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30132 discussions

view labels in native space
by Nasiriavanaki, Zahra 28 Oct '19

28 Oct '19

Hi Freesurfer experts I have a few labels that correspond to activation clusters in fsaverage space for an individual subject. I used mri_label2label to transfer them to native space of the subject. export SUBJECTS_DIR=/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR mri_label2label --srclabel ./first_levels/$subj/label/aparc/pos/lh-0001.label --trglabel lh-new.label --srcsubject fsaverage --trgsubject ${subj} --regmethod surface --hemi lh When I overlay the native label on top of the fsaverage significance map (tksurfer fsaverage lh inflated -ov sig.nii.gz), it looks like small dots all over the map. Is this because I'm viewing the native label in fsaverage space? Is there a way to view these labels in this subject's native space instead of fsaverage, something like tksurfer native(instead of fsaverage) lh inflated -ov sig.nii.gz? Thank you very much in advance Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Re: [Freesurfer] Error in glmfit-sim cache
by Renew Andrade 28 Oct '19

28 Oct '19

External Email - Use Caution I don’t know what do you mean by not knowing what it means. I said that I have tried all the values the error pinpoints to. That is I have tried mri_glmfit-sim --glmdir lh.IXI.glmdir --cache 4 abs —cap 0.05 --2spaces with "1.3", "2.0", "3.0", “4.0”. And it doesn’t work. I know it doesn’t seem to be a software issue but I cannot run this functionality of the software only for the moment everything else works fine. I have two laptops one Mac and one BMAX I have done recon-all in one and I have done glmfit in the MAC. But this I hope is only temporary because makes no sense that a software works partially. Sincerely, Andrade. ERROR: > thresh = 4,0 must be 1.3, 2.0, 3.0, 4.0 I don't know what this refers to On 10/18/19 4:45 PM, Renew Andrade wrote: > External Email - Use Caution > > I have tried all the values it pinpoints to but none seem to work. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Vertex and voxel-wise linear regression in Freesurfer
by Larry Lai 28 Oct '19

28 Oct '19

External Email - Use Caution Hello FreeSurfer Users I'm attempting to explore the correlations between the surface-based and voxel-based values and adjusted for nuisance covariate in FreeSurfer. *Correlational study:* A. Cortical thickness and VBM results B. VBM_1 and VBM_2 results *Platform:* 1) freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Ubuntu 16.0.4 Thanks for considering my request. Best regards -- *Ying-Liang (**Larry)** Lai, Ph.D. Student* Research Assistant *Ph.D. Program for Neural Regenerative Medicine* College of Medical Science and Technology Taipei Medical University and National Health Research Institutes

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b0 to T1’s co-registration without b0 inhommogeneities
by Daniel Callow 28 Oct '19

28 Oct '19

External Email - Use Caution Hello, I am trying to do a within-subject co-registration between b0 volumes and T1's for my subjects. This is an old dataset that does not have anything for correcting b0 inhomogeneities. The registration using --dti and normal parameters for bbregister led to "okay" within-subject registration. I am wondering if modifying the --dof (like 12) option for bbregister or applying some type of linear/nonlinear registration might improve the registration? Best, -- *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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Could you help me to extract my brain from MRI?
by satyr96＠o2.pl 27 Oct '19

27 Oct '19

External Email - Use Caution Hello. I have spent a lot of time testing different options in freesurfer to extract my brain for 3D printing but I could not get good results (like different parameters for skul removal and multiple images). I think the issue is with my image is to crappy because when I have used perfect MRI scan (now I think it could have been human sliced after dead) the brain looks perfect and I was able to 3D print it. I attachment I am sending the comparation between results. Link to my MRI images and final STL files: drive.google.com drive.google.com Please remove any private info if I left any. Please help me to create my own 3D model of brain. Best regards, Adam

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ERROR: Must specify input table of gradient vectors
by Renew Andrade 26 Oct '19

26 Oct '19

External Email - Use Caution Dear Anastasia Yendiki: I have tried to run TRACULA on 3 subjects as specified in configuration file attached. But the terminal output is: sh-3.2# trac-all -prep -c dmrirc.IXI domainname: Command not found. Too many ('s. INFO: SUBJECTS_DIR is /Volumes/FREESURFER/freesurfer_preprocessed INFO: Diffusion root is /Volumes/FREESURFER/freesurfer_preprocessed Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local -log /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log -cmd /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Sat Oct 26 23:06:34 CEST 2019 mri_convert --bvec-voxel /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0506412, -0.996042, 0.0730476) j_ras = (0.00618997, 0.073453, 0.997279) k_ras = (0.998698, 0.0500512, -0.00988522) writing to /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz... ERROR: Must specify input table of gradient vectors Darwin Renes-Air.home 19.0.0 Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sat Oct 26 23:06:39 CEST 2019 I don’t understand why? Because I think I have specified everything correctly. May be there is an issue with “bvecs” and “bvals” files because I added .txt format manually for it to be equal to what is specified in the tutorial of TRACULA configuration file. Sincerely, Andrade.

