dir. and one or two minutes later it stopped and prompted "recon-all finished without error at Mon Nov 14 13:44:11 CET 2011 done" and all the directories in the SUBJECTS_DIR were created with the mgz file created. thank you

2 1

mri_glmfit error
by kelsi 13 Nov '11

13 Nov '11

Hi Freesurfers, I am having problems with mri_glmfit. I am doing a one sample ttest with thickness values. However, when i enter "-surf Subject1 lh thickness.fsaverage.mgh", I receive an error message saying that the surface could not be opened. The path is correct and I entered "setenv SUBJECTS_DIR ./" in my directory before running the glm. How would I fix this error? Thank you! Kelsi Hirai

1 0

Amazon EC2 Version of FreeSurfer 5.1 Available
by Pedro Paulo de Magalhães Oliveira Junior 11 Nov '11

11 Nov '11

Some weeks ago I was asked about a public image (AMI) to run in the Amazon EC2 infrastructure If you want to use FreeSurfer in the EC2 infrastructure you can use this public AMI: *060244368407/FREESURFER51* Just for your information this AMI can run a recon-all in 23 hours in an Amazon AWS Small Instance. So with the current Amazon cost per Small Instance/Hour you'll have a recon-all for USD 2.04 Amazon request a credit card in order to create an account in http://aws.amazon.com Hope it helps, Pedro Paulo Jr. --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

4 8

using expert-options on initial run
by Michael Harms 11 Nov '11

11 Nov '11

Hi guys, There is an issue with recon-all abending if you use the -expert option on the very first call to recon-all, because recon-all attempts to copy to $subjid/scripts/expert-options before the scripts directory has been created. As an attempted workaround I manually created an empty $subjid/scripts directory so that the directory already existed. However, in conjunction with the -i flag this then triggers the error of "existing subject" and the -force option no longer exists to force the process to proceed. cheers, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

3 3

mri_glmfit search space = 0
by kevin bickart 11 Nov '11

11 Nov '11

Hi all, I am conducting a contrast of z (r) maps from 3 seed-based resting-state networks (e.g., 1 > 2 and 3). To eliminate the influence of anticorrelations on the contrast results, I thresholded the z (r) maps at 0 before running mri_glmfit, thereby eliminating voxels with negative z (r) values. The command completed successfully but the resulting sig maps did not contain voxels with any values. I have attached the fsgd and contrast files and pasted the command and output below. Can anyone identify the problem here? Thanks, Kevin *Potentially problematic portion of output:* Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to LR_Amy_lOFC2_glm2/mask.mgh search space = 0.000000 *Entire command and output: * [kreature:kbickart_fcmap_ASN_Anchor_AmyPks_buckner_YC] (nmr-stable5.1-env) mri_glmfit --y LR_Amy_lOFCpk2 _vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd /autofs/homes/006/kbickart/AmySubNet_glm/pa ired3.fsgd doss --C /autofs/homes/006/kbickart/AmySubNet_glm/paired.mat --glmdir LR_Amy_lOFC2_glm2 gdfReadHeader: reading /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 roi1_vs_roi2_vs_roi3 0 0.707107 Class Means of each Continuous Variable 1 Class_081028_BC77WB 0.0000 2 Class_081028_XE45TK 0.0000 3 Class_081028_YY28TK 0.0000 .... $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckne r_YC cmdline mri_glmfit --y LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd /autof s/homes/006/kbickart/AmySubNet_glm/paired3.fsgd doss --C /autofs/homes/006/kbickart/AmySubNet_glm/paired .mat --glmdir LR_Amy_lOFC2_glm2 sysname Linux hostname kreature machine x86_64 user kbickart FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckn er_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz logyflag 0 usedti 0 FSGD /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd glmdir LR_Amy_lOFC2_glm2 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory LR_Amy_lOFC2_glm2 Loading y from /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_Am yPks_buckner_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz llINFO: gd2mtx_method is doss Saving design matrix to LR_Amy_lOFC2_glm2/Xg.dat Normalized matrix condition is 1 Matrix condition is 44.5 Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to LR_Amy_lOFC2_glm2/mask.mgh search space = 0.000000 DOF = 177 Starting fit and test Fit completed in 0.0148667 minutes Computing spatial AR1 in volume. fMRIspatialAR1(): hit 0 voxels WARNING: no voxels in AR1 computation Residual: ar1mn = (nan,nan,nan) fwhm = (nan,nan,nan) nan Writing results paired maxvox sig=0 F=0 at index 0 0 0 seed=1321328111 mri_glmfit done -- Kevin Bickart MD-PhD Student Department of Anatomy and Neurobiology Boston University School of Medicine live UP to it

2 1

Job posting for Purdue BME (fwd)
by Bruce Fischl 11 Nov '11

11 Nov '11

FYI ---------- Forwarded message ---------- Date: Fri, 11 Nov 2011 11:58:19 -0500 From: Thomas Talavage <tmt(a)purdue.edu> Subject: Job posting for Purdue BME Hi all --- Purdue has posted a job announcement for our BME department, including (substantial) potential to hire someone into medical imaging (with an emphasis on MRI). If any of you have current or recent graduates/post-docs who might be interested in a faculty position, please encourage them to submit their materials. We will probably start looking at applications sometime in December, with interviews in the Spring. The job posting (and information about submission) may be found at: https://engineering.purdue.edu/BME/AboutUs/FacultyPositions >From the MRI perspective, with the formation of a new College of Health and Human Sciences, there is now a growing interest in expanding our present clinical/research partnership to include an on-campus, research-only facility, with the potential for us to be pushing for this to be a non-clinical strength system. I am hopeful that if we can find an outstanding MRI-centric candidate, that we can help push this agenda as a part of the search/hiring process. Tom Talavage

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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. > > > >

2 1

[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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