Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

TRACULA question- pathstats not loading
by Golan, Noa 15 Dec '15

15 Dec '15

Hi, I am currently analyzing DTI data and I am having issues with one file in particular. When I run the tracheal -path -c step, all of the files are generated except the pathstats text files. Any thoughts? Thanks! Noa

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Tracula stats COR-.info does not exist
by Simon Jones 15 Dec '15

15 Dec '15

Dear Tracula developers, I posted a problem with tracula when I ran trac-all -stat -c dmrirc_ind_mni_cvs_all_stats.all I receive this error message Loading output reference volume from /home/spj24/app/freesurfer/subjects/cvs_avg35 corRead(): can't open file /home/spj24/app/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /home/spj24/app/freesurfer/subjects/cvs_avg35 There is no file called COR-.info in the directory /home/spj24/app/freesurfer/subjects/cvs_avg35/ I have now changed the lines in the configuration file set doregcvs = 1 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # #set cvstemp = donald set cvstemp = cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects to set doregcvs = 1 set cvstemp = cvs_avg35/mri/brainmask.mgz set cvstempdir = $FREESURFER_HOME/subjects i.e. explicitly pointing to an image in the cvs_avg35 directory and the stats seem to complete without error. Is that the right thing to do? Thanks for your help, Simon

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Tracula with multi-shell data?
by Henrik Sjöström 15 Dec '15

15 Dec '15

Hi! I have some questions regarding Tracula and multi-shell DWI. -Is it possible to activate the multi-shell model within bedpostx when running it through tracula? -does anyone have experience on running multi-shell data through Tracula (2 or 3 crossing fibers)? We are planning an experiment and discussing protocols consisting of around 32 directions with b=1000 and 64 directions at b=2500 so I'm looking for opinions on this with regard to Tracula processing. Thanks! Henrik Sjöström

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Tracula Tracts density
by John Anderson 15 Dec '15

15 Dec '15

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TRACULA visualisation differences
by Worker, Amanda 15 Dec '15

15 Dec '15

Hi all, I'm just visualising tracts that have been processed using TRACULA and I'm noticing some differences that seem slightly odd. For example, when I load the ILF for one subject, the pathway looks huge and takes up a very large portion of the brain. However, when I load the same tract along with all of the other tracts it looks like a well segmented region. I have checked my registration with the T1 and it looks good, so I'm not sure why there is a difference. Looking at the stats for this tract volumes range from 300-600 approx. This is a patient vs control study so I would expect some differences in volume, but this seems like a big difference from the example given on the wiki which is around 160. But the average MD and FA seem reasonable and consistent at around 0.0008 and 0.4. This is the same for many of the subjects - would you base your quality control on the visualisation of the single tracts or all of the tracts loaded together. Is there an obvious difference/ why would they load differently? I have attached some screenshots so that you can see what I mean. Thanks in advance. Amanda

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excessive topological defect
by Elisabetta del Re 14 Dec '15

14 Dec '15

Dear FreeSurfer team, we are running FreeSurfer on 1.5T cases. For a few of them we get error messages that I am attaching. Mostly the message error relates to excessive topological defect. Any suggestions you can give to us? Thank you, regards, Elisabetta -- Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre(a)hms.harvard.edu

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ABCD postdoctoral position at Florida International University
by Anthony Dick 10 Dec '15

10 Dec '15

Dear Colleagues, Please find below an advertisement for our Postdoctoral position at Florida International University, Miami, FL. Details are also provided in the attached pdf. Thank you! Anthony >>> The Cognitive Neuroscience and Imaging Center at Florida International University (FIU) in Miami is seeking a full-time, benefits-earning Visiting Postdoctoral Fellow with expertise in magnetic resonance imaging (MRI) physics, with emphasis on functional MRI and diffusion- weighted MRI. The successful candidate will join a team of investigators to develop, support, facilitate, and coordinate daily data collection activities for the Adolescent Brain Cognitive Development (ABCD) Study: a landmark multi-site NIH study to assess the short- and long-term impact of substance use on brain development (http://addictionresearch.nih.gov) The successful candidate will develop, deploy, and optimize multiband fMRI and high angular resolution diffusion imaging (HARDI) acquisition protocols for use at 3T. She/he will contribute to deploying these MRI techniques, as well as prospective motion correction (PROMO), and fast, integrated distortion correction methods. These methods will be collectively applied in a large, longitudinal study designed to advance addiction science through a strong focus on developmentally informed assessment. The primary duties/responsibilities of the position involve direct engagement in magnetic resonance imaging (MRI) data collection efforts, including (but not limited to): protocol development and management, execution of research plan, implementation of experiments, data acquisition, and data management. Applicants must have a PhD in physics, biomedical engineering, radiological sciences, computer science, or a related field. Candidates must have a strong background in MR physics, as well as strong skills in computer programming (e.g., python, MATLAB). Applicants must have experience in MR scanner operation and software, image reconstruction, advanced data analysis (e.g., FSL, AFNI). Experience in multiband fMRI and/or HARDI imaging technology, and familiarity with data harmonization across multi-center imaging studies are highly desired. The applicant should ideally possess outstanding writing and communication skills as demonstrated by a successful publication record. The starting date for this position is January 1, 2016, and the salary will be commensurate with experience. To apply, please include all documents in one PDF file: cover letter, CV, a one-page statement describing your qualifications and research interests, contact information for two references, and copies of up to two of your publications. Applications should be sent via email to: cnic(a)fiu.edu. Review of applications will begin immediately. For informal enquiries regarding this position, please contact Dr. Angela Laird (alaird(a)fiu.edu) Additional information about the Center can be found at http://cnic.fiu.edu, and more information about the ABCD Project can be found at http://www.drugabuse.gov/news- events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain- development. MRI Postdoc -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: faculty.fiu.edu/~adick

