Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

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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Re: [Freesurfer] Running recon-all on external hard-disk?
by Shane Schofield 17 Feb '17

17 Feb '17

Hi Z K, Thanks. I had thought that the recon-all speed will run much slower on the external HD but 10 hours seems to be the average recon-all time so I am pleasantly surprised. Best Wishes, Shane

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Running recon-all on external hard-disk?
by Shane Schofield 17 Feb '17

17 Feb '17

Hello, I am new to image analysis and I have a basic question: is it recommended to run recon-all on external hard-disks (USB3.0) to save space on my laptop? Will there be any issues with regards to the performance of recon-all? I have just finished a recon-all on 1 subject and it took me 10 hours. System spec is Mac Book Pro 13” 2016 model: 2 ghz Intel core i5. 8GB ram. Thank you. Shane

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