Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

mri_vol2surf for functional 4D BOLD data only mapping 1 frame
by Robert Austin Bruce Benn 14 May '19

14 May '19

External Email - Use Caution Hi There, I’m currently trying to run mri_vol2surf on some animal data and surfaces I’ve been working with. I’m having a bit of a problem with the command mri_vol2surf. I seem to be able to project my functional volume to my surface, however I’m currently only projecting the first volume of my functional time series onto the surface. I realize the default option for frame is the first volume if output is set to a paint file, however I’m not trying to do that. Ideally I’d like to project all the volumes for later connectivity analysis. The command and terminal output are as follows: mri_vol2surf --mov rest.acp/filtered_func_data_clean.nii.gz --reg rest.acp/reg/example_func2FS.dat --surf white --projfrac 0.5 --hemi lh --o rest.acp/test.func.mgh srcvol = rest.acp/filtered_func_data_clean.nii.gz srcreg = rest.acp/reg/example_func2FS.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat -------- original matrix ----------- 0.99985 -0.01410 0.01053 2.56773; 0.01269 0.99230 0.12321 -20.18632; -0.01219 -0.12306 0.99232 0.65897; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /Volumes/brain/PCP_func/5489/anat/surf/lh.white Done reading source surface Reading thickness /Volumes/brain/PCP_func/5489/anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 2868 Writing to rest.acp/test.func.nii Dim: 19181 1 1 The actual functional volumes has 300 volumes, so I feel like I should be getting Dim: 19181 1 1 300 ? any advice? thanks, austin *************** AVISO LEGAL *************** Este mensaje va dirigido, de manera exclusiva, a su destinatario y contiene información confidencial y sujeta al secreto profesional, cuya divulgación no está permitida por la ley. En caso de haber recibido este mensaje por error, le rogamos que, de forma inmediata, nos lo comunique mediante correo electrónico remitido a nuestra atención o a través del teléfono (+34 914531200) y proceda a su eliminación, así como a la de cualquier documento adjunto al mismo. Asimismo, le comunicamos que la distribución, copia o utilización de este mensaje, o de cualquier documento adjunto al mismo, cualquiera que fuera su finalidad, están prohibidas por la ley. Le informamos, como destinatario de este mensaje, que el correo electrónico y las comunicaciones por medio de Internet no permiten asegurar ni garantizar la confidencialidad de los mensajes transmitidos, así como tampoco su integridad o su correcta recepción, por lo que el CNIC no asume responsabilidad alguna por tales circunstancias. Si no consintiese la utilización del correo electrónico o de las comunicaciones vía Internet le rogamos nos lo comunique y ponga en nuestro conocimiento de manera inmediata. *************** LEGAL NOTICE ************** This message is intended exclusively for the person to whom it is addressed and contains privileged and confidential information protected from disclosure by law. If you are not the addressee indicated in this message, you should immediately delete it and any attachments and notify the sender by reply e-mail or by phone (+34 914531200). In such case, you are hereby notified that any dissemination, distribution, copying or use of this message or any attachments, for any purpose, is strictly prohibited by law. We hereby inform you, as addressee of this message, that e-mail and Internet do not guarantee the confidentiality, nor the completeness or proper reception of the messages sent and, thus, CNIC does not assume any liability for those circumstances. Should you not agree to the use of e-mail or to communications via Internet, you are kindly requested to notify us immediately.

2 1

check FS to native registration in freeview
by Sam W. 14 May '19

14 May '19

External Email - Use Caution Hi, After bbregister, I ran mri_label2vol to convert a segmentation file to native functional space mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o aseg-in-func.nii --temp example_func.nii Now I would like to check how well the example_func and aseg file align. I tried this freeview -v s01/example_func.nii s01/aseg.mgz:colormap=lut:reg=reg.dat but it does not result in a good alignment Best regards, Sam

2 3

Research Assistant Position at Massachusetts Eye and Ear/Harvard Medical School in Boston, MA
by Bailin, Emma 13 May '19