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Re: [Freesurfer] Talairach_afd error (Bruce Fischl)
by Anna I. Garcia Diaz 09 Dec '15

09 Dec '15

Hi Bruce, Were you able to take a look at the error we discussed previously? We are very concerned about this problem, because our study depends on the preprocessing of these images. The previous e-mail with logs from the error is copied below. Any help would be very much appreciated. Thanks in advance and kind regards, Anna Garcia The recon-all.log file from the tailaraich processes on reads as follows: #@# Talairach Tue Sep 22 13:07:35 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri talairach --i orig.mgz --xfm transforms/talairach.auto.xfm /psiquiatria/home/anna/subjects/prova/mri /psiquiatria/software/freesurfer/bin/talairach --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 22 13:07:36 CEST 2015 tmpdir is transforms/tmp.talairach.22322 /psiquiatria/home/anna/subjects/prova/mri mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc input_transform(): error reading transform elem [1,1] input_transform: error reading transform. error loading transform from /psiquiatria/home/anna/subjects/prova/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.40604e-09, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-6.90488e-09, 1, 4.65661e-10) writing to transforms/tmp.talairach.22322/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /psiquiatria/software/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.22322/src.mnc transforms/talairach.auto.xfm Tue Sep 22 13:08:01 CEST 2015 talairach done INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Sep 22 13:08:02 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ltMNIreadEx: could not read row 1 from transforms/talairach.xfm (Linear_Transform = ) ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux recon-all -s prova exited with ERRORS at Tue Sep 22 13:08:04 CEST 2015 For more details, see the log file /psiquiatria/home/anna/subjects/prova/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Also, a recon-all.error file was created, and says the following: SUBJECT prova DATE Mon Sep 28 18:56:32 CEST 2015 USER anna HOST blade07 PROCESSOR x86_64 OS Linux Linux blade07 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ /psiquiatria/software/freesurfer/bin/recon-all PWD /psiquiatria/home/anna/subjects/prova/mri CMD mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 (The same exact recon-all.error file appears when using the -notal-check flag) Kind regards, Anna Garcia On Wed, Oct 28, 2015 at 2:36 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. mri_parse_sdcmdir splitting a single series into two? > (Oliver Hinds) > 2. Postdoc Positions for the Adolescent Brain Cognitive > Development (ABCD) study (Don Hagler) > 3. Re: FreeSurfer pve correction tool (Mohamed Ali Bahri) > 4. Re: A mixed effect model approach in within subject dataset > {Disarmed} (Martin Reuter) > 5. Re: FreeSurfer pve correction tool (Douglas N Greve) > 6. Understanding the brainstem AtlasMesh file structure format > (Jonathan Plasencia) > 7. Re: comparison of 4 groups: mri_glmfit or Qdec? (Sandy Schramm) > 8. Re: Talairach_afd error (Bruce Fischl) (Bruce Fischl) > 9. error finding Matlab (Jason Haberman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 27 Oct 2015 15:14:25 -0400 (EDT) > From: Oliver Hinds <ohinds(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] mri_parse_sdcmdir splitting a single series into > two? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <alpine.LRH.2.20.1510271455210.6558(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII > > Hi, > > I'm running into an issue where the slices from one DICOM series are being > parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate > series. > > A few example lines from a scan.out: > > 6 AR_t.s40.c0 ok 64 64 41 1 <long file name> > 7 AR_t.s40.c0 ok 64 64 23 1 <different long file name> > > The scan AR_t.s40.c0 was run as a single series on the scanner, with 64 > slices. Inspection of the dicom header shows that the series UID is the > same for the DICOM files in each, except there is an extra string '.0.0.0' > at the end of series UID in the DICOMS that are parsed into the second > series. > > Has anyone else experienced this behavior? If so, is there a workaround? > > Thanks, > Oliver > > > > > ------------------------------ > > Message: 2 > Date: Tue, 27 Oct 2015 13:41:36 -0700 > From: Don Hagler <dhaglerjr(a)hotmail.com> > Subject: [Freesurfer] Postdoc Positions for the Adolescent Brain > Cognitive Development (ABCD) study > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <BLU436-SMTP65024FB31221FBD3A8E848A6220(a)phx.gbl> > Content-Type: text/plain; charset="us-ascii" > > Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) > study > > > > University of California, San Diego > > > > Several funded postdoctoral positions are available in image analysis > method development, including automated cortical- and subcortical > segmentation, advanced diffusion tractography, and fMRI mapping and time > series analysis. We are looking to build a team to help build the next > generation of analysis pipelines and visualization tools for a newly funded > study to follow 10,000 children with longitudinal structural and functional > imaging across 19 sites across the US. The study will use a cross-platform > Harmonized Human Connectome Protocol, optimized for quantitative accuracy > and consistency of imaging biomarkers across scanners and time. To learn > more about the ABCD study, please see > http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan… > < > http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan… > >. > > > > Requirements: Applicants should have research experience in any of the > above fields, with a Ph.D. or equivalent degree. They should be comfortable > working in a distributed team environment, and should have a track record > of quality scientific publications. Candidates are expected to be > experienced in programming with Matlab, Python, and/or <> C/C++. Experience > with FreeSurfer, FSL, and the Human Connectome analysis pipelines is > strongly preferred. > > > > To formally apply, submit a current CV, a personal statement describing > your research experience and interests, and contact information for 2-3 > references to abcd(a)ucsd.edu <mailto:abcd@ucsd.edu>. Or feel free to email > Dr. Donald Hagler (dhagler(a)ucsd.edu <mailto:dhagler@ucsd.edu>) or Anders > M. Dale (amdale(a)ucsd.edu <mailto:amdale@ucsd.edu>) for more information. > > > > The University of California, San Diego is an Equal > Opportunity/Affirmative Action Employer advancing inclusive excellence. All > qualified applicants will receive consideration for employment without > regard to race, color, religion, sex, sexual orientation, gender identity, > national origin, disability, age, protected veteran status, or other > protected categories covered by the UC nondiscrimination policy. >

