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HCP Course 2019: Get ready for more data, and a new way of getting it
by Jennifer Elam 05 Mar '19

05 Mar '19

External Email - Use Caution *More HCP data are coming....and will be released in a new way.....will you be ready? * This spring, the first data from the Lifespan Human Connectome Projects - (HCP) Development (healthy subjects ages 5-21) and HCP Aging (ages 36-100+) will be publicly released. Yay! Also, for the first time, we will be releasing these data on the cloud, via the NIMH Data Archive (NDA). This will enable computing on the cloud to analyze HCP and Lifespan data. Come to the 2019HCP Course: "Exploring the Human Connectome" <https://store.humanconnectome.org/courses/2019/exploring-the-human-connecto…> <https://store.humanconnectome.org/courses/2019/exploring-the-human-connecto…> , July 8 – 12, 2019 in Portland, Oregon, USA to learn all about the new data, how to access it on NDA, and using HCP methods, tools, and pipelines on your own neuroimaging data. This 5-day intensive course will provide training in acquisition, processing, analysis and visualization of whole brain imaging and behavioral data of humans and non-human primates using methods and tools developed by the WU-Minn-Oxford HCP consortium. Both new and current users of HCP data, methods, and tools are welcome and the course will cover both basic and advanced topics. For more info and to register visit the HCPCourse 2019 website <https://store.humanconnectome.org/courses/2019/exploring-the-human-connecto…> . If you have any questions, please contact us at: hcpcourse(a)humanconnectome.org We look forward to seeing you in Portland! Best, 2019 HCP Course Organizers -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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Computing LGI using Octave instead of Matlab
by Natasha Sharma 05 Mar '19

05 Mar '19

External Email - Use Caution Hello all, Is there a way to run LGI commands listed below using Octave instead of Matlab? I've read somewhere on the forums of being able to get Freesurfer to use Octave instead of Matlab in FSFAST but I'm not sure if it will work with the commands below. Could I please get instructions on how to do this? mris_compute_lgi --i lh.pial mris_compute_lgi --i rh.pial Any help is appreciated! Thank you.

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Processing MEMPRAGE
by Rusche, Johann 05 Mar '19

05 Mar '19

Dear Freesurfers, Reading through the mailing list I understood how to process our nmr MEPRAGEs and I would like to double-check we are using unpacksdcmdir correctly. Unpacking with unpacksdcmdir gives me two nifti files, a 4-echo nifti file (92MB) and a 1-echo nifti file (23MB). Am I correct to understand that the smaller 1-echo nifti file is the RMS created automatically? Can you confirm that this is the file that I want to send to recon-all vis-a-vis VBM processing? >From the unpacklog: 7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso ok 256 256 176 4 MR.1.3.12.2.1107.5.2.19.45407.2014103021271096561867095 8 MEMPRAGE_tfl_mgh_multiecho_1mm_iso ok 256 256 176 1 MR.1.3.12.2.1107.5.2.19.45407.2014103021271165037167199 Thanks for your time! Johann __________________ Johann Rusche Graduate Research Student, Lazar Lab Department of Psychiatry – Neurosciences Massachusetts General Hospital

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Should I edit or reject?
by Ryan Wales 05 Mar '19

05 Mar '19

External Email - Use Caution Hi, Although there are many ways to correct for pial, WM, and segmentation defects, it seems common in the literature to forego any edits and simply either accept or reject a subject's FreeSurfer output in order to avoid subjectivity and potential over-editing. Another group rejected subjects if their defects spanned 6 or more slices, for example. Are there any guide lines on how much editing is too much editing? Should it just be edited enough so it looks tolerable by eye? Maybe by a few different raters? The defects vary in their severity, so it's difficult to know if a subject should be considered passable or requiring edits based on a minor defect. My current plan is to conduct my analysis once with excluding subjects with poor segmentation and then again, including those subjects' edited outputs. Do you agree with this logic? Thanks for your advice, Ryan -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wales(a)stonybrook.edu <ryanwales(a)stonybrook.edu>

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Re: [Freesurfer] Surface to Volume Conversion
by Bunting, Emma 05 Mar '19

