Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

overlay threshold in freeview
by Rachele Sanfelici 17 Mar '20

17 Mar '20

External Email - Use Caution Dear Freesurfer experts, I created .mgh files from a dimensionality reduction analyses (similar to parcels from a known parcellation). These matrices have low values near to 0. When I overlay each of the .mgh file in freeview, it gets automatically thresholded with what seemed to me the median or mean of all the vertices' values (i.e., when looking at the "configure overlay" option)--however, this is not the case. Thus, I wanted to ask how the threshold is precisely set, so that I can automate and incorporate it in other scripts for binarizing my matrices. Thanks a lot in advance for your help, Rachele

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Re: [Freesurfer] cent OS8 and Freesurfer 5.3 {Disarmed}
by fsbuild 16 Mar '20

16 Mar '20

External Email - Use Caution Hello Suzanne, I have not tried running Freesurfer version 5 on CentOS8, but it would not surprise me if it is not entirely compatible with the newer versions of the system libraries on CentOS8. The Freesurfer version 7 beta release just came out this February (https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1) and development is working on getting the full release out (with subsequent 7.X point releases to follow).  So I think the expectation going forward is for users to eventually migrate from freesurfer 6 to 7.  But I don’t know of any planned updates or changes to rev 5 (which is essentially 2 releases old now). If you want to maintain OS compatibility for older freesurfer releases, then one option is to use a VM or a container to keep and run older versions of CentOS.   I think CentOS6 is going to be end of life'd this coming November, but you should be able to download virtual disk images of the last release of CentOS 7, 6, 5, etc. for quite some time from osboxes.org and other sites. - R. On Mar 16, 2020, at 19:36, Suzanne Baker <slbaker(a)lbl.gov> wrote:        External Email - Use Caution        are there any plans to make Freesurfer 5.3 compatible with Linux cent os8?_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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cent OS8 and Freesurfer 5.3
by Suzanne Baker 16 Mar '20

16 Mar '20

External Email - Use Caution are there any plans to make Freesurfer 5.3 compatible with Linux cent os8?

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RAs will pick up anything with 'tutorial' in the subject line
by Morgan, Leah 16 Mar '20

16 Mar '20

The RAs will pick up any and all questions that reach the helplist over the next few weeks with 'tutorial' in the subject line. We're encouraging people to try the lectures and tutorials on their own at home and anticipate a bunch of tutorial-related questions to come through. Also, we'll be more active in tackling the data processing and troubleshooting questions for users over the next few weeks of remote work. Leah

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freesurfer- recon-all "exited with ERRORS"
by Frank Chau 16 Mar '20

16 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, I ran a recon-all on a recent batch of T1 Nifti files and all ended with "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited with ERRORS at Sat Jan 11 01:32:55 HKT 2020". I've searched the email archive list and I found other researcher encountered same problem before. However, I am quite sure their root causes are not same as my case. 3 possible causes were found in the email archive which about "exited with ERRORS": 1. The version of freesurfer (I have already used the latest 6.0.0 version) 2. Hard disk space (My computer have enough hard disk space) 3. sharing folder between virtual machine and original platform. (I use freesurfer in Mac OS which do not have this problem) I uploaded the recon-all.log to my dropbox in case it's of any use. 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) Platform: MAC OS X 10.11.6 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64 4) recon-all.log, please download at: https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Outpu… Regards Frank --------------------------- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mail : cyfrank(a)hku.hk<mailto:cyfrank@hku.hk> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong

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Error: mri-glmfit-sim
by Edith Botchway 15 Mar '20

15 Mar '20

External Email - Use Caution Hi, I'm new to FreeSurfer and working my way through the tutorial on cluster correction for multiple comparisons. I encountered an error with the --perm flag at the simulation stage but I can't find any help online regarding this. Here is the code I run: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1 And this is the error message: ERROR: Flag --perm unrecognized. Kindly advice. I am working on a windows computer and running FreeSurfer via VirtualBox. Thanks Naa Important Notice: The contents of this email are intended solely for the named addressee and are confidential; any unauthorised use, reproduction or storage of the contents is expressly prohibited. If you have received this email in error, please delete it and any attachments immediately and advise the sender by return email or telephone. Deakin University does not warrant that this email and any attachments are error or virus free.

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Using Freesurfer with post contrast MRI
by Hoang, Ricky 15 Mar '20

15 Mar '20

External Email - Use Caution Hello Freesurfer users, I have a general question regarding using freesurfer to process postcontrast MRI scans. I have tried to run recon-all with a few subject’s scans and there has been issues with the skullstripping as well as labeling high intensity areas like the venous sinuses as white matter. The runs don’t even finish usually. I was wondering if there is a method to run recon-all that helps take into account contrast. If that’s not possible, I am mainly focused on the cortical thickness of the occipital cortex. If I do a good job doing quality control around the occipital lobe, but a less robust job elsewhere, will it affect the cortical thickness measurements of the occipital cortex? Best, Ricky

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how to calculate the ROI volumes of grey matter using Desikan atlas
by Kate Marvel 15 Mar '20

15 Mar '20

External Email - Use Caution Hi Freesurfer community, I would like to know how to compute the ROI volumes of grey matter using Desikan atlas? Is there a threshold value set for this? is it 0.2? Thanks kate

2 2

Group analysis
by Hengameh Marzbani 14 Mar '20

14 Mar '20

External Email - Use Caution Hello Freesurfer developers, 1- I want to extract the uncorrected clusters from the uncorrected significance maps obtained from mri_glmfit for structural data (to illustrate cluster, size, location, and significance) like abs.sig.cluster.summary (summary of clusters (text))which is obtained from mri_glmfit-sim. Is there a way to do this? 2- I don't see any clusters when I use cluster-based correction for multiple comparisons (for example mri_glmfit-sim \ --glmdir lh.Area.glmdir \ --sim mc-z 10000 2 mc-z.abs\ --sim-sign abs --cache 4 neg \ --cwp 0.05\ --2spaces). How much is it significant if I report the uncorrected clusters? 3- Are there new ways of looking at the whole brain together (not left and right hemisphere separately)by Qdec and FSGD? 4- How can I do fdr correction in mri_glmfit-sim? what flag should I use? 5- How can I demean and normalize the covariates when I use FSGD? what flag should I use? Thanks you in advance! Best regards, Hengameh

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tracula error too many ('s
by Renew Andrade 14 Mar '20

14 Mar '20

External Email - Use Caution Dear FreeSurfer experts: I mentioned an error that I still cannot fix. I don’t think is the “\” because as you can see in the file attached everything seems correct. I cannot fix the issue with TRACULA I attach the configuration file so you can check in effect is correct. Sincerely, Andrade.

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