Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Inconsistent Morphology Output
by Chen, Christine 11 Nov '19

11 Nov '19

External Email - Use Caution Hello, My lab has been running T1 (MPRAGE) data through run_subject (uses recon-all, autorecon, mris_volume and mris_wm_volume) then through run.r (pulls freesurfer.r and pedbirn.r) using the Desikan-Killiany atlas to output measures of cortical morphology. We've always gotten consistent output when rerunning data, however, lately when rerunning data using the exact same files as before, the output measures are different, sometimes significantly so, compared to when they were previously run. We recently installed the development version of FreeSurfer in a path different from $FREESURFER_HOME, which is still set to usr/local/freesurfer. We've also confirmed that all these runs have been using FreeSurfer v6.0 by looking at the /scripts/build-stamp.txt file. So the inconsistency in output might not be due to the FreeSurfer version used. Additionally, we are collecting a new dicom format, however when rerunning files collected in the previous dicom format through the pipeline and comparing this output to the output from when it was previously ran, the measures are still different, so the inconsistency in results might not be due to the dicom format. Do you have any ideas why this sudden change in outputs is being observed? Is there a flag we can add to the scripts to ensure results are identical and consistent with what they were previously, such as -norandomness or -seed 1234? Any help or guidance would be greatly appreciated. Thank you in advance. Best, CC ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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FDR for aseg
by Benjamin Ineichen 11 Nov '19

11 Nov '19

External Email - Use Caution Dear Freesurfer experts, I run the command mri_glmfit --table aseg.volume.stats.dat --fsgd GLM7.fsgd dods --C contrasts6.mtx --glmdir NFL.aseg.glmdir This gave me the output sig.table.dat. Is there a way to implement an FDR to this analysis in Freesurfer or do I have to use another statistical program for that? Many thanks for your support! Best regards, Ben

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Question about convert fsaverage to fsaverage5
by chenyang jiang 11 Nov '19

11 Nov '19

External Email - Use Caution Dear Fs Developers Hi, I am new to freesurfer, after I ran the recon-all command, I want to align the individual surface to fsaverage5 space. and then extracted the cortical thickness of each vertex. Should I use mri_surf2surf to do it, What's the specific parameter I should set up? like srcsurfval , trgsurfval and so on. would it be possible to give me entire command setting. Thank you so much! Chenyang

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T2 white matter surface refinement
by Defenderfer, Matthew K 11 Nov '19

11 Nov '19

External Email - Use Caution Hi, Looking through the documentation, there are extra options to include a T2 image to refine the pial surface boundary, but I was wondering if FreeSurfer can use a T2 in conjunction with a T1 to help refine the white matter/gray matter boundary? As in, gray matter with higher myelin content than average could cause the white matter boundary to be placed further out than normal when just using a T1; can FreeSurfer currently use a T2 image to help prevent that at all? Thank you -Matt Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology

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Longitudinal Analysis for functional connectivity data?
by Barbour, Tracy,M.D. 11 Nov '19

11 Nov '19

Hello Freesurfer experts! I see that there is a longitudinal processing pipeline for volume/cortical thickness. I was wondering if the same pipleline could be used for resting state functional connectivity based analysis? Best, Tracy

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mri_surfcluster error -- FsFastTutorialV6.0
by 王如雪 11 Nov '19

11 Nov '19

External Email - Use Caution Hi Sir/Madam: I got an error when executing the new version "mri_glmfit-sim" correction for multiple comparisons with permutation at the group level according to FsFastTutorialV6.0. This was the command I used: "mri_glmfit-sim --glmdir my-glm --perm 1000 1.3 pos --cwp .05 --2spaces" But it prompted: mri_surfcluster: could not read surface /home/freesurfer/subjects/fsaverage4/surf/lh.white No such file or directory after "mri_glmfit simulation done" However, I've verified that /home/freesurfer/subjects/fsaverage4/surf/lh.white existed and that I had read permission to it. And after I loaded it with freeview -f /home/freesurfer/subjects/fsaverage4/surf/lh.white, the lh.white file was opened in the freeview window while the command line prompted "Did not find any volume geometry information in the surface". Can you help me with this error? Thank you very much! Best, ---------------- Ruxue Wang PhD Student, Tsinghua University

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nuisance factors
by Georgina Angelopoulou 11 Nov '19

11 Nov '19

External Email - Use Caution I am sorry, please let me rephrase. I want to compare patients vs controls in Surface area and grey matter volume. I have already checked age slope and it is not significant for either GMV or SA. However eTIV slope is significant in both cases (we do check for eTiv slope first as we did for age, right?) So in that case that we have two nuisance variables (age and eTiv), eTIV is significant but age isn't, how are we going to formulate the contrast? Would 1 -1 0 0 0 0 be correct? Thanks once again, Georgina

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Post-doc position in fMRI research available at karolinska institute
by Erik Lindberg 11 Nov '19

11 Nov '19

External Email - Use Caution Hi we are looking for a new post-doc in neuroimaging at Karolinska Institutet at the Department of NVS. The Department of Neurobiology, Care Sciences and Society (NVS) conducts world leading research in aging, dementia, epidemiology and care sciences. For this position we are looking for someone that has experience in analyzing functional magnetic resonance images. Working with resting-state and experimental fMRI will be the applicants main duty in this project. The applicant may also work with different imaging modalities such as structural, diffusion tensor- and functional magnetic resonance imaging (fMRI) and its applications to Alzheimer’s disease and frontotemporal dementia. In particular, the person is expected to take an active role in applying advanced imaging methods. There are also possibilities to initiate individual research projects, based on the person´s interests and in collaboration with the University of Gothenburg. The successful candidate should show a high level of independency, be able to work in a team and be willing to supervise students. Further information can be found at: https://ki.varbi.com/se/what:job/jobID:295452/type:job/where:4/apply:1

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4d nifti probabilistic atlas of Thalamic Nuclei and Brainstem sub structures
by Mageshwar Selvakumar 11 Nov '19

11 Nov '19

External Email - Use Caution Dear all, I am interested in the probabilistic thalamic nuclei atlas and the brainstem substructure atlas. I downloaded the beta version of freesurfer to get acces to them, however i only see the thalamic nuclei one. Furthermore, Is there a way to convert the meshes into a 4d nifti probabilistic atlas. Or does someone already have a nifti that i could have access to? Thank you for your time Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898

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Brain connectivity postdoctoral position @ CIMeC University of Trento, Italy
by Jovicich, Jorge 11 Nov '19

11 Nov '19

External Email - Use Caution POSTDOCTORAL RESEARCH FELLOW (call open till December 6, 2019) - Development, testing and validation of MRI microstructural and functional connectivity methods to advance human neuroscience. - Center for Mind/Brain Sciences (CIMeC), University of Trento, Italy. - More details in the link below. Feel free to contact me for further information. Call Outline: https://r.unitn.it/en/cimec/mri/opportunities Application: http://bit.ly/CIMEC-MRI-Postdoc-Call-2019a Best, Jorge -- Jorge Jovicich, Ph.D. Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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