05 Mar '19

External Email - Use Caution Hi Bruce, Yes, the brains were registered in fsaverage space. The issue I am facing is my sig.mgh output from GLM will not convert into a .nii file using mri_convert. I am trying to load them both as overlays not view them directly. The sig.mgh file loads fine, it is the .nii file that sees the problem. Similarly, if I do GLM directly with a .nii output, I see the same issues. You asked me to run mri_info on both the .mgh and .nii.gz files, which I gave in my previous email. Please let me know how to proceed from here! Best wishes, Bruce Fischl<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 04 Feb 2019 06:31:00 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Hi Emma the dimensions (163842 x 1 x 1) mean that these are overlays on the fsaverage surface. Can you remind me what issue you are trying to solve? cheers Bruce External Email - Use Caution Hi Bruce, I ran the mri_info command on the sig.mgh and the sig.lh.nii.gz files for participant 124 and got these outputs... For sig.mgh: Volume information for sig.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 For sig.lh.nii.gz: Volume information for sig.lh.nii.gz type: nii dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -68267.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -2.5000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 13653.5000 0.0000 0.0000 1.0000 -3.0000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 13653.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 3.0000 -0.0000 -0.0000 -0.0000 1.0000 Please let me know if you need any other information in order to help with our problem, Best wishes, Emma Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ 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: Monday, February 4, 2019 5:00:09 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 180, Issue 5 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. gray matter volume of the entorhinal cortex (Laboratorio de Neurociencia Funcional) 2. Re: problem using recon-all (Shachar Gal) 3. Re: problem using recon-all (Glasser, Matthew) 4. Re: Surface to Volume conversion (Bunting, Emma) 5. Re: gray matter volume of the entorhinal cortex (Bruce Fischl) 6. Re: Surface to Volume conversion (Bruce Fischl) 7. Re: gray matter volume of the entorhinal cortex (Laboratorio de Neurociencia Funcional) 8. free surfer install issues (Jordan Fowler) 9. Re: free surfer install issues (Greve, Douglas N.,Ph.D.) 10. (no subject) (Jordan Fowler) ---------------------------------------------------------------------- Message: 1 Date: Mon, 4 Feb 2019 10:08:06 +0100 From: Laboratorio de Neurociencia Funcional <neuroaginglnf(a)gmail.com> Subject: [Freesurfer] gray matter volume of the entorhinal cortex To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CABUYonO85t9vP8NBw9HtWuET2n4i-9s-Q_LevCxZ_rK3U4YAew(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfers, gray matter volume of the entorhinal cortex (EC) can be obtained either in the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all our T1 images were manually edited on a slice-by-slice basis to correct pial surface misplacements and erroneous white matter segmentation, which volume measure of the EC would be more precise? I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats were thresholded at a specific probability value (% of case overlapping). Which probability value was used? Is there a reference paper explaining how probabilistic maps of EC were built based on ex vivo MRI contrast? Thank you in advance. Best, Jose L. Cantero

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Surface Misplacement
by Banu Femir 05 Mar '19

05 Mar '19

External Email - Use Caution Hi, I've a problem about surface placement. For my PhD thesis, I've been analyzing T1 images of 103 AD, MCI and SCI subjects. I'm using FS 6.0 stable version on Linux. Some of my data, especially AD data have a surface problem. White matter includes both white and gray matter, and CSF is included as a gray matter. So, it looks like the surfaces has shifted. (The MR images do not have any lesion). Until now, I tried to clean dura for one subject, but nothing changed. I also run reconall again for another subject, got the same result. All done in FreeView. I do not know what to do in this case. It looks like troubleshooting does not solve my problem, since mine is very complicated. I would be so happy if anyone has an idea of what can I try to do? Many thanks in advance, Banu.

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mri_vol2surf sample inside and outside of pial
by Michael Jordan 05 Mar '19

05 Mar '19

External Email - Use Caution Hi, I have a short question concerning the mri_vol2surf command. Do the following parameters of the command return the maximum volume value (for each vertex) which occurs between 10 mm outside and 10 mm inside the pial surface (along normal vector)? --projdist-max -10 10 0.25 --interp nearest --surf pial Thank you very much!! Regards Michael

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postdoc opportunity
by Bruce Fischl 04 Mar '19

04 Mar '19

see the attached job opening description. If interested contact Michael (contact info below and in attachment) Michael Zeineh, M.D.-Ph.D. Assistant Professor, Dept. of Radiology Associate Chief of Neuroradiology for Operations and IT Stanford University, Lucas Center for Imaging, Rm. P271 1201 Welch Road, Stanford CA 94305-5488 t: 650-721-1419, c: 650-722-2235, f: 650-723-1523 http://med.stanford.edu/zeinehlab.html [med.stanford.edu]

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Omitting aseg regions from segmentation
by zalewk 04 Mar '19

04 Mar '19

External Email - Use Caution Hello Freesurfer team, I am currently working processing the volumetrics of exvivo brains, many of which do not have a brainstem/cerebellum. It seems this often results in a subcortical alignment that isn't optimal, and fails to create the pial/wm surface where freesurfer attempts to label more ventral non-zero voxels as brainstem/cerebellum. Currently, I have to manually edit the aseg.auto_noCCseg.label_intensities.mgz and aseg.presurf.mgz to fix this. Is there a way to omit aseg labels (like the brainstem/cerebellum) from the processing stream that I've overlooked? If not, would there be a potential alternate solution such as creating a second atlas from the original sans these ROIs and have the cross-sectional stream still run normally? Best, Kody Zalewski

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Interpolate one volume into raster coordinate system of a second volume
by Stockmann, Jason 02 Mar '19

02 Mar '19

Hello, I apologize for asking such a basic question, but I can’t find the right tool to interpolate a NIFTI brain volume (or DICOMs) into the raster coordinates of a second volume. I simply want a naive interpolation into the second volume’s coordinate system without performing registration. For my application I do not want to actually register the two volumes, just interpolate/resample. I tried using mrivol2vol.m in Matlab but it crashes because it can’t find the field ‘mov.vox2ras0’ in my NIFTI headers (I use either mri_convert or dicm2nii to convert Siemens DICOMs to NIFTI). I then tried manually calculating the raster coordinates for the two volumes by creating integer voxel coordinates for (i,j,k) and then multiplying them by the NIFTI vox2ras matrix to get (x,y,z). I then use ‘scatteredInterpolant’ in Matlab to interpolate one volume into the second volume’s coordinate system, but this has only worked for me some of the time. I have been able to interpolate 2D axial MRI slices into an oblique 2D coordinate system, but I’m having trouble with 3D acquisitions like MPRAGE, etc. Does anyone know of a “foolproof” and simple standalone tool for this task (ideally for Matlab)? --- Jason -- Jason Stockmann Instructor in Radiology Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown, MA 02129 jstockmann(a)mgh.harvard.edu<mailto:jstockmann@mgh.harvard.edu> +1 315 450 3309

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