Freesurfer

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30088 discussions

About recon-all
by bowang21＠mail.ustc.edu.cn 06 Mar '12

06 Mar '12

Dear all, I have just ran the command 'recon-all'. recon-all -i 3098704 -s BianYP -sd /home/wb/test/ -all In the parameters,3098704 is a function slice,but this parameter need a anatomical volume.Could it can find the correct ones itself? Whether the anatomical volume is just 3D slice or 2D ?

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Flags to align per-run motion-corrected functional volumes?
by Alex Kell 06 Mar '12

06 Mar '12

Hi Freesurfers, I am using preproc-sess in Freesurfer/Fsfast 5 with per-run motion correction (these subjects have a lot of between-run motion), and I want to analyze the volumes in each subject's individual space (I'd prefer native functional space, but I am happy to do it in each subject's anatomical space). Do preproc-sess, mkanalysis-sess, or selxavg3-sess have any built-in flags that would automatically align the functional volumes using the 6 rigid parameters generated from bbregister? Or do they have a built-in way to align and to upsample the functional volumes to the subject's anatomical space (not the surface)? I am happy to upsample each run's functional volume to anatomical space with an mri_vol2vol call, and then to estimate my glm with selxavg3-sess on these volumes. But I figure there may be some flags that do this automatically. I've looked through the documentation and I haven't found these flags. Is this possible to do automatically? Thanks, guys! Alex Kanwisher Lab Manager McGovern Institute for Brain Research MIT

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Experiences with GPU-assisted recon-all
by Abdulkadir Ahmed 06 Mar '12

06 Mar '12

Dear SPM community, Freesurfer supports GPU acceleration since version 5.0. To assess the utility of this functionality, particularly the gain in performance, I performed `recon-all` with and without the option `-use-gpu`. I'd like to share the result and also hope to get some answers to the question that came up. The Video card used was a GeForce GTX 460 and the CPU was an Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz. 1) cudadetect did not recognize the video card Detecting CUDA... *** No CUDA enabled device(s) detected! *** 2) mri_em_register_cuda called without parameters gave following output nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0.2.1221 Driver : 3.20 Runtime : 3.20 Acquiring CUDA device Using default device CUDA device: GeForce GTX 460 ... 3) Running mri_em_register_cuda was about 4 times faster than mri_em_register. During execution of mri_em_register_cuda, the GPU load was at 20% as indicated by `nvidia-smi -a` 4) Running `recon-all` with `-use-gpu` option took 6:49 hours and without the option it took about 20 Minutes longer. A summary of the processing steps taken from `recon-all-status.log` is attached to this email. Note, that these times represent wall clock times, not CPU times. Hopefully this information will be helpful. The processes "EM Registration" and "CA Normalize" were significantly accelerated by the GPU, as expected. Also "SubCort Seg" ran much faster. "Surf Reg rh" ran 3.4 times faster with GPU acceleration while the accelerated version of "Surf Reg lh" was slower than the regular. What binary was used in these steps? What could be the reason for the difference between hemispheres (I assume lh/rh means left/right hemisphere)? Bug? Problem with the data? According to `-recon-all`, following binaries support GPU acceleration mri_em_register, mri_ca_register, mris_inflate and mris_sphere. Cold someone point out what binaries correspond to the 64 steps reported in the "scripts/recon-all-status.log"? This would enable to identify the steps that have GPU-accelerated variants. The GPU performance was at 20% while CUDA binaries were executed. What could be the reason for this, i.e. why not 100%? Is this even expected on the GeForce GTX 460? What are the limitations when running multiple GPU-accelerated instances of `recon-all`? How many GPU memory does a single instance take at max? What could be the reasons that `cudadetect` failed to detect any CUDA devices, yet CUDA binaries worked as expected? Best regards, Ahmed Abdulkadir -- Master Student, Life Sciences, Semester 4 Medical Image Processing (MIP) Lab École Polytechnique Fédérale de Lausanne Student Assistant Functional Brain Imaging (FBI) Department of Neurology University Medical Center Freiburg Breisacher Str. 64, D-79106 Freiburg --

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Re: [Freesurfer] Output volume defined by pial surface/red line
by Douglas N Greve 06 Mar '12

