Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

Error in selxavg3-sess
by Nina Khatibi 12 Jan '21

12 Jan '21

External Email - Use Caution Hi, I'm using a functional analyse with selxavg3-sess, i have 25 subjects and each subject contains 15 runs, I've done plenty of analyses with different paradigm files, but now with a paradigm file of 5 conditions, I face an error on subject 22 run 12, which I can not solve.I wonder if you can help me. I'm using macbook pro 2018, macOS Mojave 10.14.6 and freesurfer-darwin-macOS-7.1.1-20200811-8b40551 outanadir = /Volumes/ADATA/FunctionalData/Subject22/bold/fsaverage5Con2Sec.lh/pr012 Excluding 4 points ERROR: fast_st2fir: two or more presentations are simultaneous ERROR: creating FIR design matrix for Condition01 Dot indexing is not supported for variables of this type. Error in flac_customize (line 354) if(~isempty(flacnew.TFmtx)) Error in fast_selxavg3b (line 179) flac = flac_customize(flac); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Regards, Nina

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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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recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}
by Ben Deen 08 Jan '21

08 Jan '21

External Email - Use Caution Hi all, I'm encountering an issue with surface reconstruction quality in ventromedial prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted input data to recon-all. I'm using the following command, with Freesurfer 7.1.1 running on Mac OS 10.15.7 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551; the options file specifies "mris_inflate -n 30"): recon-all -s ${subject} -i T1w.nii.gz -all -hires -expert ${optsFile} -T2 T2w.nii.gz -T2pial Across four participants I've tested with this approach, there is a consistent reconstruction issue with the gyrus rectus and medial orbital gyrus, in which they are cut off in the white and pial surfaces (see images at https://secure-web.cisco.com/1YjHwYMb6FHlCVkbgjtpceoj_IZMMa8YVArerusSJpfEDY… it's particularly clear against the T2 image). I've tried to correct the issue by manually modifying wm.mgz to include all wm voxels in these gyri. However, when I do so and rerun autorecon2-wm, the orig surface improves to incorporate the edits to wm.mgz, but the white/pial surfaces do not. By debugging individual steps of recon-all, I've found that the -white step seems to be to blame for this: when I rerun this step, the output white.preaparc surface doesn't change to incorporate my edits to wm.mgz. Any thoughts as to what might be causing these issues - both the initial reconstruction problem, and the failure to update with manual edits? There is some signal dropout in the T1 image in this region, which may contribute to the issue, although I would hope the T2 image could compensate for this. Thanks, Ben

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tkregister-sess: no windows pop up
by Kazuhisa Shibata 04 Jan '21

04 Jan '21

External Email - Use Caution Dear the developers. I have been trying to check the quality of registration between functional and structural images by using tksurfer-sess. Although it says “tkregister-sess completed”, no windows pop up. I have confirmed that Xquartz is working (xclock shows the clock). I’d be extremely grateful if you could give me your advise on this. For your reference, I have attached a log file and showed what was displayed on the terminal below. I use Mac OS11.1. Best, Kaz -- Kazuhisa Shibata Team Leader Lab for Human Cognition and Learning Center for Brain Science RIKEN https://secure-web.cisco.com/1_DTkcMx0GtpUOQXiw7nzTp30ywRlb3dnZPqeNvkA-BtbU… kazuhisa.shibata(a)riken.jp kazuhisa.shibata(a)gmail.com

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talairach.lta coordinate spaces
by Tisdall, Dylan 03 Jan '21

03 Jan '21

External Email - Use Caution Hi list, I'm trying to understand whether the talairach.lta transform is from the image-axes RAS to talairach or the scanner-axes RAS to talairach. Basically, if I rotate the imaging FOV and scan the same subject, should I expect that to change talairach.lta or not? My confusion stems from the discrepancy between what the scanner terms RAS coordinates (aligned to the gradient axes) vs. what might be plausibly called RAS in the image coordinates (aligned to the FOV axes). The underlying goal here is to try to evaluate how gradient-axis-aligned someone's head was when they were loaded in the scanner. Thanks, Dylan --- Dylan Tisdall, PhD Research Assistant Professor Department of Radiology Perelman School of Medicine University of Pennsylvania Room D406 Richards Medical Labs 3700 Hamilton Walk Philadelphia, PA 19104

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Re: [Freesurfer] error in running tkregisterfv (Greve, Douglas N., Ph.D.)
by Peter de Best 03 Jan '21

03 Jan '21

External Email - Use Caution Dear Dr. Greve, Thank you so much for the information. However, after adjusting the registration file to *.lta, I get the same error message. It will probably help me correctly coregister func & anat in the future, but the issue seems more likely to be connected to some setting that I cannot seem to find... Do you have any suggestions/ tips? Best regards (and happy new year), Peter

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Access to datasets used for validation of sbTIV and eTIV measures
by Erus, Guray 03 Jan '21

03 Jan '21

External Email - Use Caution Hello FreeSurfer Developers, I'm working on the validation of a method that calculates ICV. The wiki pages on eTIV and sbTIV: https://secure-web.cisco.com/1NfwRceKeD3VTf9pMcEK-JbxIvMnSdQdPlMoLFc8Asj7-1… https://secure-web.cisco.com/1NnGHZWJ6QIknzbA50Q86PSKxQrceCNCSBmR1j4U6EVMlc… include very useful information related to my work. These pages refer to 2 datasets (SASHA and ADNI30) with manual ICV masks. The text also indicates a path for one of these datasets: "... These subjects are found in /space/freesurfer/subjects/atlases/SASHA ..." If I understand correctly, this is a local/restricted path that is not publicly available. Is that correct? Is there a way I can get access to these datasets for my validation experiments? Thank you and happy new year! Guray Guray Erus, PhD Senior Research Investigator Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Richards Building 3700 Hamilton Walk, 7th Floor Philadelphia, PA 19104

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segmentation fault
by Wei Koo 03 Jan '21

03 Jan '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon2 for a number of subjects, but one of my subjects I get the following error when I run the mri_tesellate command: Removing intersections Segmentation fault FreeSurfer version: freesurfer-darwin-macOS-7.1.1.

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Question about a feature introduced in FS 7.0
by Aaron Tanenbaum 03 Jan '21

03 Jan '21

External Email - Use Caution I am curious about a feature introduced in FS 7.0 In the release notes it says, "Ability to freeze the surface at points labeled 247 in the aseg.presurf.mgz" I was interested to know what this feature can do. Do you have any examples of when this should be used? Aaron Tanenbaum

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Re: [Freesurfer] Password Request for VirtualBox Ubuntu
by fsbuild 30 Dec '20

30 Dec '20

External Email - Use Caution Hello Kanon, I am sending the information to your email address shortly. - R. On Dec 30, 2020, at 02:09, 藤本花音 <fujimotokanon86(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I am attempting to start Ubuntu via VirtualBox on Windows 10, but  Ubuntu requests a login password for the "Developer" account, while installation guide assumes automatic login.Can I ask for the password or is there any other way to successfully start Ubuntu?  For the installation and setup, I followed  the Windows VM Install & Setup, using the virtual disk image of the VM Ubuntu_710_clone_2.7z (downloaded on Dec 29, 2020).Thank you very much,Kanon Fujimoto-- --------------------------------------------------------------藤本花音TEL:09081307404E-mail:fujimotokanon86@gmail.com_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer December 2020