Freesurfer

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30132 discussions

GLM analysis question
by Ferraro, Pilar 23 Sep '19

23 Sep '19

External Email - Use Caution To the kind attention of the FreeSurfer team, I have some questions concerning a GLM analysis I’m running and any help would be greatly appreciated! I’m interested in identifying cortical regions where older age is associated with greater atrophy. However, unlike the example reported in the tutorial page, I do not have two groups (male and females) but just one group (patients, regardless of their gender). - Firstly, I’ve generated an “age.fsgd" file with the following structure: Class Main Variables Age Input subj 1 Main 61 Input subj 2 Main 73 …. And so on. - Secondly, I’ve assembled the data using the mris_preproc command (including resampling, concatenating and smoothing). - Thirdly, I’ve proceeded with the glm analysis using the mri_glm command. However, here I’ve changed the fsgd option, and in particular: —fsgd age.fsgd doss (I thought the DOSS design was more appropriate in my case). FIRST QUESTION: is this correct? Then, I’ve set the contrast in the "lh-Avg-thickness-age-Cor.mtx” file as: 0 1. SECOND QUESTION: is this correct? In this case I’ve set the intercept value as 0 and the slope value as 1. Many thanks for your help, Pilar

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talairach.m3z not found
by Dev vasu 23 Sep '19

23 Sep '19

External Email - Use Caution Dear all, When i run recon-all , i am encountering an error transforms/ talairach.m3z not found during registration phase, could some one please let me know how to resolve this?. Thanks Vasudev

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Fwd: Talairach Failure Dection error for recon-all
by Hang Zeng 23 Sep '19

23 Sep '19

External Email - Use Caution mT1.nii <https://drive.google.com/file/d/1ABR_hATWJP7QisH3TIw1_yZjVaxaucgn/view?usp=…> Dear Freesurfer users, I am trying to run the recon-all command for a T1 imge. The image is bias corrected using spm-segmentation (see attached). And the Talarich Failure Dection error occurred (see the log file). I ran the same analysis with the non-processed T1 and it worked. Any information would be appreciated Best, -- Hang ZENG Institute of Neuroscience and Medicine (INM-3) Forschungszentrum Juelich, Leo-Brandt-Str. 5 52425 Juelich Email: h.zeng(a)fz-juelich.de <zenghang14(a)gmail.com> & zenghang14(a)gmail.com Telefon: +49 2461/61-85328

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freeview command line options
by Rockers, Elijah D. 23 Sep '19

23 Sep '19

External Email - Use Caution Hello, it's possible I found a bug in freeview: I'm using the overlay_color option with freeview. Specifically I am trying to use both the "truncate" and "inverse" options in a command line call to freeview for a pipeline I am building. The documentation says that I can apply more than one, delimited by commas .... however I have found that if I attempt to use both truncate and inverse, it seems to be only applying whichever one appears last on the list. In an interactive instance of freeview, doing everything manually, I have no problems. Just seems to be an issue with the command line call. Any suggestions on how I might proceed in this case? -Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Hippocampal Subfields Atlas
by ZZY 23 Sep '19

23 Sep '19

External Email - Use Caution Dear Freesurfer developer:               I have a group of multimode MRI data, including functional MRI, T1WI and diffusion MRI. We want to analyze the functional and structual connectivity between the hippocampal subregions. Now, we have obtained individual-level atlas of hippocampal subfields for each subject by using FREESURFER 6.0 on the T1 image. What should we do next step? How do get a group-level atlas of hippocampal subfields and apply it to functuional and diffusion data? Best, zhiyong

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Default GCA atlas FreeSurfer 6?
by Brehler, Michael 20 Sep '19

20 Sep '19

External Email - Use Caution Hello FreeSurfer experts, can someone tell me what the default GCA atlas for recon-all in FreeSurfer 6 is and where I can find the image? Regards, Michael

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Course in Advanced Neuroimaging (Barcelona)
by Erick Canales 20 Sep '19