06 Mar '12

Yes, you can do this in a few steps. Use mri_binarize to convert the ribbon.mgz into a binary mask of just the cortex (use the --match option). Then use mri_binarize with aseg.mgz to get the hippocampus (17 for left, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then add them together with fscalc. Then use mri_mask with brain.mgz as the input and the result from above as the mask. doug octavian lie wrote: > Dear Bruce and Doug, > > I want to clarify what I need. > I would need to export to nii.gz a brain volume which has to be : > - T1, > - contain gray and white matter inside the pial surface, without > white-gray segmentation (the source analysis program downstream in the > pipeline needs to complete this step in order to function). > - in addition to the pial contents, it should contain > hippocampi/amygdala as per aseg process, but exclude cerebellum > - the volume inside the pial surface has to be "real", not binary.(if > binary, gray should be darker than white, and not sure if this would > work with the source analysis program I run). > > If I try to export volumes such as brain.mgz, or brain.finalsurf.mgz, > the extra dura/scalp *outside* of the pial surface (red line, fig) is > also exported. Again, I am working at editing the pial surface to > remove extra dura inside the red line; this is a work in progress, > including customizing early recon-all steps/ implenting Andre's > protocols. My problem is how to exclude tissues* outside* the pial > surface/ red line, except hippocampi/amygdala. > Can I create a pial/hippocampal mask excluding everything outside the > red line/hippocampal/amygdalar volumes, which then I could align to a > "real" brain, such as brain.mgz to get the brain inside the calculate > pial surface? If so, how you would proceed? > > Thank you for your suggestions. > > See also my previous message: > > > Dear All, > > I am increasingly fascinated by freesurfer. > Here is a rookie issue: I use a source imaging program that is rather > simple-minded in its MRI processing steps. To be able to use the > inverse solution tools of that program, I need to use 2 volumes: > - a head MRI to be used to electrode coregistration > - a skull-stripped brain MR without cerebellum, including both the > gray and white matter; the program needs to perform its own white > matter extraction to generate the gray matter volume to be used as > source space. > - both MRs have to be subject to the same transforms, if any, and have > to have the same origin and coordinate systems (like real > head/brain pairs). > > So first, I am in the search of the "best" brain extraction possible, > with as little dura included as possible. Besides trying to > implement Andre's dura protocols, and editing the pial surface for > brainmask.mgz, then running the rest of the recon-all steps, I need > to be able to export in nii.gz format a volume having its pial surface > as calculated by freesurfer. > When exporting brain.finalsurfs.mgz with mri_convert, it looks that > the calculated pial surface (red line) as visualized with tkmedit subjid > brain.finalsurfs.mgz -surfs is ignored in the nii.gz file. When the > output nii volume is imported in programs such as Bioimage Suite, > I essentially see what looks like the outside (surface) brainmask.mgz > volume as in tekmedit but not accounting for the calculated pial > surface. How can I export brain.finalsurfs.mgz with its calculated > pial surface as a nii volume? In other words, I would need a > ribbon.mgz type volume to include the white matter on the inside. I > suppose it comes down to adding options to the mri_convert > brain.finalsurfs.mgz step after surfaces have been generated, but I > would need some guidance > Please advise. > > > Octavian. > > > > > > 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. > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Matched sample
by Jacquelynn Nicosia Copeland 06 Mar '12

