Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 36 Topic 14. Error with command: mri_em_register: RB40_talairach_2005-07-20.gca. No such file or directory (Greve, Douglas N., Ph.D.)
by Camerino, I.L. (Ileana) 12 Jan '21

12 Jan '21

External Email - Use Caution Dear Douglas, Thank you so much for your reply. After trying: mri_em_register -mask brain.mgz -p .5 nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta I got the following error: using MR volume brain.mgz to mask input volume... using top 50.0% wm points as control points.... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/6.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... mghRead(/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/mri/brain.mgz, -1): could not open file mri_em_register: could not open mask volume brain.mgz. In fact the the file brain.mgz is not present in the mri folder. I am a bit lost since I am getting a different error every time I try to solve the previous one and I do not understand what is the problem exactly. The first error I got after running recon all on this subject (with a massive stroke on the left hemisphere) is a watershed error. So I added the control points and run: recon-all -autorecon2-cp -autorecon3 -subjid /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056. After which I got the error: mghRead(/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/mri/norm.mgz, -1): could not open file assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... mri_normalize: could not open source file norm.mgz Finally to solve the above error I run: mri_em_register -mask brain.mgz -p .5 nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta but I got yet a new error: -1): could not open file mri_em_register: could not open mask volume brain.mgz. Please could you let me know how can I understand what is the problem and how can I solve it? Best regards Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

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Transform rescaled non-pvc PET to surface
by Julie Ottoy 12 Jan '21

12 Jan '21

External Email - Use Caution Dear Freesurfer team, I have a question related to petsurfer. On the website, it is stated that "If you are not using PVC, you can use the template.reg.lta to sample the PET volume onto the surface using mri_vol2surf, then apply standard surface-based analysis." However, I was wondering how to do this for PET data that I first want to normalize to a reference region (to perform group-wise glm analyses afterwards). For example, I want to transform the "non-pvc and pons-rescaled PET volume" to the surface. Is there a way to easily do this? Or should I use the --scale flag with vol2surf and input the non-pvc reference region value for each subject reading from the gtm.stats.dat file, which I got from the mri_gtmpvc with --psf 0 --no-tfe --no-rescale? Thank you for the help! Best regards Julie

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Fw: recon-all -hires option
by S.R. Poortman 12 Jan '21

12 Jan '21

External Email - Use Caution Dear list members, As a PhD student working on longitudinal child and adolescent T1-weighted data (.75x.75x.8 mm3) acquired at 3T (age range: 8 - 18 at baseline; 11 - 24 at follow-up), with the aim of doing cortical laminar analyses eventually, I am interested in getting the most of our lab's submillimeter resolution data. Therefore, in addition to a default recon-all run (with the -3T option enabled), I ran a separate recon-all with both the -3T and the -hires option enabled (with mris_inflate -n 50 added to the expert file), resulting in the following two runs: recon-all -all -i ${subj} -subjid ${SUB_ID} -3T and recon-all -all -i ${subj} -subjid ${SUB_ID} -3T -hires -expert $EXPERT_FILE Now, the surfaces (i.e., lh.pial, lh.white, rh.pial, rh.white) seem to be calculated more accurately for most brain regions, indeed, which looks very promising. However, the brainmask.mgz turns out to be of poor quality for a number of our subjects, cutting away a substantial portion of the brain. See the image below for an example of the same subject, on which both runs have been performed. The same slices are shown for each run. As can be seen in the image, a part of the the temporal region of the brain has been excluded in the brainmask.mgz of the -hires run (left in the image). [cid:b4d26f40-11bb-4d8f-888c-ab4da9fea062] Is there anything I can do, such as adjusting certain parameters, to prevent this from occurring? It would be a shame if I couldn't make use of the -hires option due to this, as it does seem to be a promising option in all other aspects. Thank you for considering my question. I look forward to hearing from you. Good holidays to you! Kind regards, Simon Poortman (Erasmus MC, Rotterdam, the Netherlands)

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Segmentation Fault During mri_convert running FS 5.0
by Dowling, Kevin Francis 12 Jan '21

12 Jan '21

Hello FreeSurfer experts, We have some old clinical structural data we processed using version 5.0 and had extensively edited manually. We’re now hoping to re-process the data in version 5 to regenerate copies of the subjects that are free of manual edits. So far (because of the below core dump error), I’ve tried doing this two ways, first by running recon-all -autorecon-all -clean -s <subject> on copies of our manually edited data and, secondly, by using from the original, unaltered MPRAGE files and running recon-all -i ./path/to/MEMPRAGE.nii -s <subject> (which fails before we would then run recon-all -autorecon-all -s <subject>). In both cases I’ve run into an error I never encountered when last working with this data 2 years ago in version 5. Specifically I get a “Segmentation fault (core dumped)” when mri_convert is invoked. I’ve enclosed a copy of the recon-all.log and recon-all.error files as attachments and provided the specific commands that seem to trigger the core dump below (from recon-all.error file). I looked on the mail archive but I wasn’t able to find any answers. I’m running version 5.0 (as that is the version our manually edited data was processed in): setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 I’m running Red Hat Enterprise Linux Release 6.7 (Santiago) The specific commands that appear to be causing the (Segmentation fault) core dump in each of the two different cases are below (taken from recon error log): When running: recon-all -i ./path/to/MEMPRAGE.nii -s <subject> the error occurs with.. mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii /autofs/cluster/roffman2/users/RPDR_FromRaw_No_Edits/00033/mri/orig/001.mgz When running: recon-all -autorecon-all -clean -s <subject> the error occurs with.. mri_convert /autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/rawavg.mgz /autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/orig.mgz --conform Notably, when I tried running the same commands (bolded above) in version 5.3 (source/usr/local/freesurfer/nmr-stable53-env) they both exit without errors, leading me to wonder if this is a software-version interaction issue. (In case it has any bearing, I’m running all of this while ssh’d into the Martinos servers.) I suspect I may have missed something very simple, but I would be very grateful for any suggestions for how I might try to overcome this issue. I’m happy to provide clarification or any additional information that may be helpful. Thank you, Kevin Kevin F. Dowling Per-Diem Clinical Research Coordinator Brain Genomics Laboratory Department of Psychiatry Massachusetts General Hospital MD/PhD Candidate University of Pittsburgh & Carnegie Mellon University MSTP

