Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Re: [Freesurfer] PET tools in FS dev v6.0
by Pradeep 19 Nov '15

19 Nov '15

Hello Doug, I am in the process of testing the FS PVC procedure and I was wondering if there is a way to do this procedure with single frame PET data and get the partial volume corrected SUVR image. I know that this is still new and not all the processes is documented yet, but any inputs on this would be appreciated. I have successfully ran steps 1 and 2 from the process you have outlines above. Thanks, Pradeep On Mon, Sep 28, 2015 at 10:03 PM, Jonathan DuBois < jonathan.m.dubois(a)gmail.com> wrote: > Hi Doug, > > I uploaded the files you requested. I'm not sure if it matters, but one > thing I forgot to mention was that in order to get the pet file in the > right format and orientation, I ended up using (ecattominc pet.v pet.mnc) > and (itk_convert --inv-y --inv-x pet.mnc pet.nii). I couldn't find a good > tool to convert directly form ECAT to NIFTI, but perhaps this conversion > process interferes with the pet processing? > > Best, > Jonathan > > >> Message: 7 >> Date: Mon, 28 Sep 2015 18:07:18 -0400 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] PET tools in FS dev v6.0 >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <5609BA16.2090006(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> Can you upload the FS subject, pet data, and .lta? >> https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> >> >> On 09/28/2015 12:08 PM, Jonathan DuBois wrote: >> > Hi Doug, >> > >> > I was told you were away last week so I'm reposting this message. >> > Thanks for sending me the information on the PET scripts. I >> > ran gtmseg, and bbregister successfully (I inspected both and they >> > look accurate), but I am getting a segfault with mri_gtmpvc at the >> > auto mask step. >> > >> > I copied the command and the error below. I thought that it could be a >> > memory issue due to the size of the matrix (I ran it on a mac with >> > 8gb) but I also tried to run it with the --tt-reduce and got the same >> > error. The data is from an HRRT PET scanner with a PSF of 4mm. For the >> > auto-mask input I used 6 .01, as your instructions were PSF+2. Is this >> > correct? >> > >> > Thanks >> > Jonathan >> > >> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg >> > /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.mgz --reg >> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output >> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale >> > Loading input pet.nii.gz >> > done loading input 26 frames >> > >> > $Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $ >> > setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub >> > cd /Volumes/my_passport/external/Documents/fssub2/test >> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg >> > /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.mgz --reg >> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output >> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale >> > sysname Darwin >> > hostname Jons-MacBook-Air.local >> > machine x86_64 >> > user jonathandubois >> > vgthresh 0.001000 >> > nReplace 18 >> > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 >> > 4 avail.processors, using 1 >> > Creating output directory gtmpvc.output >> > Loading seg for gtm >> > /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.mgz >> > Loading seg ctab >> > /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.ctab >> > Reading /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.lta >> > Replacing 18 >> > Pruning ctab >> > done with seg vol >> > maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10 >> > Computing auto mask >> > Segmentation fault: 11 >> > >> > >> > Message: 13 >> > Date: Tue, 08 Sep 2015 14:34:11 -0400 >> > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu >> > <mailto:greve@nmr.mgh.harvard.edu>> >> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0 >> > To: freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:freesurfer@nmr.mgh.harvard.edu>Message-ID: >> > <55EF2A23.3070705(a)nmr.mgh.harvard.edu >> > <mailto:55EF2A23.3070705@nmr.mgh.harvard.edu>> >> > Content-Type: text/plain; charset=windows-1252; format=flowed >> > Yes there are both. For KM we have MRTM1 and MRTM2 so far. They >> > are not >> > well documented yet. >> > 1. To start, run >> > gtmseg --s subject >> > This will take a couple of hours and produces some files needed >> > for GTM >> > PVC (which is used for GTM, MG, RBV). >> > 2. You'd then register the PET to the anatomical with bbregister >> (with >> > --t2 weighting). Make sure to save the output as an LTA (--lta). I >> > usually use the mean TAC as the input. You can do this in parallel >> > with #1. >> > 3. You'd then run mri_gtmpvc, something like >> > mri_gtmpvc --i tac.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg >> > gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o >> > gtmpvc.output >> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale >> > PSF is the point-spread FWHM of the scanner; reg.lta is the >> > registration >> > from #2. --km-hb specifies the highbinding region for MRTM2. >> --km-ref >> > specifies the reference region. --mgx specifies to output a >> > muller-gartner map (not necessary for GTM ROI analysis). >> > 4. For the GTM (ROI) MRTM1 KM analysis, you would then run >> > mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat >> --o >> > mrtm1 --no-est-fwhm --nii.gz >> > where time.dat is a text file withe acquisition time of each time >> > point >> > in the tac. >> > 5. For the MRTM2 analysis >> > set k2p = `cat mrtm1/k2prime.dat` >> > mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat >> > $k2p --o >> > mrtm1 --no-est-fwhm --nii.gz >> > If you want to run a voxel-wise analysis, then you can use the mgx >> > volume as input (--y). Probably you'll want to sample this to the >> > surface using mri_vol2surf and the registration file >> aux/anat2pet.lta, >> > then smooth on the surface. >> > >> > >> > doug >> > >> > >> > >> > On 09/08/2015 02:11 PM, Jonathan DuBois wrote: >> > > Hi FS experts, >> > > >> > > In FS development package I see that there have been tools added >> for >> > > partial volume correction of PET data, but I was wondering if >> there >> > > were also kinetic modeling tools similar to those described in >> > Doug's >> > > 2014 paper? If you could let me know what PET processing tools >> have >> > > been included in the dev package, I would be interested to test >> and >> > > compare them. >> > > >> > > Thanks, >> > > Jonathan >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > >> > _______________________________________________ >> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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] selxavg3-sess error empty conditions in paradigm file
by Douglas Greve 19 Nov '15

