Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

Graduate student positions available
by Stephanie Otto 21 Oct '20

21 Oct '20

External Email - Use Caution Greetings Freesurfer Community! The Cognitive and Brain Sciences<http://groups.unr.edu/unr_psych_cbs/CBS_grad_program/> (CBS) group in the Department of Psychology at the University of Nevada, Reno have graduate positions open for Fall 2021, specifically in the labs of Dr. Edward Ester, Dr. Lars Strother, Dr. Marian Berryhill, and Dr. Sarah Haigh. The CBS program has a strong concentration in vision science with 11 faculty working in different areas of vision. We strongly encourage students from diverse and under-represented backgrounds to apply. Please see additional opportunities through the Graduate School<https://www.unr.edu/grad/initiatives>, including the NSF GAIN Scholars program. Students can apply either to the Cognitive and Brain Sciences Program or the Graduate Program in Integrative Neuroscience. UNR was recently awarded Carnegie R1 status and has a fast-growing multi-disciplinary Neuroscience program. Resources for neuroimaging are provided through the Center for Integrative Neuroscience (an NIH COBRE award), including 3T fMRI, high-density EEG, fNIRS, and Adaptive Optics. The Center also houses a research core supporting applications of Virtual and Augmented Reality, and a core for Cellular and Molecular Imaging including confocal and 2-photon microscopy. Reno is located next to the Sierra Nevada near Lake Tahoe, and has been rated one of the best small cities in the US for outdoor recreation and overall quality of life. Read below for information on specific labs that are recruiting graduate students: Dr. Ester is recruiting a student to work on an NSF-funded project<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nsf.g…> that explores relationships between short-term memory and motor control. The student will have the opportunity to learn multiple techniques used to measure human brain activity (EEG, fMRI, and tDCS) and gain a strong quantitative skill set. The Strother lab studies visual perception and object recognition using behavioral experiments and fMRI. We are currently investigating neural mechanisms that allow us to perceive and recognize stimuli and support social and linguistic behaviors (e.g. faces, bodies and words). We are seeking Ph.D. students to develop and implement: (a) psychophysical experiments that measure visual performance during various perceptual tasks; and (b) fMRI experiments that rely on multivariate analysis of the data to measure the neural coding of visual object information in the brain. Dr. Berryhill<https://packpages.unr.edu/mberryhill/> and Dr. Haigh<https://packpages.unr.edu/shaigh/> are seeking two joint students to work on an NIMH-funded project focusing on biomarkers of schizophrenia that are evident in individuals with high schizotypy (subclinical individuals who exhibit schizophrenia-like behaviors). Students will learn and conduct studies using behavioral psychophysics and electroencephalography (EEG), to investigate sensory and working memory. _____ Dr. Sarah Haigh Assistant Professor, University of Nevada, Reno, Department of Psychology and Center for Integrative Neuroscience, 1664 N. Virginia Street Reno, NV 89557-0296 Tel: +1 (775) 682-9885 https://packpages.unr.edu/shaigh/ Follow us @HaighLab

1 0

Help to create flattened images of the whole brain
by Ornaith O Reilly 21 Oct '20

21 Oct '20

External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting to get a flattened patch of an entire hemisphere. Below is a page outlining how to use mris_flatten to achieve this: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I am just trying to achieve this with the tutorial data to start with. 1. First problem is that when I run the command 'tksurferfv bert lh inflated'; I am getting the error outlined in Image 1. 2. I realised that I could create a patch using freeview instead of tksurfer. However I attempted to follow the instructions on the page above to do this and ran into some problems. Image 2 shows an example of the patch that I created and image 3 shows the error that I get when I attempt to press the Press Fill Uncut Area button (I tried this many times and got the same result). 3. However one time I did succeed in making a patch (I don't know what I did differently this time?) - see image 4 attached. I saved it as lh.full.patch.3d. When I tried to run the command mris_flatten below I got the error outlined in image 5. mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d The version of Freesurfer and the platform that I'm using is outlined below: 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: macOS High Sierra 10.13.6 (17G7024) If anyone could shed some light on any of these errors or suggest an alternative method it would be greatly appreciated. Thanks a lot. Kind Regards Ornaith O'Reilly

