Freesurfer

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19 participants
30088 discussions

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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Obtaining MNI Coordinates for HCP annotations
by Dev vasu 19 Sep '19

19 Sep '19

External Email - Use Caution Dear all, I would like to obtain MNI coordinates for HCP annotations , i have annotation files for both lh and rh ( which are attached ) , i would like to obtain MNI coordinates for them . I was going through the post https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2015-November/042446… , but i could not get a better understanding on how to generate MNI values for each label in annot files , that i would like to use for graphical analysis. Thanks Vasudev

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Recon-all on a cluster error
by Lauricella, Michael 19 Sep '19

19 Sep '19

External Email - Use Caution Dear Freesurfer Experts, I have a an error when running recon-all on a computing cluster. I've checked the environment and so have some of my more knowledgeable colleagues but we can't see anything wrong with the environment. I was wondering if anyone else has experienced difficulties like the one below when trying to run recon-all on a computing cluster and might have some advice. Error of my run is below and the full log file is attached. Thank you in advance for your help! "Iteration 1 Wed Aug 7 13:53:08 PDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.18980/nu0.mnc ./tmp.mri_nu_correct.mni.18980/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18980/0/ -iterations 1000 -distance 50 [mlauricella@qb3-id115:/mnt/freesurfer_subjs/SUBJECT_ID/mri/] [2019-08-07 13:53:08] running: /mnt/neuroimaging/FreeSurfer/V6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18980/0/ ./tmp.mri_nu_correct.mni.18980/nu0.mnc ./tmp.mri_nu_correct.mni.18980/nu1.imp Assertion failed at line 742 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux qb3-id115 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SUBJECT_ID exited with ERRORS at Wed Aug 7 13:53:09 PDT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" Best, Michael

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fsPALM - Path Issue?
by Harikumar, Amritha 19 Sep '19

19 Sep '19

Hello, I had emailed the Freesurfer Forum a few weeks back about trying the PALM analysis for permutation testing. I recently tried fsPalm again on running some of our subcortical analyses for the caudate, putamen, and nucleus accumbens, and we performed the following steps: * Set our respective ROIs (e.g. caudate, putamen, nucleus accumbens) * Set the paths for fsPalm to run for each of the ROIs * Ran mri_glmfit as noted in the Freesurfer Help documentation for fsPalm for the three ROIs We ran into several issues. When we looked in the ‘run_palm.m’ output file under the subfolder for our first ROI that we tried to run PALM analysis for, it mentions ‘error in run_palm: zthresh = fast_p2z(pthresh)'. We are not sure where this function fast_p2z is supposed to be called from, as it is not located in any of the Matlab scripts when downloading the package for fsPalm (e.g. the palm-alpha115 file from Freesurfer). My question is - are we missing a path, or several paths that we have to put into the Matlab script, or does fsPalm no longer work for running such analyses? fsPalm has worked in the past for one of my colleagues using the palm-alpha112 file, but we are now having trouble running this using the palm-alpha115 file version. Any help 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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Cortical thickness (spc) extraction
by AKUDJEDU, THEOPHILUS 19 Sep '19

19 Sep '19

External Email - Use Caution Dear FreeSurfer, I used QDEC for the longitudinal two‐stage model analyses, where temporal data within each subject was reduced to a symmetrised percent rate of change (spc) maps using the long_mris_slopes function for data acquired at two time-point. I observed an abnormal region with different spc in patients relative to controls over time. How do I extract the spc for this region in each individual? What scripts do I use? Thanks Theo

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