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(no subject)
by Daniel Callow 26 Oct '19

26 Oct '19

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Open Faculty Position in Psychology at the University of Nevada, Reno
by Stephanie Otto 25 Oct '19

25 Oct '19

External Email - Use Caution Greetings Freesurfer Group, I'm not sure if it is acceptable to post open positions here, but our department is currently seeking to fill an Assistant Professor position and we would be grateful if you could share this information with the Freesurfer community. Thanks in advance! The Department of Psychology at the University of Nevada, Reno, is seeking applications for a tenure-track Assistant/Associate Professor in Cognitive Neuroscience. The level will be determined by the Department and will be commensurate with the selected candidate’s experience, knowledge, skills, and abilities. We are particularly interested in candidates whose research includes advanced techniques in neuroimaging and/or computational approaches. The candidate’s area of research should complement the strengths of the department in visual and multisensory processing. Successful candidates will be expected to establish a nationally recognized, extramurally funded research program, train graduate students, and participate in undergraduate teaching. Competitive startup funds are available. Required Qualifications PhD in Neuroscience or related field; postdoctoral research experience. Preferred Qualifications A strong publication record; potential for strong teaching skills; expertise that complements and expands the research capacity of the department; the potential to develop a nationally-competitive research program. Compensation Grade Assistant Professor -- Rank II Associate Professor -- Rank III Total Compensation The total compensation package includes a negotiable competitive salary, moving allowance (if applicable), a rich retirement plan, health insurance options that include dental and vision, life insurance, long-term disability, along with many other benefits. Additionally, there is a grant-in-aid educational benefit for faculty and dependents. For more information, please visit: UNR Benefits Faculty Dual Career Assistance Program The University of Nevada, Reno recognizes the importance of addressing dual-career couples’ professional needs. We offer a dual career assistance program to newly hired faculty spouses/partners that provides resources and assists them to identify career opportunities in Northern Nevada. Dual Career Program Department Information The department contributes to both the undergraduate and graduate interdisciplinary training programs in Neuroscience (approximately 440 undergraduates and 35 doctoral students). The department has 32 tenure-ladder faculty, four teaching faculty, and a corps of administrative staff; it is home to the Psychology major (900 students) and graduate programs in Cognitive and Brain Sciences, Behavior Analysis, and Clinical Psychology (120 students across three programs). A wide array of resources for neuroimaging is 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. Contact Information Sharee Williams at (775) 682-8795 or shareew(a)unr.edu Required Attachment(s) Please attach the following documents to your application. 1) Resume/CV 2) Cover Letter 3) Contact information for five professional references 4) Statement of Research and Teaching Interests 5) Please write a brief statement (one page maximum) about how you would contribute toward our mission of creating a culturally inclusive environment in the role for which you are applying Best, Stephanie Otto Doctoral Candidate, Cognitive and Brain Sciences Program Department of Psychology, MSS 414/MS0296 University of Nevada, Reno sotto(a)nevada.unr.edu

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Thalamic subnuclei color table
by Crawford, Anna 25 Oct '19

25 Oct '19

External Email - Use Caution Hello, Just a quick question. We recently installed the new thalamus segmentation subroutine. It's really wonderful, and much promise to our work. I can't find a lookup table with the numerical labels from the FS output to the thalamic nuclei. The numbers around between 8103-8133 on the right, and 8203 and 8233 on the left. Can you point me in the right direction for this? For other FS segmented volumes I always use the following, but it doesn't include these thalamic subnuclei http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfe… Thank you, Anna Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Mri_mask producing only zeros
by Sims, Sara A (Campus) 24 Oct '19

24 Oct '19

External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then into a surface with 1s inside the label and 0s outside the label. I want to make a connectivity map surface overlay with values only within my label overlay. However when I run it, it creates a surface overlay with only zeros. There is definitely values within the label surface overlay (I triple checked). Code I used: Mri_mask original_surface_overlay label_mask new_masked_output It doesn’t output any errors. Here is what it looks like in freeview: Original surface overlay (label is outlined in green) [cid:image001.png@01D5821A.1324B130] The label made into a surface overlay (same as the one shown in green above): [cid:image002.png@01D5821A.1324B130] But this is the output: all zeros even though there was data within the mask. [cid:image003.png@01D5821A.1324B130] Help! Sara A. Sims

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