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fmri_readreg
by shahin＠nmr.mgh.harvard.edu 09 Feb '18

09 Feb '18

Dear Surfers, Previously we had a matlab function fmri_readreg.m (author: Doug Greve) that could extract the regmat from the register.dof6.dat files. But version 6 does not generate dof6.dat anymore. Rather it generates a dof6.lta that fmri_readreg can not read. I was wondering if there is an updated version of fmri_readreg.m to read lta files. If no, would you tell me how to extract regmat from this lta file. regards _____________________________________ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129

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[freesurfer] Extracting values of cortical thickness in each vertex.
by 박경일 09 Feb '18

09 Feb '18

Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung

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How to analyze fMRI in native volume space
by Tuominen, Lauri Johannes 09 Feb '18

09 Feb '18

Dear Freesurfers! I would like have my fMRI runs in the native T1 volume space and do the first level analyses there. I can only find -self flag for surface based analyses in preproc-sess. What would be there recommended way to do the analyses in the T1 volume space? This is 7T data and I’d like to use the individual segmentations as ROIs. Thank you so much! Lauri Tuominen

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Multiple regression FreeSurfer
by Martin Juneja 09 Feb '18

09 Feb '18

Hi, I am interested in correlating cortical volume measures with behavioral data X1, after regressing out the effect of age and sex. For that I ran following commands: mri_glmfit --y lh.X1.CV.15.mgh --fsgd X1.fsgd dods --C Corr-X1-cor.mtx --surf fsaverage lh --cortex --glmdir lh.X1_CV.glmdir mri_glmfit-sim --glmdir lh.X1_CV.glmdir --cache 2 abs --cwp 0.05 --2spaces where X1.fsgd is following: GroupDescriptorFile 1 Class Male Class Female Variables X1 Age Input S001 Male 127 36 .... so on and Corr-X1-cor.mtx is 0 0 0 0 1 I was wondering how can I use multiple regression approach e.g. how can I correlate CV and X1 after accounting for thickness and area or how can I correlate gyrification and X1 after accounting for CV and thickness etc. I am not sure what will be my commands for that and what will be fsgd and mtx files? Thanks for your help.

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Gray matter mask
by Hanna Vasilevskaya 09 Feb '18

09 Feb '18

Hello FS team, I am new to FS and using version 5.3 on a Mac. I have minimal programming background and this might be a very easy question, however I was not able to find a similar one in the archive. I have T1 MRI images from multiple subjects and I need to extract the brain gray matter mask (just cortical regions, without cerebellum). I will then use this mask as an ROI to extract PET activity. Would you happen to know a way for this? Thank you greatly, Anna

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mri_aparc2aseg labelwm not labelling wm
by Sims, Sara A 09 Feb '18

09 Feb '18

Freesurfers, I am trying to use a cortical label to label wm. I am using the following command line: mri_aparc2aseg --s $patient --annot 8V1 –labelwm And most of the time in most subjects this works, however sometimes the output file doesn’t label any wm with the 3000+N or 4000+N like it usually does. I have tried changing the -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I could find but it won’t budge even though doing other labels in the same person works fine. Fyi: The original cortical label is also correctly place in the cortical ribbon. Any ideas? Please! Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin(a)uab.edu

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pre-smoothing coomand line
by Avideh Gharehgazlou 09 Feb '18

09 Feb '18

Hi Freesurfer experts, I found the answer to my previous question on FreeSurfer Wiki regarding pre-smoothing command line for LGI ( I am interested in looking at between-group differences in vertwex-wise LGI values). I am now aware that the following command line must be used: recon-all -s <subjid> -qcache -measure pial_lgi However, if I also want to look at surface area differences between groups later on, is using the above pre-smoothing command line correct? OR do I have to use the following command line considering that I Am not only looking at LGI values : recon-all -s <subjid> -qcache Would really appreciate your advice, Thanks, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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Wm.mgz editing
by Emily Schwartz 09 Feb '18

09 Feb '18

Hi FreeSurfer community, I am relatively new to manually editing and am having some questions dealing with editing the wm.mgz. Occasionally, white matter and grey matter are being incorrectly cut out, but I cannot edit WM voxels in the area (lh postcentral) because they are already considered WM in the heat map (but excluded from the boundary). I have attached images. How would I go about fixing this? Would control points work here? And would the segmentation error in slices 79-81(lh postcentral) be edited by adding wm voxels (I can't really add any to slice 79)? (This is an elderly brain.) Thank you, Emily

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FW: Memorandum: Call for CASE Distinguished Postdoctoral Scholar {Disarmed}
by Anthony Dick 09 Feb '18