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The lookuptable value of Virchow–Robin space
by Aaron Tanenbaum 12 Jan '21

12 Jan '21

External Email - Use Caution Ideally, what should Virchow–Robin space be labeled as.

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eTIV=0.0 on volumes where control points have been added manually
by Julia Lam 12 Jan '21

12 Jan '21

External Email - Use Caution Dear all, I received values of 0.0 on variables BrainSegVolNotVent and eTIV when running aparcstats2table on volumes where I've added control points. Why is that? I really appreciate any help you can provide. Yours sincerely Julia Lam

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FW: Faculty Positions in BME School of ShanghaiTech University
by Fischl, Bruce 11 Jan '21

11 Jan '21

Hi All See the attached faculty openings in Shanghai Cheers Bruce From: Dinggang Shen <dgshen(a)shanghaitech.edu.cn> Sent: Sunday, January 10, 2021 9:48 PM To: Fischl, Bruce <BFISCHL(a)mgh.harvard.edu> Subject: Re: Faculty Positions in BME School of ShanghaiTech University External Email - Use Caution Hi, Bruce, Happy New Year! I am now in ShanghaiTech University, helping build School of Biomedical Engineering. If you know any qualified candidates who may be interested in faculty position in ShanghaiTech BME School, please help recommend. More details about faculty positions are provided in the attachment. Thanks. Please also feel free to forward this email. Best, Dinggang Shen

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BIDS-PET extension request for comments - closes on Friday (Jan. 22nd)
by Franklin Feingold 11 Jan '21

11 Jan '21

External Email - Use Caution We are happy to announce that the Positron emission tomography BIDS extension is finally nearing it’s completion. Hence, we are seeking final community feedback for the PET BIDS standard. We are looking for feedback on GitHub and specifically to the BIDS-PET extension proposal<https://secure-web.cisco.com/1bByOsPwW5V4ULpYAowQ2tJ3GsVakW2j6M0vRnBq3X6q1n…>. We have also developed an extension for the validator<https://secure-web.cisco.com/1kOebq-NBdHXE2Rhmum4xlBgBZ_6NCwVFa7N9bs1FDO-pG…> and added PET examples into BIDS examples<https://secure-web.cisco.com/1ioWTTq8pZ9DXpmgxJQjHceibnPTCb-ANN3JLVJgiNtD5b…>. The community review will close on Friday (Jan. 22nd) at 11:59pm PT (pacific time). This BIDS extension seeks to establish how PET data and additional metadata are organized within the BIDS structure. This encompasses the recent guidelines for brain PET data in publications and in archives provided in the consensus paper (Knudsen et al. 2020<https://secure-web.cisco.com/1yCSN92-EIL-vkLQ5_FhgmscyuZQXdmTxGu3UQONhJNegf…>), including blood and metabolite data. The final review entails a two week period for public commenting, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (Please see our release protocol<https://secure-web.cisco.com/1QWVanNWx0rbij03q3usRZFdY7frxdHRgmDBpKoXk_cHE-…> for more details) We are looking forward to hearing from you, Melanie Ganz (BEP 009 lead) and team

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Correcting pial surface with Flair sequence
by Georgia Kapizioni 09 Jan '21

09 Jan '21

External Email - Use Caution Hello Freesurfer Developers, I am conducting a group analysis between a patients and a control group. I have accomplished recon-all individual analysis and I want to correct pial surface using 3D Flair. I would like to ask two specific things: 1. Is 3D Flair appropriate or only T2 Flair is recommended for such correction. From what I have read on previous posts, it is usually recommended to use T2 Flair. 2. For my data, for most of my 3D data slice thickness is 1 mm, but for some of them is 1.48 mm. Is that difference going to affect analysis results? Thank you in advance, Georgia

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write .annot files
by Octavian Lie 08 Jan '21

08 Jan '21

External Email - Use Caution Dear All, These are probably rookie questions. 1. I can read an .annot file with read_annotation.m, is there a way to write one? (for example read it to matlab, modify, and save, or create a combined (lh+rh) aparc.annot file etc. 2. On the same line, how one combines all the Brodmann labels into a Brodmann parcellation, if not done already.. Thank you, Octavian

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