19 Nov '15

On 11/19/15 9:53 AM, Danielle Miller wrote: > Hi Doug, > > Thanks for your response. So you are saying to rename a correctly > identified condition as the empty condition? That is if I have a > correct trial, rename it to an incorrect trial? Won't this pull onset > times from the wrong conditions? This is what I'm suggesting. Not sure what you mean by onset times from wrong condition. > > When you say it should have little effects on the final results, are > you only thinking about this in terms of one or two subjects? What if > there are more subjects in this situation? If you have many corrects, then it will not affect the estimation of the HRF for the "correct" condition regardless of the number of subjects. If you plan to study the incorrects or some contrast that includes the incorrects, then you won't be able to use these subjects anyway. doug ps. please remember to post to the FS list and not to us personally. thanks! > > Thanks, > Danielle > > -- > Ph.D. Program in Behavioral Neuroscience > Boston University School of Medicine L-815 > 72 E. Concord St > Boston, MA 02118 > > > VA Boston Healthcare System Jamaica Plain > Memory Disorders Research Center > 150 South Huntington Ave D11-103 > Boston, MA 02130 > OFFICE:(857) 364-2130 >

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Error using mkdir for the segmentation of hippocampal subfields using FreeSurfer 6
by Fengji Geng 19 Nov '15

19 Nov '15

Dear FreeSurfer Users, I was trying to segment hippocampal subfields using FreeSurfer 6 with data that have already undergone the FreeSurfer 5 pipeline recon-all -all. According to the usage described on the webpage of HippocampalSubfields (http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) I ran the command: recon-all -s ${Mysubject} -hippocampal-subfields-T1 Then the following errors occurred. It seems that the program 'segmentSubjectT1_autoEstimateAlveusML (line 113)' was trying to make a directory in a Read-only place. But the error message did not indicate where this place was. I have tried to look codes in 'run_ segmentSubjectT1_autoEstimateAlveusML.sh" . But it does not have this information either. As segmentSubjectT1_autoEstimateAlveusML is a binary file, I could not dig out any more info. Does anyone know how to solve this error? Or know where the program was trying to mkdir? Thank you. Here begins the error message: hippocampus:/<2>hippocampus/HMN/data/FG_Temp: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Nov 18 21:57:45 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Nov 18 21:57:50 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError End of error message. Best Regards! Fengji --- Fengji

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lgi value aberrantly to high, maybe due to topological defects
by Oana Georgiana Rus 19 Nov '15

19 Nov '15

Dear freesurfer users, I run the command *'recon-all -lgi' *for my participants and for two of them I get the following error message: ... remeasuring lGI value for vertex iV = 39301. It may take a few minutes. WARNING -- Problem for vertex iV = 39301, lGI value is aberrantly high (lGI=44.2971)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/data_august/Geo/freesurfer_OCD/subjects_converted/KuTo67/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! On the freesurfer weppage (http://freesurfer.net/fswiki/LGI) it is supposed to be a known issue and they suggest to relaunch *mris_compute_lgi *, quote: /In case of topological defects of the pial surface (run mris_euler_number), mris_compute_lgi crashes. Usually, simply relaunching mris_compute_lgi is sufficient to overcome this issue. / I already tried that several times and i still get the same error . The script always crashes at the same vertex. However when I check the mris_euler_number for the subject's rh.pial it interestingly does not show me any topological defect. Has anybody encounter the same problem? or what should be a possible solution? Thanks a lot in advance for your answer. Best Georgiana -- Oana Georgiana Rus PhD Student Neuroimaging Center TUM-NIC Klinikum rechts der Isar Technische Universität München Einsteinstr.1 81675 München Raum 5.8 Tel. 089 4140 7971

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failure to start tksurfer
by Lars M. Rimol 19 Nov '15