09 Feb '18

Hello, Please see below for a very time-sensitive opportunity for postdoctoral scholars in developmental neuroimaging in the Center for Children and Families (ccf.fiu.edu) Please contact me directly (adick(a)fiu.edu<mailto:adick@fiu.edu>) with any interest. Good salary/benefits in a great city (Miami, FL) and renewable for multiple years. Thanks! Anthony -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Florida International University MM Campus AHC4 454 Department of Psychology and Center for Children and Families<http://www.ccf.fiu.edu/>, an FIU Preeminent Program<https://beyondpossible.fiu.edu/preeminent-programs/> 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu<mailto:adick@fiu.edu>; Webpage: http://dcn.fiu.edu<http://dcn.fiu.edu/>; Join the SSHD<http://www.sshdonline.org/> ##### Check out the new book<http://www.routledge.com/9781138960039>: Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, Theory, and Method. Taylor & Francis. From: Alina Delgado <alidelga(a)fiu.edu> on behalf of Michael Heithaus <heithaus(a)fiu.edu> Date: Friday, February 9, 2018 at 11:26 AM Subject: Memorandum: Call for CASE Distinguished Postdoctoral Scholar [cid:image001.png@01D320DC.8C56F780] MEMORANDUM To: All Faculty From: Michael R. Heithaus, Dean Date: February 9, 2018 MULTIPLE POSTDOCTORAL POSITIONS IN RESEARCH AREAS Florida International University is classified by Carnegie as a R1: Doctoral Universities - Highest Research Activity and recognized as a Carnegie engaged university. It is a public research university with colleges and schools<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…> that offers 196 bachelor’s, master’s and doctoral<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage.c…> programs in fields such as engineering, computer science, international relations, architecture, law and medicine. As one of South Florida’s anchor institutions, FIU contributes almost $9 billion each year to the local economy. FIU is Worlds Ahead in finding solutions to the most challenging problems of our time. FIU emphasizes research as a major component of its mission. FIU has awarded more than 220,000 degrees and enrolls more than 54,000 students in two campuses and three centers including FIU Downtown on Brickell, FIU@I-75, and the Miami Beach Urban Studios. FIU’s Medina Aquarius Program<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…> houses the Aquarius Reef Base, a unique underwater research facility in the Florida Keys. FIU also supports artistic and cultural engagement through its three museums: Patricia & Phillip Frost Art Museum<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage.c…>, the Wolfsonian-FIU<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…>, and the Jewish Museum of Florida-FIU<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage.c…>. FIU is a member of Conference USA<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…> and has more than 400 student-athletes participating in 18 sports. For more information about FIU, visit http://www.fiu.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…>. Position Title: Distinguished Postdoctoral Scholar Location: Florida International University, Miami, Florida Rank: Postdoctoral Research Associate Application Deadline: February 28, 2018 Description: The College of Arts, Science & Education<http://case.fiu.edu/> (CASE) at Florida International University (FIU), Miami, FL (USA) is seeking multiple candidates to serve as Distinguished Postdoctoral Scholars in fields of study relevant to CASE’s scholarly research areas in the sciences, humanities and education. Additionally, scholars may work with one of our preeminent centers including the Institute for Water & Environment, the Center for Children & Families, and the STEM Transformation Institute. The CASE Postdoctoral Scholars will work with a mentor/scholar of their choice. While the primary focus for the Postdoctoral Scholars will be to conduct scholarly activities and research, they will also be expected to interact with graduate students, participate in outreach efforts, and submit competitive research proposals where appropriate. The Postdoctoral Scholars will have the opportunity to teach if desired and will also be able to interact with faculty from across the College, as well as additional FIU faculty and external partners affiliated with the university. Appointments will have a term of one year starting in Summer or Fall 2018 and are renewable contingent upon excellent performance. The Scholar will receive a salary of $50,000, plus benefits and a discretionary fund of up to $5,000/year for research and travel expenditures. Applicants from underrepresented minority groups are highly encouraged to apply. Candidates will be selected based on demonstration of research excellence and potential future impact on their respective field of study. To apply, please send a cover letter that includes the name of the proposed faculty mentor, a proposed research plan, CV and the names of three references to alidelga(a)fiu.edu<mailto:alidelga@fiu.edu> . Please make sure you have contacted a potential supervisor who would be willing to be your mentor. [cid:image003.png@01D3A197.8B2B4A00]Cheers, Dr. Michael Heithaus Dean, College of Arts, Sciences & Education Florida International University

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smoothing command line- LGI
by Avideh Gharehgazlou 08 Feb '18

08 Feb '18

Hi, I am interested in looking at between-group differences in in LGI on Qdec (I will look at surface area as well later). I have a question regarding the smoothing stage. My recon-all for all subjects has completed, and I have LGI values for each subject. For smoothing, I was going to run the following command line: Recon-all –s <subjid> -qcache However, I saw in an archive post someone mentioning running the following line instead: recon-all -s <subjid> -qcache -measure pial_lgi Will you please tell me which command line I have to run? Thanks so much, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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