Freesurfer March 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
161 discussions

mri hippocampal subfields:output file
by Loreto, Flavia 18 Mar '20

18 Mar '20

External Email - Use Caution Dear FreeSurfer experts, Version: FreeSurfer 6.0 Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave We have run hippocampal subfields segmentation analyses and we are now having problems exporting the volumetric outputs. We have run Iglesias’ ‘obsolete’ script to obtain hippocampal volumes, as our system does not support the dev version of Freesurfer. recon-all -all -s bert -hippocampal-subfields-T1 Then, to gather volumes from our analysed subjects, we have run this script quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory> In particular, this is how it looks in our terminal: -bash-4.2$ quantifyHippocampalSubfields.sh T1 hippo_demo.txt /rds/general/project/amyloidpet/live/freesurfer Gathering results from subjects in: /rds/general/project/amyloidpet/live/freesurfer Using the suffix name: T1 And writing them to: hippo_demo.txt However, we are not able to find the output anywhere. Could you help us figuring out what could be the reason why can’t find it? I have attached the recon-all.log for one of our analysed subjects. Many thanks for your help. Kind regards, Flavia

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longitudinal FreeSurfer help
by Swati Rane 17 Mar '20

17 Mar '20

External Email - Use Caution Dear FreeSurfer experts, I simply do not understand the LME setup for longitudinal analyses. Here is what I have: 3 groups each with variable longitudinal data (in terms of umber of time points and interval between timepoints). I am interested in detecting if the rates of longitudinal atrophy in each of the 3 groups and whether it is significantly different between the 3 groups. 1. My Qdec file contains: fsid, fsid_base, time, age, group, gender 2. I read in the relevant files with (output of surf2surf, lh.cortex, lh.sphere) 3. I read the Qdec file removed the first column, obtained the subject IDs, keep numerical data and get a sorted ‘M’ matrix 4. X=[intercept time grp1 time*grp1 grp2 time*grp2 grp3 time*grp3 age@timepoint1 gender] 5. After that, should I use voxel wise mass-univariate model or spatiotemporal mass-univariate model lme_mass_fit_vw or lme_mass_fit_EMinit? 6. After that I don’t understand the subsequent steps. Can you help me understand? Any help is appreciated. Thanks! Swati

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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

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Freesurfer March 2020