Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

Error
by Kirill Elin 10 Jan '20

10 Jan '20

External Email - Use Caution Dear FreeSurfer Developers, I am trying to run the script and the recon-all command and getting Exited with errors output. 1. FreeSurfer Version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2. Platform, VM Ware Workstation 15, host OS: Windows 10, Guest: Ubuntu ubuntu-18.04.3-LTS, 64 Bit, 2 GB RAM 3. See the log file and the screenshot. In the script I have not found any other errors so I am not even sure, what I should be looking for. If it plays a role, my MRI folder, where original T1s are as well as the output folder are in the shared folder (shared between the host windows OS and the virtual machine). I would be grateful if you could help me out with this. Thank you in advance. Sincerely yours, Kirill

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Right Lateral Ventricle Omitted from white and pial surfaces
by Rachel Hoel 10 Jan '20

10 Jan '20

External Email - Use Caution Dear Freesurfer Developers, In one of our recons I'm seeing that the right lateral ventricle is partially excluded from the white matter and pial surfaces (screenshots attached). The aseg.mgz has no label for the omitted region. We are using v6.0. What is recommended for fixing this type of error? Filling in the wm.mgz where the omission is? Thanks in advance, Rachel

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single-trial analysis of BOLD data in FSFAST
by Katsumi, Yuta 10 Jan '20

10 Jan '20

Dear Doug, I would like to perform GLM on a trial-by-trial basis in FSFAST. That is, I'm interested in obtaining beta estimates per trial and using them as input for group-level analyses of activation patterns (e.g., MVPA) or functional connectivity (e.g., beta series correlations). I've done this in the past using SPM to analyze data in volume space, and now would like to take a similar approach using FSFAST to analyze data in surface space. Would you please advise how I might be able to implement this? Thanks in advance for your input. Best, Yuta

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funcroi-sess annotation issue
by Lewis, Lydia R. 10 Jan '20

10 Jan '20

Hello Freesurfer Team, I am running the fsfast analysis stream for resting state data and recently came across an issue with the funcroi-sess command. I originally used funcroi-config to configure the rois with the -annot aparc.a2009s $ROI flag to seed each of the regions from the 2009 annotation. But when I tried to do funcroi-sess I got the following error ERROR reading $projectdir/sess01/rest/lh_G_and_S_frontomargin.fc/tmp.funcroi-sess.lh.G_and_S_frontomargin/label/lh.lh_G_and_S_frontomargin.label It seems like this is because first command (mri_annotation2label) generates labels with slightly different names, such as $projectdir/sess01/rest/lh_G_and_S_frontomargin.fc/tmp.funcroi-sess.G&S_frontomargin.fc/label/lh.G&S_frontomargin.label. For instance, if I edit the config file to: roiname lh.G_and_S_frontomargin annot aparc.a2009s G&S_frontomargin fillthresh 0 analysis lh_G_and_S_frontomargin.fc the funcroi-sess command works fine. As a solution, I edited my script to change the annotations to 1) remove the hemisphere from the prefix, and 2) replace G_and_S with G&S. With these changes, the funcroi-sess command seems to be working correctly. I just wanted to get some feedback on whether this was a valid solution, or if this error is occurring because of some other larger issue that I will need to fix/be aware of. For reference I am using the stable6 version of freesurfer. Thanks for your time, Lydia Lewis

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Please help! Talairach Fail error message
by Isabella Leung 10 Jan '20

10 Jan '20

External Email - Use Caution Hello Freesurfer Community, I have been processing my T1 data through the Freesurfer dev version. Recon all has worked for the majority of the scans but for a couple of them, it gives me an error message saying "Talairach Failed". Essentially, I want to do the HA segmentations after. Is the Talairach step necessary for that? Or can I skip it? If not, is there a way to fix this error? Any help would be greatly appreciated!!! Best regards, Isabella Isabella Hoi Kei Leung | PhD Candidate Brain & Mind Centre | Central Clinical School | Faculty of Medicine THE UNIVERSITY OF SYDNEY Room 408, Level 4, Bldg M02K | 94 Mallett St, Camperdown NSW 2050 Australia M +61 404 066 903 E isabella.leung(a)sydney.edu.au

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average subject with 5th order icosahedron tesselation
by Marina Fernández 10 Jan '20

10 Jan '20

External Email - Use Caution Dear Freesurfer experts, Now, I would like to downsample the average subject of a dataset (that is a 7th order icosahedron tesselation) to have surfaces with 10242 vertices (5th order icosahedron tesselation). How can I do that? Thank you in advance. Best regards, Marina.

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Volume correction with Intracranial volume
by Steve Petersen 10 Jan '20

10 Jan '20

External Email - Use Caution Dear Freesurfer experts, I would like to perform external analysis with the hippocampus, parahipocampus and entorhinal volume. As I understand its the hipocampo volume should be corrected using the subject´s intracranial volume. 1. How do you recommend correcting the volumes (hippocampus, parahipocampus and entorhinal cortex) with the intracranial volume? Maybe correcting the volume by scaling with the EstimatedTotalIntraCranialVol? 2. Is necessary to correct the cortical thickness measurements with the intracranial volume? Thanks for your help. Best regards,

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Lesion Correction
by Horn, Mitchell Jacob 10 Jan '20

10 Jan '20

Hi Freesurfer Team, I have a couple cases with large hemispheric ICH that have caused my recon to hit the default wall-time of 96 hours. It seems to get hung up on the correcting topology defects step for the affected hemisphere. My goal is to have the recon at least finish so I can analyze the unaffected hemisphere. I have tried WM-edits, and just recently tried generously covering the ICH in the aseg.presurf with the WM-hypointensity label 77. I then submitted the recon to start just after the aseg.presurf generation with the following tags, < recon-all -autorecon2-cp -autorecon3 -subjid $subject >. However, when it gets to the fix topology point for the affected hemisphere, it hangs at this point with a huge defect as shown below: reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.2324 (-4.6162) -vertex loglikelihood: -6.5360 (-3.2680) -normal dot loglikelihood: -3.5251 (-3.5251) -quad curv loglikelihood: -6.0339 (-3.0169) Total Loglikelihood : -25.3274 CORRECTING DEFECT 0 (vertices=26285, convex hull=5359, v0=0) Is there something I can do to at least skip the correction of the affected hemisphere? Thanks in advance, Mitch

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Freesurfer 7T MPRAGE
by Manoj Saranathan 10 Jan '20

10 Jan '20

External Email - Use Caution Hi, I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In previous threads, a few people have suggested using SPM to correct for bias first and then running recon-all. Alternatively I saw a thread which suggests modifying the mri_nu_correct command https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html Can I edit the recon-all to run this alternative command and simply run recon-all? The threads are all really old and SPM is now SPM12 which integrates things. Is this modified bias correction inside FS as good as SPM ? I am mainly interested in thalamic segmentation. Are there others with the same issue? Thanks manoj Manoj Saranathan Associate Professor, Dept. of Medical Imaging University of Arizona Ph: 520-626-6531

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pcc.mgh files from mri_glmfit using --pvr
by Emilie Reas 10 Jan '20

10 Jan '20

External Email - Use Caution I am running mri_glmfit using the --pvr option and do not get a pcc.mgh file with the output. I found an old thread from 2017 in which Douglas Greve explained that "mri_glmfit will not generate a pcc file with --pvr. I think I just did not get around to adding support for this." Have there been any updates to fix this? Is there a workaround to get pcc files using --pvr? -- Emilie Reas, PhD Postdoctoral Fellow, UC San Diego ereas(a)ucsd.edu

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Freesurfer January 2020