Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

longitudinal recon-all
by Lisa Delalande 20 Nov '15

20 Nov '15

Hi, I would like to know if, in doing a longitudinal study (i.e. 2 or 3 MRI each subjects), this is usual to have many file for one subject (see the picture, 5 file for one subject with two MRI : a0009_1 = MRI 1 and a0009_2 = MRI 2) ? Because in the future I will have around 100 subjects with 3 MRI each so I will have a lot of file to handle with ... Thanks in advance ! Friendly Lisa

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Error message with lh.BA1.label
by BAUTISTA-PERPINYA Maximilia (ETU VIE) 20 Nov '15

20 Nov '15

Dear all, I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments: FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860…) Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects. output of bugr: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 --------------------------------------------------------------------- 1) subject name: it happens with any subject 2) the entire command-line executed recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid where: $g = /path/to/nii/file and $subjid = subject ID 3) the error message generated from the recon-all.log: SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015 from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Best regards, Max -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg maximila.bautista-perpinya(a)etu.unistra.fr

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Unsupported TransferSyntax in DICOMs: problem with "mri_convert"
by Baker, Justin T.,M.D.,Ph.D. 19 Nov '15

19 Nov '15

Hi FreeSurfer list, Lately, we have noticed that a bunch of DICOMs obtained on our 3T Tim Trio (at McLean Hospital) are getting labeled with TransferSyntax IDs that are causing DICOM unpacking scripts (like mri_convert) to fail. In particular, the offending TransferSyntaxIDs appear to be "1.2.840.10008.1.2.4.90" and "1.2.840.10008.1.2.4.91", according to what we can glean from the DICOM headers. It seems like the "JPEG Lossless Only" syntax is the real problem, but in any case, we are not finding any suitable workarounds for this issue. Any advice on how to proceed would be much appreciated. We are hoping that a patch to "mri_convert" would solve the problem. Best, Justin

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Generating a correlation map from a functional contrast ...
by Joseph Andreano 19 Nov '15

19 Nov '15

Hi Freesurfer experts, I'd like to generate a correlation map showing the strength of correlation between a behavioral value and the value of a functional contrast between two conditions. >From previous cortical thickness analysis, I know that if I use the -notask tag on mkanalysis, I can use a file that includes all of my behavioral values and correlate them with, say, a thickness value. But when I use -notask, I can't specify a paradigm file, without which I can't specify contrasts. Is there a way to make this correlation map versus a functional value drawn from a contrast? This seems simple, conceptually, but I haven't been able to implement it. Thanks in Advance, Joe _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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modify QDEC smoothing options
by Hirsch, Gabriella 19 Nov '15

19 Nov '15

Hey Freesurfer experts, I had a quick question. Is there any way to modify QDEC in such a way to have other options other than 0, 5, 10, 15, 20 etc, for smoothing? I know I would also have to -qcache the data for the desired smoothing too but I was wondering if anyone had done this before? Any ideas would be appreciated! Thanks, Gabriella * Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.

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Skullstripping leaves a little bit of dura
by Guido Orlando Pascariello 19 Nov '15

19 Nov '15

Hi Experts I'm using Freesurfer to quantify some subcortical volumes and cortical areas. I have been preprocessing my data using 'recon-all autorecon1' I have a question About Skullstripping. It is leaving a little bit of dura behind the head. I found '-gcut' which is useful to solve it but it has some cons. I don't want to view the data, I just want to get the quantifications, so I wonder if this pices of dura could affect the '-tessellate' step. I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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FSFAST First-Levels: Fast_selxavg3() ERROR
by Afzal, Afsana 19 Nov '15

19 Nov '15

Hi, I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3(): Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical. Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it. Thank you for any help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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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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