06 Mar '12

Hi there FreeSurfers, I was thinking about using a propensity matched control sample for a study I am conducting that includes FS data. I would want to match each patient (i.e., MCI) with a specific control (re-using some controls multiple time(s) using the propensity matching, and then using paired sample statistics. However, when looking on FS about qdec and group analyses using the command stream, I didn't see any information about if/how to set up a paired sample. Is it possible to do a matched paired sample (reusing control pts) with FS? If so, where I could get more information on it? Thank you, Jacquie Jacquelynn N. Copeland, M.A. Doctoral Candidate Medical/Clinical Psychology Program Department of Psychology University of Alabama at Birmingham Email:jcopeland@uab.edu ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Tuesday, March 06, 2012 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 97, Issue 8 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. controls points in 5.1 (Chris Hyatt) 2. mri_vol2surf error writing to nifti volume (Tina Jeon) 3. mri_cvs_register on a 64-bit Mac crash PETSC ERROR (Rey Ramirez) 4. (no subject) (Ryan) 5. overlaying sig.mgh onto normalized individual brains (Catherine Wan) 6. Re: (no subject) (Bruce Fischl) 7. Ask question about QAtools (chenchunhuichina) 8. Re: pwd: permission denied (Marcel Zwiers) 9. Re: mri_cvs_register on a 64-bit Mac crash PETSC ERROR (Bruce Fischl) 10. about QAtools (chenchunhuichina) 11. About recon-all (bowang21(a)mail.ustc.edu.cn) 12. Re: About recon-all (Bruce Fischl) 13. Research scientist in MRI imaging ? three-year contract available immediately (Fr?d?ric Andersson) 14. Re: about QAtools (Louis Nicholas Vinke) 15. PhD / Post-Doctoral position ? Neuroimaging of language and audition, University of Geneva (Narly GOLESTANI) ---------------------------------------------------------------------- Message: 1 Date: Mon, 05 Mar 2012 16:48:24 -0500 From: "Chris Hyatt" <Chyatt(a)harthosp.org> Subject: [Freesurfer] controls points in 5.1 To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4F54EE580200002D0002B061(a)gwmail1.harthosp.org> Content-Type: text/plain; charset=US-ASCII Bruce, You had posted that there is a 'backwards compatibility flag' regarding control points manually specified to the aseg normalization in Freesurfer version 5.1 (see your thread from 1/27/12 below). You said that Nick might know about this flag. I too had noticed very different behavior after adding control points in v5.0 and v5.1, as many more regions were tagged as white matter in v5.1 than in v5.0. Would anyone know if this flag exists and how to use it? Thanks, Chris Re: [Freesurfer] control point guidanceBruce Fischl Fri, 27 Jan 2012 11:58:38 -0800 Hi Mikeit's a bit hard to state the region of effect for the control points. Essentially we go through and label voxels as control points or not based on their intensity, intensity gradient and connectivity (that is, the must be 6-connected to other control points) then build a Voronoi diagram and each control point sets the scaling for its Voronoi triangle. Thus if you have a control point surrounded by others its region of effect is small, but one control point all by itself can have a large region of effect.Also, 5.1 applies the manually specified control points to the aseg normalization (norm.mgz), whereas older versions didn't. Not everyone is happy with this, so I think there is a backwards compatibility flag. Nick would know.Bruce ------------------------------ Message: 2 Date: Mon, 5 Mar 2012 21:55:38 +0000 From: Tina Jeon <Tina.Jeon(a)utsouthwestern.edu> Subject: [Freesurfer] mri_vol2surf error writing to nifti volume To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <C567682DBD3D104CA75A281451264BA301E4B5FC(a)swmsmailstu.swmed.org> Content-Type: text/plain; charset="us-ascii" Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing "SetSlice $gnVolSlice [set gnVolSlice]" invoked from within ".w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc" (command bound to event) ________________________________ UT Southwestern Medical Center The future of medicine, today.

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overlaying sig.mgh onto normalized individual brains
by Catherine Wan 06 Mar '12

06 Mar '12

Dear Freesurfer-list, Please excuse me if this question sounds very simple. I work with lesion brains and I want to overlay the group level result (sig.mgh) onto individual brains to check whether it covers the lesion (which we don't want). I first used mri_surf2vol to convert sig.mgh to a volume. I then mri_vol2vol to normalize the individual T1.mgz to the fsaverage T1, but when I overlaid the sig.mgz onto the normalized T1, it didn't look well-registered (see attached jpeg). However, when I overlaid the same sig.mgh onto the fsaverage T1, it looked completely fine. I'm wondering if anyone could tell me how to better register the individual T1 so I can check whether the individual lesion overlaps with the group level results? Some of the brains went through tkregister2 and the segmentation looked fine afterwards. Any guidance would be much appreciated! Regards, Catherine

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PhD / Post-Doctoral position – Neuroimaging of language and audition, University of Geneva
by Narly GOLESTANI 06 Mar '12

06 Mar '12

PhD / Post-Doctoral position – Neuroimaging of language and audition, University of Geneva ------------------------------------------------------------------------------------------------------------- Applications are invited at the PhD or at the Post-Doctoral level at the Department of Clinical Neuroscience at the University of Geneva in Switzerland, under the supervision of Professor Narly Golestani. Projects will include developing new methods to analyze aspects of brain morphology using structural MRI, and applying these in the context of normal variability, disease, and expertise. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field, and experience with analysis of structural MRI data and with programming are highly desirable. Applicants should have a strong interest in neuroscience and ideally also in research on language and audition. The position can start as early as April 1st 2012, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani@unige.ch(https://webmail.unige.ch/horde/imp/message.php?index=6)). Applications including a CV, a statement of research interests, and the names and full contact details of two referees should be sent to: Narly.Golestani@unige.ch(https://webmail.unige.ch/horde/imp/message.php?index=6).

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Research scientist in MRI imaging – three-year contract available immediately
by Frédéric Andersson 06 Mar '12

