Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

Geometric distortion
by Martin Juneja 14 May '19

14 May '19

External Email - Use Caution Hi experts, I have following question from one of the reviewers regarding recon-all pipeline: *"Was geometric distortion corrected? If not, this should be discussed or mentioned in the study limitation."* I was wondering if the reviewer is referring to following step in the recon-all pipeline. Could you please help me in addressing this concern by the reviewer? Thanks. MJ Cortical Parcellation (-<no>cortparc, -<no>cortparc2) Assigns a neuroanatomical label to each location on the cortical surface. Incorporates both geometric information derived from the cortical model (sulcus and curvature), and neuroanatomical convention. Calls mris_ca_label. -cortparc creates label/?h.aparc.annot, and -cortparc2 creates /label/?h.aparc.a2005s.annot.

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How to obtain the CSF mask
by Yaoshen Yuan 14 May '19

14 May '19

External Email - Use Caution Dear Freesurfer team, I am planning to get the CSF binary mask using Freesurfer. I saw previous discussion about combining several labels in aparc+aseg.nii to create the CSF mask. I am now using Freesurfer v6.0.0. I am wondering does FS now offer a direct mask for CSF using recon-all (I saw gm.mask.mgz and wm.mask.mgz under \mri folder ) or do I still need combine different labels to get the CSF mask? Thank you in advance! Yaoshen Yuan

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Re: [Freesurfer] How can I visualize cortical thickness data on a brain template?
by albertotricker 14 May '19

14 May '19

External Email - Use Caution I hava a data set of 240 patients, 60 Healthy Control, 60 MCI, 60 cMCI and 60 AD, with 429 cortical and subcortical features. 68 of this features are cortical thickness standard desviation features (ie, lh_bankssts_thicknessstd, lh_caudalanteriorcingulate_thicknessstd, … , rh_insula_thicknessstd). I have calculated the average of each of this features for each group (HC, MCI, cMCI, AD) and I want to represent this data over a brain template. For now I am doing this with visbrain, a Python open-source package, but I was wondering if I could do the same with FreeSurfer. I have not found any way to do it in a simple way in the FreeSurfer wiki, but there has to be some way to do it. Thanks you for the help! -- 1/8/1996 Huétor Tájar Alberto Martín Martín _Estudiante de Ingeniería Electrónica Industrial_ UGR _Ingeniero en proceso (de volverse loco)_

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ERROR: flirt in bbr Matlab Execution
by Pfannmoeller, Joerg Peter 14 May '19

14 May '19

Hello, I have a problem with bbregister and the option --init-best. In the current dev version of freesurfer 6 the processing stops with the error message: terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt if I run bbr using Matlab and the Matlab command 'system', where Matlab was started from a terminal in which all FreeSurfer environment variables are set as described on your webpage. However, if I execute the same bbr command from the terminal in which I started Matlab it seemingly runs without any problems. The output files look okay. There is just one output in the log-file which I do not understand: (standard_in) 1: illegal character: K (standard_in) 1: syntax error I got two questions: 1.) Is the run started from the terminal okay? 2.) What do I need to do to get the run started from Matlab to work? The data used worked fine in the stable version for bbregister with fsl flirt initialization in Matlab. However, --init-best did not work in the stable version. In the example discussed here a single slice was registered to the brain anatomy. Here is some information on my operating system: lsb_release -a Distributor ID: CentOS Description: CentOS Linux release 7.6.1810 (Core) Release: 7.6.1810 Codename: Core Can you help me with this issue? Best Joerg

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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.

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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

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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.

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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

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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)_

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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

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Freesurfer May 2019