13 May '19

The Laboratory for Visual Neuroplasticity at the Massachusetts Eye and Ear Infirmary (Harvard Medical School), located in Boston, MA is seeking a full-time research assistant to start between July and September 2019. Candidates who would be able to commit to the position for a minimum of two years would be strongly preferred. Led by Dr. Lotfi Merabet, the computational neuroscience lab studies how the brain adapts to blindness and visual impairment. Major research focuses include brain imaging technologies (including MRI and EEG) to investigate structural and functional neuroplasticity as well as development of behavioral stimuli (virtual reality) for research into cerebral and ocular visual impairments. Detailed information about the lab can be found at http://scholar.harvard.edu/merabetlab. Responsibilities: The research assistant will assist with behavioral and MRI data management and analysis (~75% of the time), conduct experiments (~10%), and perform various administrative tasks (~15%). Qualifications: Ideal candidates will have a bachelor's degree or equivalent in neuroscience, computer science, or psychology. An interest in working with people with disabilities would be highly desirable. Some research experience in a neuroscience and or an experimental psychology lab would be good, but not required. Strong organizational and communication skills and attention to detail are an important must. The candidate should be self-motivated and able to solve problems independently while also being comfortable working with others. Applicants with a background in programming (e.g. Unix, Python, MATLAB), statistical analysis software (e.g. R, SPSS, Stata) and/or neuroimaging software (e.g. FreeSurfer, FSL, SPM, etc.) are strongly encouraged to apply. To Apply: Please send a CV and a cover letter to Emma Bailin (emma_bailin(a)meei.harvard.edu<mailto:emma_bailin@meei.harvard.edu>), with the subject line "Research Assistant position application". The letter should describe your research experience (if you have any), interests and include why you think you would be a good fit for the lab. Please also include the name and contact information of two references. Applications will be reviewed on rolling basis until the position has been filled. Emma Bailin Research Coordinator Laboratory for Visual Neuroplasticity Schepens Eye Research Institute Mass. Eye and Ear Infirmary Harvard Medical School Emma_Bailin(a)MEEI.harvard.edu<mailto:Emma_Bailin@MEEI.harvard.edu> Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at (800) 856-1983. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.

1 0

MP2RAGE recon using Siemens Terra 7T scanner
by Fuller-Deets, Josh (NIH/NEI) [C] 13 May '19

13 May '19

External Email - Use Caution Hi Freesurfer users, we have a new Terra 7T scanner and I'm having issues collecting a clean MP2RAGE scan and subsequently reconstructing it. Does anyone with experience with this scanner have any suggestions about modifications to the standard Siemens provided sequence? Alternatively, does anyone have any suggestions for any expert file/input settings for recon-all other than what is in the high field recon and submillimeter recon help pages? Thanks for your time, Joshua Fuller-Deets Computer Systems Analyst [C] Laboratory of Sensorimotor Research National Eye Institute 49 Convent Drive, Rm. 2B75 Phone: 301-496-3708 Fax: 301-402-0511 Email: josh.fuller-deets(a)nih.gov

2 1

How can I visualize cortical thickness data on a brain template?
by albertotricker 13 May '19

13 May '19

External Email - Use Caution Hello FreeSurfer technical staff I hava a data set provided by ADNI initiative, which is formed by a set of pre-processed T1-weighted MRI using FreeSurfer. The feature space consists of cortical thickness and subcortical volumes. Well, I want to visualice the cortical thickness features on a brain template to obtain something like this: https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inl… It is possible to do that with FreeSurfer, or I have to use other tool? I am sorry if the question if not complete, please tell me if you need more information. -- 1/8/1996 Huétor Tájar Alberto Martín Martín _Estudiante de Ingeniería Electrónica Industrial_ UGR _Ingeniero en proceso (de volverse loco)_

2 1

tractstats2table error
by Daniel Callow 13 May '19

13 May '19

External Email - Use Caution Hello, I just ran trac-all on my data and am trying to use tractstats2table to run some tract-based group level analysis. I have created a text file with the full paths to each conditions stats file (attached below and tried to run the following command tractstats2table --load-pathstats-from-file /Volumes/DANIEL/trac/stats_info/stats_rh.unc.txt --overall --tablefile /Volumes/DANIEL/trac/stats_info/rh.unc.All.table However, I get the following error message. Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer_dev/bin/tractstats2table", line 347, in <module> pathway_subj, measure_value_map = parsed.parse() File "/Applications/freesurfer_dev/bin/fsutils.py", line 288, in parse val = float(strlist[1]) ValueError: could not convert string to float: 'y' Could someone please provide me some guidance on how to troubleshoot this? *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

