Freesurfer

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30133 discussions

apply CVS morph to a list of coordinates
by Donos, Cristian 20 Feb '17

20 Feb '17

Hi, I have registered a patient’s MRI over the ColinN27 with mri_cvs_register and now i need convert an electrode (or voxel) coordinate from the subject’s space to the N27 space. I found an old post in the mailing list, but it did not work for me. The coords.txt file is just one line containing 10 10 10. What am i doing wrong? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39971.html Here are the commands i used and the results : > createMorph --out fullCSVmorph.tm3d --template /Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz --subject /Volumes/Sector2/surfaces/TandonLang/TS076CD/mri/orig.mgz --in gcam /Volumes/Sector2/surfaces/TandonLang/TS076CD/TS076CD/csv/combined_toColin27_elreg_aseg.m3z atlas geometry = 256 , 256 , 256 image geometry = 256 , 256 , 256 vox 2 ras atlas = -1.000 0.000 0.000 127.000; 0.000 0.000 1.000 -111.000; 0.000 -1.000 0.000 147.000; 0.000 0.000 0.000 1.000; ras 2 vox image = -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 138.000; -0.000 1.000 -0.000 143.000; 0.000 0.000 0.000 1.000; product = 1.000 0.000 0.000 1.000; 0.000 1.000 0.000 -9.000; 0.000 0.000 1.000 32.000; 0.000 0.000 0.000 1.000; transform at origin 1.000; -9.000; 32.000; 1.000; invalid voxel count = 9071323 saveTransform code writing transform size = 49918625 writing morph to file fullCSVmorph.tm3d > applyMorph --template /Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz --transform fullCVSmorph.tm3d point_list coords.txt transformed_coords.txt linear Template name:/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz After loading template Template name:/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz After loading template extension = tm3d Exception caught while loading transform VolumeMorph load - failed to open input stream Thank you, Cristian Donos, PhD Postdoctoral Research Fellow, Department of Neurosurgery 6431 Fannin Street | Suite G.550D | Houston, Texas 77030 Phone: 979-633-9208 Email: cristian.donos(a)uth.tmc.edu<mailto:cristian.donos@uth.tmc.edu>

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Longitudinal proceesing for Pediatric data
by Dongnandi 20 Feb '17

20 Feb '17

Dear freesurfer exports, As it is mentioned in the documentation that 'pediatric data violates the fixed head size assumption' for the current longitudinal stream. Is there any solution for the issue now? Thanks Dong

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Re: [Freesurfer] issues with -T2pial option in v.5.3
by Antonin Skoch 20 Feb '17

20 Feb '17

Dear Petr, according to the screenshot, the problem is that there is quite low signal intensity in the cut-out parts of gray matter on T2 images. Apart from HCP pipelines, you can try to increase -nsigma_below parameter of mris_make_surfaces to prevent this cut-out. The default value is 3, try something higher. Or you can try dev version of freeSurfer and experiment with explicit setting of T2 intensity threshold using -T2_min and -T2_outside_min parameters. Regards, Antonin Skoch You could try with the HCP Pipelines and see if that helps: https://github.com/Washington-University/PipelinesPeace, Matt. From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Petr Bednarik <bedna...(a)umn.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, February 20, 2017 at 12:26 PM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] issues with -T2pial option in v.5.3 Hi everyone, I am using Freesurfer version 5.3. I tried to refine the pial surfaces by using -T2pial option: recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial -autorecon3 This step was helpful - e.g. it removed nicely residuals of venous sinuses, but in some subjects it also removed part of the parietal or frontal cortex, while the white matter is appropriately segmented. https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?dl =0 The T2-space images had the same resolution as T1-MPRAGE (1x1x1mm) and were acquired in the same session (3T Siemens Trio, standard 32 channel coil). The problem does not seem to be caused by T2 misregistration : https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0 Question : What could cause this error and how could I extend pial surfaces and get correct final segmentation ? Thanks a lot ! PB

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issues with -T2pial option in v.5.3
by Petr Bednarik 20 Feb '17