1 0

Estimating the memory footprint of Longitudinal Stream?
by Paul Wighton 21 Oct '20

21 Oct '20

External Email - Use Caution Hi FreeSurfers, Is there any guidance on how to estimate the memory footprint of the Longitudinal steam? We are trying to process the MacLaren test-retest dataset [1] (40 timepoints per subject) with the longitudinal stream in v7.1.1 and are running into memory errors during `mri_fuse_segmentations`. Thanks, -Paul [1]: https://openneuro.org/datasets/ds000239/versions/00001

2 2

replace the vertex_label_index in .annot file
by 1248742467 20 Oct '20

20 Oct '20

External Email - Use Caution hello, Previously, rh.white and rh.aparc.2009s.annot were used to generate vertex_id and vertex_label,  ' from freesurfer_surface import Surface from freesurfer_surface import Label from freesurfer_surface import Annotation surface = Surface.read_triangular('rh.white') surface.load_annotation_file('rh.aparc.a2009s.annot') with open("rhlabels.txt","w") as f: for vertex_index, vertex in enumerate(surface.vertices): vertex_label_index = surface.annotation.vertex_label_index[vertex_index] vertex_label = surface.annotation.labels[vertex_label_index] #print(vertex_index, vertex, vertex_label) #f.write("vertex_index:{} vertexlabel:{} \n".format(vertex_index, vertex_label)) f.write("vertex_index:{} vertex_label:{}\n".format(vertex_index, vertex_label)) ' the output:vertex_index:0 vertexlabel:Label(name=S_precentral-sup-part, index=70, color=#1514c8) and the label_index obtained after a certain algorithm was updated to replace the vertex_labe_index in rh.aparc.2009s.annot, and then load the result with freeview. But I don't know how to replace the vertex_label_index value in .annot? 

2 1

white and pial surfaces appearing outside gray matter boundary
by Batool Rizvi 20 Oct '20

20 Oct '20

External Email - Use Caution Dear FreeSurfer experts, I wrote in this question around a week ago, but haven't heard back. I'm attempting again without attaching an image, since I didn't see this getting posted the first time. I'm seeing this type of error reoccur for around half of the subjects I've reviewed so far for a study. The pial and white surfaces are merging to the outermost boundary of the brain, and almost completely overlapping each other. Provided that these are older subjects, but I didn't see this error in my experience editing older subjects in other studies. Is there perhaps a preprocessing command I could perform since this error is systematic throughout the brain, not specific to a region? I tried segmenting out the dura/CSF, and rerunning with a cleaner brain mask, and that helped a little but not too much. I also tried running it with a T2 input, but that also didn't fix the issue, though there was a little improvement;. Trying to run it with a FLAIR now, since the T2 didn't include the whole brain. Thank you for any input! Batool

1 0

Error running mris_ca_label
by Rollo, Patrick 20 Oct '20

20 Oct '20

External Email - Use Caution Experts, My group runs an older version of Freesurfer so that when we run recon-all, it creates the 2005 FS atlas. I've installed the current version of FS on a new machine and I'm trying to go back and create DKT atlases for each of our previous patients. I use the following code, hoping to generate an .annot file but get the following output: mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz < subjid > lh ../surf/lh.sphere.reg /Applications/freesurfer/average/lh.DKTatlas40.gcs ../label/lh/aparc.DKTatlas.annot GCSAread(../surf/lh.sphere.reg): file magic #fffffe63 != GCSA_MAGIC (ababcdcd) mris_ca_label: could not read classifier from ../surf/lh.sphere.reg if I run it without the file path for the lh.sphere.reg file I get the following: mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz < subjid > lh lh.sphere.reg /Applications/freesurfer/average/lh.DKTatlas40.gcs ../label/lh/aparc.DKTatlas.annot GCSAread(lh.sphere.reg): could not open file No such file or directory mris_ca_label: could not read classifier from lh.sphere.reg No such file or directory Thank you for your help!

