Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

recon-all input
by Xinfa Shi 04 Sep '14

04 Sep '14

Hello, Now I have a subject data,including 156 dicom images(MR0001~MR0156),amd they were converted into a .nii.gz file(eg.CON_T1_01.nii.gz) .I am wondering whether they are the same : recon-all -i MR00001.dcm -s con01 -all recon-all -i CON_T1_01.nii.gz -s con01 -all Many Regards. Xin-Fa Shi.

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invalid=96777 in recon-all
by Pom Sailasuta 04 Sep '14

04 Sep '14

Hello, I am using FreeSurfer version 5.3.0 in 64bit desktop, I got these errors at the begining of recon-all but the reconstruction is not stop, keep on going with lots of invalid=96777. **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.849, neg=0, invalid=96777 0001: dt=129.472000, rms=0.789 (7.080%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.765 (3.083%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.759 (0.766%), neg=0, invalid=96777 0004: dt=517.888000, rms=0.749 (1.353%), neg=0, invalid=96777 0005: dt=92.480000, rms=0.744 (0.567%), neg=0, invalid=96777 0006: dt=369.920000, rms=0.740 (0.600%), neg=0, invalid=96777 0007: dt=73.984000, rms=0.738 (0.229%), neg=0, invalid=96777 0008: dt=73.984000, rms=0.737 (0.148%), neg=0, invalid=96777 0009: dt=73.984000, rms=0.735 (0.250%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.733 (0.313%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.730 (0.371%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.727 (0.408%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.724 (0.430%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.721 (0.450%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.718 (0.450%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.714 (0.455%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.711 (0.442%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.708 (0.424%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.705 (0.403%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.703 (0.388%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.700 (0.347%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.698 (0.329%), neg=0, invalid=96777 thanks for the comments. Pom -- Pom

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Re: [Freesurfer] problems with tracula pre-processing (bvecs)
by Michele Cavallari 04 Sep '14

04 Sep '14

Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp <bakk.hbg(a)googlemail.com> wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. _______________________________________________ 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. _______________________________________________ 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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problems with tracula pre-processing (bvecs)
by Michele Cavallari 04 Sep '14

04 Sep '14

Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help.

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Re: [Freesurfer] tracula: bvec-error
by Barbara Kreilkamp 04 Sep '14

04 Sep '14

Dear all, Robby, are you still having the problem? Did you solve it? I am really having the same problem, just that I am using nifti files instead of dicoms. I am using the same version as Robby. Please find my command+output, trac-all.log and configuration file in the attachment. I would also appreciate any help. Thank you, Barbara On Tue, Aug 26, 2014 at 8:21 AM, Robby De Pauw <Robby.DePauw(a)ugent.be> > wrote: > >> Hi Anastasia, >> >> I’m using this version of tracula. >> >> trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp >> >> I’ve attached the log-file you requested. >> >> Robby De Pauw, dra. >> *Ghent University* >> Department of Physiotherapy and Rehabilitation Sciences >> 3B3 >> De Pintelaan 185 >> B-9000 Ghent >> >> Robby.DePauw(a)Ugent.be >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> 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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watershed surface to volume rendering repost
by Sherwood, Matt 04 Sep '14

04 Sep '14

Freesurfer, Sorry for the repost, but I did not get any further details: We have scans that have recon-all completed. Following recon-all, we completed watershed (under the MNE toolbox) to extract skull and scalp from the T1 scans. The outputs of this algorithm are outer brain, inner skull, outer skull and outer scalp surfaces. We are particularly interested in these volumes for our study. Is there a way to convert these surface to volumes representative of CSF (layer between brain/skull), skull (inner to outer skull surface) and skin (outer skull to outer scalp)? Matthew Sherwood Medical Research Engineer Wright State Research Institute 4035 Colonel Glenn Hwy. Dayton, OH 45431 PH: 937.705.1025 FAX: 937.705.1095 EMAIL: matt.sherwood(a)wright.edu<mailto:matt.sherwood@wright.edu>