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Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum
by UQAM 09 Dec '15

09 Dec '15

Hi Zeke, We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer. Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc Could you also please explain how to edit the ColorLut.txt file Finally, what is the precise script of the mri_segstats to generate stats tables. Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: > Hello Genevieve, > > Below is a link to the newest version of mri_cc. Please copy it to your > FREESURFER_HOME directory and backup the original. > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc > > Hope this help. > > -Zeke > > > On 11/24/2015 05:56 AM, UQAM wrote: > >> Hi Bruce, >> >> DELL R910 >> Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) >> 32 Go RAM >> CentOS release 5.10 (Final) >> kernel 2.6.18-371.3.1.el5 >> >> On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> Hi Genevieve >> >> I just tracked this down and it is a bug in mri_cc. If you tell Zeke >> your hardware/software environment he can get you a new version that >> should work >> >> cheers >> Bruce >> >> >> On Mon, 23 Nov 2015, UQAM wrote: >> >> Hi Bruce, >> Please find the two files attached. >> >> Genevieve >> >> >> >> On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> >> wrote: >> Hi Geneviève >> >> if you send us the $SUBJECTS_DIR/CColorLUT.txt and >> $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a >> look >> >> cheers >> Bruce >> On Mon, 23 Nov 2015, UQAM wrote: >> >> Hi, >> This a a "re-posting" of a question I've raised >> last week ; ) >> >> I would like to segment the corpus callosum >> into twelve even lenght segments >> instead of the five segments that freesurfer >> includes by default. >> >> - First I ran a mri_cc on subject e0070: >> >> mri_cc -aseg aseg.auto_noCCseg.mgz -o >> aseg.12segmentsCC.mgz -d 12 e0070 >> >> - Then I edited the ColorLUT.txt file and renamed >> it CColorLUT.txt (see >> attachment, segments 251 to 262). >> >> - Finally I ran a mri_segstats to compute the >> statistics on segmented >> volumes. >> >> mri_segstats seg >> $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab >> $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid >> 0 sum >> --e0070_CC12.aseg.stats >> >> The e0070_CC12.aseg.stats file still displays only >> five segments of the >> corpus callosum. >> >> Any tips or clues on how I could do things >> differently to get 12 segments? >> >> Thanks in advance, >> >> Geneviève >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>

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3dClustSim and Gaussian filter width
by Emma Thompson 08 Dec '15

08 Dec '15

Dear Freesurfers, I am trying to use 3dclustsim in AFNI to determine the minimum number of voxel in a cluster to reach significance, my understanding is that in the command line the -fwhm s flag refers to the gaussian filter width and NOT the Gaussian Kernel, can anyone point me to how I might be able to obtain this for each hemisphere in freesurfer? I am using my own average brain that I created, but it would help to know how to do this for the fsaverage as well. Many thanks for your help! http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html

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Freesurfer November 2015