1 1

Longitudinal processing
by falk.luesebrink＠med.ovgu.de 13 May '19

13 May '19

External Email - Use Caution Dear all, I'm a beginner in using the longitudinal processing pipeline (as well as statistical analysis) and it would be great to get some insights or hints to analyze my data. I have a dataset consisting of 11 subjects each acquired at 7 different time points with an isotropic resolution of 1 and 0.8 mm at 3T using a 64-channel head coil. Using that dataset I want to investigate short term differences in e.g. cortical thickness with the goal to assess the degree of biological variance during that time period. I have plotted the mean cortical thickness of each time point of every subject (using lme_timePlot and lme_lowessPlot) showing a somewhat random distribution across time and from my perspective fairly high standard deviation. I wanted to have a look at the individual percent change by overlaying the symmetric percent change on fsaverage, but wasn't quite sure of the scale. Is it in percent? So in case I set the scale bar between 1 and 5, the color relates to 1 to 5 percent? What other ways would make sense to have a look at? I definitely cannot compare groups, as there is just one. The days and time of acquistion are rather randomly choosen, so I potentially cannot use either as a covariate. Best, Falk ............................................... [klinikum_logo_schmal_e-mail_blau] University Clinic for Neurology Otto-von-Guericke-university Magdeburg Medical faculty Leipziger Str. 44 39120 Magdeburg Phone +49-391-6117-512 falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> http://www.kneu.ovgu.de/kneu.html

2 2

Longitudinal Gray/white Contrast Measure
by WON JONG CHWA 13 May '19

13 May '19

External Email - Use Caution Dear FreeSurfer experts, I am currently running a longitudinal analysis in FreeSurfer v5.3 to look at changes in volume and gray/white contrast. I ran all the processing steps and used this command below to look at results for volume: long_mris_slopes --qdec ./qdec/qdec.table.dat --meas volume --hemi lh --do-label --do-rate --time years --qcache fsaverage --sd $SUBJECTS_DIR We also would like to look at change in gray-white matter intensity ratio over time (between 2 timepoints) as well, but there is no separate measure defined for it. I was wondering what we can do to calculate this. Thank you. William

2 1

How to get the difference between motion, NU
by chen 13 May '19

13 May '19

External Email - Use Caution Hi expert, I selected hippocampus and amygdala as ROIs to estimated the reliability of a well-controlled multi-site study. The travelling volunteers were scanned in each site with the same type scanners and scan protocol. But, amygdala volume (generated by FreeSurfer) presented a relatively poor ICC scores between sites. So, i want to found the reasons from sites or scanners. According to previous studies, the variation might come from across-site difference and the structure itself. And the major sources of between-site variation might be related to field inhomogeneity and other issues idiosyncratic to individual each scanners. Due to this reason, i want to check my data to confirm the field inhomogeneity located in amydala area or not. How can i get the difference between the originate image and the images after motion and NU intensity? I am looking forward to your suggests. Cheers, Jiachen

1 0

recon-all errors at Talairach
by QN Z 12 May '19

12 May '19

External Email - Use Caution Dear Experts, I got recon-all errors at Talairach both on my own data and sample file (nii.gz) converted from the FreeSurfer installation tutorial. I reinstalled my platform and FreeSurfer 5.3.0 a few days ago, however the errors still exited. My code is as follows: export SUBJECTS_DIR=/home/zqn/freesurfer/subject recon-all -s ST_LS_004 -i /home/zqn/freesurfer/subjects/ST_LS_004.nii recon-all -s ST_LS_004 -all The errors appeared after the third command line was input and the errors are as follows: #-------------------------------------------- #@# Talairach 2019年 05月 13日星期一 10:11:56 CST /home/zqn/freesurfer/subjects/ST_LS_004/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux zqn-Precision-Tower-3620 4.18.0-18-generic #19~18.04.1-Ubuntu SMP Fri Apr 5 10:22:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ST_LS_004 exited with ERRORS at 2019年 05月 13日星期一 10:11:57 CST ----------------------------------------------- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Platform: Ubuntu 18.04 recon-all.log: see attached file I am brand new to FreeSurfer and I read the recon-all.log but could not find out what the errors exactly are and the way to solve it. Any reply or suggestion is highly appreciated. Thank you so much! Qiannan Zhao

1 0

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