20 Sep '19

Dear colleagues, I am pleased to announce our upcoming Course in Advanced Neuroimaging held annually in Barcelona. It takes a practical approach and does not require qualifications or previous experience in neuroimaging. It will be taught in Spanish. The multidisciplinary programme provides thorough training in the analysis of brain images from different MRI modalities and data modeling techniques, including voxel-based morphometry, cortical thickness, diffusion tensor imaging, fibre tracking, functional MRI and brain connectivity, as well as the statistical methods behind these techniques including elements of meta-analysis, and more. The course consists of a five-month online theoretical module (starting on November 6th) and a period of practical face-to-face training (split between two days in November and two weeks at the end of April) held in Barcelona. For further information, please visit the website: www.cursoneuroimagen.com Best regards, Erick J. Canales-Rodríguez Joaquim Radua Raymond Salvador Edith Pomarol-Clotet FIDMAG Research Foundation and Sociedad Española de Neuroimagen *www.fidmag.com <http://www.fidmag.com/>*

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mgz to nifty {Disarmed}
by 郑凤莲 20 Sep '19

20 Sep '19

External Email - Use Caution Hi experts, I am using FS for some studies. Now, I have a question about format convertion. How can I convert .mgz file to .nii file. Is there any way to complete? Thanks for your contention in advance. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Researcher Position in Artificial Intelligence on Magnetic Resonance Imaging for Alzheimer's Prevention
by Juan Domingo Gispert López 20 Sep '19

20 Sep '19

External Email - Use Caution The Barcelonabta Brain Research Center (BBRC <https://barcelonabeta.org/>) is looking for a researcher to develop deep learning methods to predict preclinical Alzheimer’s disease based on Magnetic Resonance and wet biomarkers, as part of its Alzheimer’s Prevention Program. This is a full-time position and the person selected will report to the Neuroimaging´s group leader. Main Responsibilities: - To develop and apply Machine/Deep learning (ML/DL) techniques to MRI data to predict preclinical AD stages on the ALFA/ALFA+ datasets from the BBRC - To develop the ML/DL algorithms so that they are compatible with use in real-world scenarios - To liaise with third parties to validate the performance of the developed algorithms - To write technical reports, journal articles and present results in scientific conferences We offer: - The research position is scheduled initially for two years (open to renewal). - Salary will be in accordance with qualifications and experience Further information and application instructions: https://fpmaragall.org/wp-content/uploads/2014/07/Researcher-Position-in-De… -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> 08005 Barcelona <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> www.barcelonabeta.org www.fpmaragall.org ------------------------------ Confidencialitat correu electrònic BBRC <https://www.barcelonabeta.org/ca/politica-privacitat-web>. Confidencialidad correo electrónico BBRC <https://www.barcelonabeta.org/es/politica-privacidad-web>. E-mail confidentiality BBRC <https://www.barcelonabeta.org/en/privacy-policy-web>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

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PALM Analysis
by Harikumar, Amritha 19 Sep '19

19 Sep '19

Hi there, I am trying to run a Permutation Analysis of Linear Models (PALM) for analyzing subcortical areas in the nucleus accumbens, caudate, and putamen. Upon trying to run the script after reading the Freesurfer wiki, I am not sure what it is referring to regarding applying fsPalm in MATLAB. My questions are - do we a.) copy paste the existing fspalm command in Matlab and run it after setting the two Freesurfer paths listed in the wiki, or what is the correct procedure to run it? I tried running it in terminal as well, but didn’t have any luck. My existing Matlab script has set up the two Freesurfer paths, and is trying to run the fsPalm command for each subcortical area of the three ROIs mentioned above, but that isn’t working either. Any help in running fsPalm would be greatly appreciated! Thanks, Amritha Amritha Harikumar Clinical Research Coordinator Holt Emotion and Social Neuroscience Lab Department of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital ___________________________ 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: 617-724-3283

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