2 1

Error during skullstripping: numerical result out of range
by Hye Min Shin 20 Oct '20

20 Oct '20

External Email - Use Caution Hi experts, While running recon-all on subjects with 3T T1 scans, I ran into an error with one subject during skullstripping stage. Recon-all was running with 3T flag. The error message is the following: register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 56, 29) --> (216, 255, 255) using (103, 122, 142) as brain centroid... mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find MRI wm before smoothing, mri peak at 73 robust fit to distribution - 72 +- 7.4 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf Numerical result out of range I tried the following suggestion in https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12605.html but to no avail. It's just strange because only one subject has this issue and the subject's scan looks fine- no part of the brain seems cutoff. Any suggestions would be helpful. Best, Julia Shin

2 1

Re: [Freesurfer] Problem with dcmunpack on freesurfer
by fsbuild 20 Oct '20

20 Oct '20

External Email - Use Caution Hello Praveen, The first line of dcmunpack script should indicate it calls the tcsh interpreter.  However, neither csh or tcsh interpreters are installed by default on Ubuntu.  The "which" command will probably report it is not found on your system thru your $PATH. $ which tcsh tcsh: Command not found But you can install the C shells manually via, $ sudo apt-get install tcsh csh .... after the install try the which command again. I am a working on a debian installer package so these manual installs will no longer be necessary. - R. On Oct 20, 2020, at 01:10, Praveen Raghunathan <praveenvr28(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer developers,Sorry if I'm making a simple mistake that I've overlooked. I am currently trying to do the freesurfer tutorials available at http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorialsand am having problems with the dcmunpack command on freesurfer. Whenever I try to run the dcmunpack script (whether it's dcmunpack -help or dcmunpack -src . -scanonly scan.log), I get the following error message :bash: /home/praveen/freesurfer/bin/dcmunpack: /bin/tcsh: bad interpreter: No such file or directoryI have installed freesurfer, added the license and am able to use freeview to open .mgz and .pial files so I'm not sure why dcmunpack is missing. I'm not able to find any online documentation on how to install or source that particular script either. I've searched the list archive and no similar errors have been reported. Please advise and let me know what I should do or what I'm doing wrong.I am currently running freesurfer on a virtual machine using Oracle Virtualbox 6.1 on my Windows laptop. The OS on the virtual machine I'm using is:Ubuntu 20.04.1 LTS and the freesurfer version is: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551I am using a Bash shell to run the commands.Thank you so much for your help! Please let me know if you need any other information.SincerelyPraveen V. Raghunathan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Problem with dcmunpack on freesurfer
by Praveen Raghunathan 20 Oct '20

20 Oct '20

External Email - Use Caution Hi Freesurfer developers, Sorry if I'm making a simple mistake that I've overlooked. I am currently trying to do the freesurfer tutorials available at http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials and am having problems with the dcmunpack command on freesurfer. Whenever I try to run the dcmunpack script (whether it's dcmunpack -help or dcmunpack -src . -scanonly scan.log), I get the following error message : bash: /home/praveen/freesurfer/bin/dcmunpack: /bin/tcsh: bad interpreter: No such file or directory I have installed freesurfer, added the license and am able to use freeview to open .mgz and .pial files so I'm not sure why dcmunpack is missing. I'm not able to find any online documentation on how to install or source that particular script either. I've searched the list archive and no similar errors have been reported. Please advise and let me know what I should do or what I'm doing wrong. I am currently running freesurfer on a virtual machine using Oracle Virtualbox 6.1 on my Windows laptop. The OS on the virtual machine I'm using is: Ubuntu 20.04.1 LTS and the freesurfer version is: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 I am using a Bash shell to run the commands. Thank you so much for your help! Please let me know if you need any other information. Sincerely Praveen V. Raghunathan

1 0

why can't I receive a reply from others in my mailbox?
by 1248742467 19 Oct '20

19 Oct '20

External Email - Use Caution Hello,  After i asked a question, why can't I receive a reply from others in my mailbox?

1 0

← Newer
1
...
7
8
9
10
11
12
13
...
18
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2020