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FreeSurfer NVIDIA card drivers with CentOS 6.5
by raij＠nmr.mgh.harvard.edu 04 Sep '14

04 Sep '14

Hi, Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to use the "noveau" drivers that come with CentOS 6.5 or would it be better to go with the proprietary drivers from NVIDIA? I would imagine that since FS 5.3 does not use GPU for analysis, this is mainly relevant for visualization (freeview etc) requiring 3D rendering of volumes, surfaces, and tractography results simultaneously. In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here. Thanks! Tommi --- Tommi Raij, MD, PhD

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Re: [Freesurfer] trac-all -prep error field map error
by Eileen Moore 04 Sep '14

04 Sep '14

Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example? As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map. I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file). Thanks, Eileen. > ------------------------------ > > Message: 10 > Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1407170411110.12767(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Eileen - All image formats that mri_convert (and thus any freesurfer > program) can read will do, you don't need dicom. Try giving trac-all the > phase difference maps you have and let's see what happens. > > Best, > a.y > > On Wed, 16 Jul 2014, Eileen Moore wrote: > > > Hi Anastasia, > > > > OK - our imaging physicists had developed a wrapper script around > epidewarp > > which takes our dicom images and converts them into the phase difference > map > > (it is based on the script that was authored by Doug Greve for the fBIRN > > consortium). It looks like the tracula script requires dicom images. Is > > there a way for me to do epidewarp manually and then follow through with > the > > remaining steps using trac-all? > > > > Thanks, > > Eileen. > > > > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > Message-ID: > > <alpine.LRH.2.03.1407141119560.23459(a)nmr.mgh.harvard.edu> > > Content-Type: text/plain; charset="utf-8" > > > > > > Hi Eileen - That step is run with the program epidewarp.fsl, > > which you can > > run on the command line to see the available options. The input > > phase map > > volume is expected to have either 2 frames (2 separate phase > > maps) or 1 > > frame (the difference phase map). This error from trac-all means > > that it > > found that your input phase map has something other than 1 or 2 > > frames, so > > it doesn't know how to handle it. > > > > Hope this helps, > > a.y > > > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > > I'm tyring to > > > run tracula on some? images acquired from a GE scanner. I am > > running into > > > problems when I try to perform the registration-based > > B0-inhomogeneity > > > compensation, getting an error in the terminal output: "ERROR: > > Unrecognized > > > format of phase map". However, trac-all -prep runs fine when I > > skip the > > > B0-inhomogeneity compensation step. Is there something else I > > need to do to > > > use field map correction? > > > > > > I've attached the trac-all.log and a copy of the terminal > > output. > > > > > > Thanks, > > > Eileen. > > > > > > > > > > > > > > > > > > > >

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Tracula - May update version
by Peggy Skelly 04 Sep '14

04 Sep '14

I have a few questions about the May 2014 update to Tracula: 1. Between the 2013-12-04 trac-all version 1.53 and 2014-05-26 trac-all version 1.56, the longitudinal stream now uses the aparc+aseg.mgz from the *.long.* directories, and all output is saved there, too. Are the <subj_tp>.long.<subj_base>/dlabel/anat and anatorig transformed into the base space like other images from the longitudinal recon-all, or are they in the original space of the timepoint T1 image? 2. Are there any changes to the bedpostX step, other than using a different mask? I've already run bedpostx in the Dec 2013 version (with lowb_brain_mask). Can the results be used with the new version by moving the <subj>/dmri.bedpostX directory to <subj_tp>.long.base/dmri.bedpostX? 2a. (Maybe pertains to both versions) The link to .../dmri/nodif_brain_mask.nii.gz seems to be made during the -prep stage using .../dlabel/diff/aparc+aseg_mask.bbr.nii.gz or lowb_brain_mask.nii.gz depending on usemaskanat's value in the dmrirc file. The bedpost stage seems to use the target file as its mask no matter what usemaskanat is in the dmrirc file used when calling trac-all -bedp. (I'm trying to use aparc+aseg_mask for -prep and -path, but lowb_brain_mask for -bedp in anticipation of using the bedpostx output for other seed-base tracking in FSL.) 3. May 2014 version: trac-all -prep -notensor fails when it gets to computing the priors because dmri_train includes the --fa flag and the dtifit_FA.nii.gz is not present. Running trac-all -prior without a computed FA also fails the same way. I could compute the tensor, but thought I would save some time. I didn't realize computing the priors would use it. Does it improve the accuracy? Thanks, Peggy