19 Nov '15

Hi, I'm unable to initiate tksurfer. Can anyone tell me why this happens? [10:57 lmr@dmed4870 lmr] > tksurfer fsaverage lh inflated subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /home/lmr/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/lmr checking for nofix files in 'inflated' Reading image info (/home/lmr/subjects/fsaverage) Reading /home/lmr/subjects/fsaverage/mri/orig.mgz surfer: Reading header info from /home/lmr/subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: tkoInitWindow(fsaverage) Received X error! Error code : 2 Request code : 154 Minor code : 3 Error text : 'BadValue (integer parameter out of range for operation)' Can't create a context! surfer: failed, trying double buffered window Received X error! Error code : 2 Request code : 154 Minor code : 3 Error text : 'BadValue (integer parameter out of range for operation)' Can't create a context! surfer: failed, no suitable display found sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Re: [Freesurfer] freesurfer vs ITK build from sources on ubuntu(LUCID)
by Nedialko I. Krouchev 18 Nov '15

18 Nov '15

To follow up on my previous message: the FS build is not facilitated by the scarcity and incompleteness of build instructions. For example ITK, PETSC (and possibly other packages) which are not even mentioned explicitly as FS prerequisites (!) need to be installed at a (version-matching!) dev-level (in ubuntu this can be done through the package-mgmt system), and the corresponding directories skillfully linked to the FS build configure options. This - paired with the scarcity of binaries for the various unix platforms hardly contributes for expanding the circle of FS users, unless the users in question are accomplished unix gurus familiar with all the inner workings of a modern code maintenance. Please contact me offline for further details and exchange.

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recon-all script order
by Lauren Bystrom 18 Nov '15

18 Nov '15

Hello all, I am trying to run freesurfer on a set of subjects that have tumors in their brain. To get around the tumor, I only want to run freesurfer on one of the hemispheres. When I use hemi -?h, freesurfer exits once it hits the other hemisphere. This is a problem because it doesn't go back to finish the rest of recon-all for the hemisphere I want. Is there a way to change the order of files created with the recon-all script so all of the volumetric, and all of the wm, and all of broadmann's area, etc. is completed for one hemisphere before being run for the other? Thanks! Lauren Bystrom

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FreeSurfer question
by Tsapanou, Angeliki 18 Nov '15

18 Nov '15

Hello, I am dealing with a problem on FreeSurfer a couple of days now. I want to fix the scull strip and I run the following commands: cd /users/Angeliki/studyname export SUBJECTS_DIR=studyname/subjid/session/T1/ recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid FreeSurfer Then, the command works and the part of the cerebellum that I don't need turns brown. I close it and I save the script with: gedit ~/FreeSurfer/Angeliki/run_reconalls_aut1.sh And type at the script for echo: recon-all -autorecon2 -autorecon3 -subjid FreeSurfer Finally, I submit it to the cluster with the command: ~/FreeSurfer/Angeliki/run_reconalls_aut1.sh The problem is that even though it runs properly (and I tried to add some control points and they work), the brown part of the cerebellum does not disappear, but remains there. Is there something I have to change? Thank you, Best, Angeliki Tsapanou

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gender as nuisance factor
by Tesse, Marcello 18 Nov '15

18 Nov '15

Dear FreeSurfer experts, > > > I a PhD student at King's college London. > > I am running cortical thickness analysis with QDEC. > > I would like to investigate some cortical thickness differences > between 2 groups, > > using as nuisance factors 'age' and 'gender'. > > > No problem at all with age. But the gender as dicotomic variable is > > listed on fixed factor in qdec, in design window. > > My question is: > > how can I run the analysis using 'gender' as nuisance factor?? > > > > thank you very much > > MARCELLO

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selxavg3-sess error empty conditions in paradigm file
by Danielle Miller 18 Nov '15

18 Nov '15

Hello Freesurfer Experts, I am reposting this as this has not come up on the mail archive thread. I keep running into the following error (see below) when selxavg3-sess gets to my third subject. I am assuming this is because this subject does not have all of the conditions modeled (that is, this particular subject does not have any incorrect responses). Is there a way to model an empty condition to get around this? I want a general contrast of Incorrect > Correct, but some subjects do not make any errors and therefore would not have this condition in their paradigm files. Any advice would be greatly appreciated. #@# CC_003_recon ############################### /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer-5.3/matlab/MRIread.m ------------------------- outtop = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST Extension format = nii.gz INFO: key PerSession unrecognized, line 6, skipping INFO: key ApplySubCortMask unrecognized, line 12, skipping 1 Correct-v-Incorrect.mat 2 Incorrect-v-base.mat nruns = 4 autostimdur = outanadir = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305 Found 57600/537168 (10.7) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 740, nX = 27, DOF = 713 Saving X matrix to /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 39 s = svd(A); Error in ==> fast_selxavg3 at 254 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

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Freesurfer November 2015