06 Mar '12

Research scientist in MRI imaging – three-year contract available immediately The Physiology of reproduction and behaviour combined research unit at the INRA centre of Tours is recruiting a research scientist specialised in MRI for its imaging platform. This internationally recognised facility for imaging of medium sized domestic animals will be equipped with a 3T MRI, an X-ray scanner and an ultrasound echography machine. The facility employs seven staff including a veterinary surgeon, and technical staff to prepare the animals, anaesthetise, and provide pre- and post-operative care. The recruited scientist will carry out MRI imaging experimentations on different domestic animal models (pig, sheep, goat and rabbit). The main areas of investigation are the abdomen and the central nervous system. The successful candidate will have contact with many different people involved in the protocols of the different research teams. Within the department he/ she will be in charge of developing and adapting the imaging protocols (MRI) for domestic animals. The job will involve analysing the imaging needs of the different research teams and developing innovative and appropriate methodologies to meet these needs. The recruited scientist will take part in training and teaching sessions. He/ she will be required to integrate the national and European medical imaging networks, and to draw up close links with the imaging teams from the Medical School and Teaching Hospital of Tours, where these imaging techniques are developed on clinical models, integrating the network of skilled staff for these structures. This position does not involve any specific constraints. The job will involve: • Studying the needs related to the research aims of resident and partner teams; • Proposing suitable imaging strategies (from acquisition to analysis) for the research problematics of these teams, in terms of acquisition protocol, sequences and parameters; • Optimising the existing MRI acquisition procedures for humans for use with animal models; • Developing original MRI sequences corresponding to the scientific problematics of the users; • Ensuring technological intelligence in the field of MRI sequences; • Promoting original developments within the scientific community of MRI “methodologists”; • Training users in original acquisition procedures developed for their needs; • Liaising with the manufacturers of the MRI system for software updates, upgrading and maintenance; • Organising and checking preventive maintenance and repairs in liaison with the manufacturers; • Carrying out quality checks on acquisitions; • Coordinating use of the system; • Overseeing measurement taking, interpretation of results and their validation for scientific analysis in compliance with the quality system; • Managing the technical resources allocated to a research project or protocol; • Presenting, disseminating and promoting achievements and results. Taking part in teaching both in higher and continuing education, contributing to training of students through research, training and advising users on the deployment of the experimental systems; • Managing technical documents relating to the domain; • Taking part in the research projects of the Unit’s teams. Skills required: - In-depth knowledge of NMR physics, and in vivo NMR imaging and spectroscopy; - In-depth knowledge of MRI instrumentation and sequence programming; - Ability to analyse images and process signals; - Interest in programming; - Good relational skills in a multi-displinary context; - An operational level of scientific and technical English (good oral and written comprehension); - Skills in X-ray imaging would also an advantage; - Basic knowledge of physiology would be an advantage. Know-How - Quality control; - Technological intelligence/ literature search; - Scientific promotion; - Organisational management; - Ability to integrate various elements relating to different technological fields (magnetism, computing, electronics, etc); - Know-how in experimental imaging of large animals would be an advantage. Required training/ professional experience - PhD in biophysics, physics, image analysis or signal processing, and/or an engineering degree in the same fields with skills in nuclear magnetic resonance (NMR); - Experience in NMR sequence programming for in vivo imaging; - A qualification in animal experimentation is recommended. - Post-doc professional experience is highly recommended. Personal qualities: Capacités personnelles : - Good human skills and ability to work in a team in a multi-disciplinary context; - Good communication and organisational skills; - Good animal skills; - Thorough. Contact: Send your CV and cover letter to: Yves Tillet, INRA-PRC, UMR7247, Directeur de l'FR135 "Imagerie Fonctionnelle", 37380 Nouzilly mail : yves.tillet(a)tours.inra.fr Tel : 02 47 42 77 98 (secretary)

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About recon-all
by bowang21＠mail.ustc.edu.cn 06 Mar '12

06 Mar '12

Dear all I just want to ask a sample question.What's the best number of the parameter of 'recon-all' , -i invol1 -i invol2.That is, how many slices should we use?If the invol1 is the fist slice of the fMRI series or any one of the data? Yours

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mri_cvs_register on a 64-bit Mac crash PETSC ERROR
by Rey Ramirez 06 Mar '12

06 Mar '12

Dear colleagues, especially Lilla Zollei, I am trying to run mri_cvs_register on a 64-bit Mac but it crashes at the same place where other people had reported a problem. I tried updating mri_cvs_register from ftp as recommended in: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018786.html but that didn't help. The problem seems to be the exact same problem mentioned on this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-December/021457… I paste a small chunk of the log below at the point the PETSC ERROR occurs. I attach the whole log file. Has anyone come up with a solution? Thanks so much for your help, Rey ... setting bc 51.75 25.0698 42.9884 -> 0 0 0 instead 51.76 25.0798 42.9984 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 77063 Total BCs = 527338 no-eqs = 209160 surf2vol(51421) malloc: *** mmap(size=251830272) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 251828644! ... -- Rey R. Ramírez, Ph.D. MEG Brain Imaging Center Institute for Learning & Brain Sciences Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 e-mail: rrramir(a)uw.edu Tel: (206) 543-6484 Fax: (206) 221-6472 Cell: (619) 709-3590

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