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Job Posting: Assistant Professor of Psychology at the UC-Davis Center for Mind & Brain
by Steven J Luck 04 Sep '14

04 Sep '14

The Center for Mind & Brain and the Department of Psychology at the University of California, Davis, invite applications for a tenure-track position in Mind & Brain Sciences. The appointment will be at the Assistant Professor level. Applications are sought from scholars who have strong and innovative research portfolios that focus on both the human mind and the human brain and that would complement the existing research at the Center for Mind & Brain (http://mindbrain.ucdavis.edu ). This could involve any state-of-the-art methodological approach (including but not limited to imaging, electrophysiology, stimulation, modeling, genetics, neuropsychology, behavior/psychophysics, and child/life-span development) and any content area that integrates mind and brain and is synergistic with existing research at the Center for Mind & Brain. Applicants must have a Ph.D. in psychology, neuroscience, statistics, biomedical engineering, or related field, or an M.D. with specialization in neurology, psychiatry, radiology, or a related field (must be completed by the first day of courses, September 24, 2015); a strong commitment to high quality teaching; and the potential to attract, or an established record of attracting, substantial extramural funding. The successful applicant will hold an academic appointment in the Department of Psychology and will contribute to the graduate and undergraduate teaching programs of that department (and will likely participate in the University-wide Neuroscience Graduate Program). The individual’s laboratory will be located at the Center for Mind and Brain, an interdisciplinary research center with 18 core faculty and a dedicated research staff. The Center offers an impressive array of modern research equipment, including several high-density EEG/ERP recording labs and a transcranial magnetic stimulation laboratory. Center faculty also have access to three research-dedicated MRI scanners at the Imaging Research Center (http://ucdirc.ucdavis.edu ), including a new 3T Siemens Skyra system and a BrainAmp MR system for simultaneous EEG/MRI. The cognitive neuroscience community is extremely well integrated across campus, with exceptionally collegial interactions and collaborations among members of the Center for Mind & Brain, the Center for Neuroscience, the MIND Institute, and the Imaging Research Center. We also have close ties with many academic departments and with the UC-Davis Medical Center. Applicants should submit a curriculum vitae, statements of research and teaching interests, representative reprints and/or preprints, and at least three letters of recommendation electronically at: https://recruit.ucdavis.edu/apply/JPF00384 The position will remain open until filled. Applications submitted by November 1st, 2014 will receive full initial consideration. For information, contact the Search Committee Chair, Dr. Steve Luck, sjluck(a)ucdavis.edu. The University of California, Davis, the Center for Mind & Brain, and the Department of Psychology are interested in candidates who are committed to the highest standards of scholarship and professional activities, and to the development of a campus climate that supports equality and diversity. The University of California is an affirmative action/equal opportunity employer. -------------------------------------------------------------------- Steven J. Luck, Ph.D. Director, Center for Mind & Brain Professor, Department of Psychology University of California, Davis Room 109 267 Cousteau Place Davis, CA 95618 (530) 297-4424 E-Mail: sjluck(a)ucdavis.edu Web: http://mindbrain.ucdavis.edu/people/sjluck Calendar: http://www.google.com/calendar/embed?src=stevenjluck%40gmail.com&ctz=Americ… --------------------------------------------------------------------

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Freesurfer September 2014