20 Feb '17

Hi everyone, I am using Freesurfer version 5.3. I tried to refine the pial surfaces by using -T2pial option: recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial -autorecon3 This step was helpful - e.g. it removed nicely residuals of venous sinuses, but in some subjects it also removed part of the parietal or frontal cortex, while the white matter is appropriately segmented. https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?d… <https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?d…> The T2-space images had the same resolution as T1-MPRAGE (1x1x1mm) and were acquired in the same session (3T Siemens Trio, standard 32 channel coil). The problem does not seem to be caused by T2 misregistration : https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0 <https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0> Question : What could cause this error and how could I extend pial surfaces and get correct final segmentation ? Thanks a lot ! PB

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hippocampal subfields in average space
by Tuominen, Lauri Johannes 20 Feb '17

20 Feb '17

Hi everyone, Is there a template of the hippocampal subfields in some average space? Best Lauri Tuominen

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Hippocampus eTIV correction (LONGITUDINAL)
by Sebastian Huhn 20 Feb '17

20 Feb '17

Dear Freesurfer community, I wondered, how you correct the longitudinal hippocampus segmentation for total intracranial volume. Our cross-sectional analysis is corrected for total intracranial volume as described, for example, in Kerti et al. 2013 Neurology ( http://dx.doi.org/10.1212/01.wnl.0000435561.00234.ee ). They used this formula: adjusted volume = raw volume - b*(ICV - mean ICV). The coefficient b represents the slope of regression of a region-of-interest volume on ICV. Now I am curious how to perform such a correction for intracraial volume for our longitudinal data. Do I correct for example the longitudinal hippocampus volume for timepoint 1, for eTIV found in SUBJECT.long.template/stats/aseg.stats, or for eTIV of the template, or anything else? Or are such corrections even neccessary for longitudinal runs? Thanks a lot for helping me out of my confusion. Best, Sebastian

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Hipposubfield outputs 6.0
by stdp82＠virgilio.it 20 Feb '17

20 Feb '17

Hi list,I wonder whether in the 6.0 the hipposubfield outputs needs for nomalization (by diving for 3 the volumes as well as the 5.3) or they are already corrected?Thanks Stefano

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Trying to download FreeSurfer 6
by Jose Enrique Romero Gómez 20 Feb '17

20 Feb '17

Hello, I'm trying to download FS6 but always get a timeout error. This is the link I'm using: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz And this is the error message *Connection to 132.183.202.158 failed.* The system returned: *(110) Connection timed out* The remote host or network may be down. Please try the request again. Thanks! Jose

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Neurohackweek 2017: a summer school in human neuroscience and data science, September 4th-8th
by Ariel Rokem 18 Feb '17

18 Feb '17

We are happy to announce a call for applications to participate in the Neurohackweek summer school for neuroimaging and data science. This 5 day hands-on workshop, held at the University of Washington eScience Institute in Seattle, will focus on technologies used to analyze human neuroscience data, on methods used to extract information from large datasets of publicly available data (such as the Human Connectome Project, OpenfMRI, etc.), and on tools for making human neuroscience research open and reproducible. Morning sessions will be devoted to lectures and tutorials, and afternoon sessions will be devoted to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. For more details, see: http://neurohackweek.github.io/ We are now accepting applications from trainees and researchers in different stages of their career (graduate students, postdocs, faculty, and research staff) to participate at: https://form.jotformeu.com/70342294106348 Some experience in human neuroscience and at least basic knowledge in programming is desired, but we welcome applications from participants with a variety of relevant backgrounds. Accepted applicants will be asked to pay a fee of $200 upon final registration. This fee will include participation in the course, accommodation in the UW dorms, and two meals a day (breakfast and lunch), for the duration of the course. A limited number of fee waivers and travel grants will be available. We encourage students with financial need and students from groups that are underrepresented in neuroimaging and data science to apply for these grants (see application form for details). Important dates: April 18th: Deadline for applications to participate May 6th: Notification of acceptance June 1st: Final registration deadline On behalf of the instructors, Ariel Rokem, UW eScience Tal Yarkoni, UT Austin

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How to measure hippocampal, ventricle and temporal lobe volume & thickness
by Jing Gu 17 Feb '17

17 Feb '17

Dear FreeSurfer Developers, I am trying to measure hippocampal, ventricle and temporal lobe volume & thickness. Could you let me know the coding? Freesurfer Version : 5.0, unix Have a good weekend. Gina

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