Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

Masking A Surface Overlay
by Jacoby, John 29 Jun '21

29 Jun '21

Hi all, I've used mri_glmfit to run some GLMs on surface data. Now I would like to visualize the "gamma.mgh" output in freeview, but only with vertices colored if they're above or below a certain value according to the "z.mgh" output of mri_glmfit. In other words, visualize the gamma file normally but keep non-significant vertices uncolored. So far, I tried using mri_binarize on z.mgh to create a file with ones on the significant vertices and zeros everywhere else. Then I used mris_calc "masked" option to mask the gamma file by the binarized z file. This sort of works, but by "masking" it just sets the output file to zero outside the mask, and zero is still colored like any other number in freeview. I want non-significant areas to be entirely un-colored. Is this possible? Thanks in advance for any help. Best, John

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Recon-all soft errors
by Rosalia Dacosta Aguayo 29 Jun '21

29 Jun '21

External Email - Use Caution Dear Freesurfer team, I am inspecting the different participants I have run recon-all -all and I have found different errors I would like to discuss with you before proceeding as I am new with this software. 1. I have found dura at some regions of the brain. I should use gcut or delete voxels? 2. I have found discontinuity in GM and what I should do with this (attached photo 2) 3. In photo 1, not sure at some regions were to consider wm as it is not clear for me...any suggestion with this one? I think it should be done with cp, right? https://secure-web.cisco.com/1jRruz6TGD-rKjtwk6y7Fou9kvVTddyJdG7ncgi9OGDrLH… Kind regards, Rosie

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Question regarding tissue segmentation
by Guy Fons F Rens 28 Jun '21

28 Jun '21

External Email - Use Caution Dear FreeSurfer community, I was wondering whether someone could please help me. Background In my supervisor’s lab, we are currently doing neuroimaging with functional Near-Infrared Spectroscopy (fNIRS). Parts of our data analysis are performed in Homer3 & AtlasViewer, software designated for fNIRS analysis. In order to perform analyses on individual (and not template) brains, AtlasViewer can read brain segmentation files generated by FreeSurfer. Accordingly, only anatomical and no functional files are needed. Current status * I am running Freesurfer 7.1.0-1 on my windows 10 computer through a Linux terminal (centos7). * I am able to process single participants’ anatomicals through the recon-all command * I can export the datasets from the Linux environment back to the Windows environment * I can load the generated freesurfer files into AtlasViewer. The issue The recon-all command is highly convenient for generating the required files that can be read into AtlasViewer. However, some of the included processing steps interfere with proper analysis in AtlasViewer. These steps are: 1. Automatic defacing of the anatomical: As we need anatomical landmarks (such as nasion) for fNIRS analysis, defacing makes defining this landmark tedious (if not impossible) 2. Transformation into normalized space: The dataset is automatically transformed into Talairach space. As we need to process our data in native space (because the fNRIS montage is in native space), this step is interfering with our ability to align the anatomical scan and the fNIRS montage. The specific questions For our data analysis in AtlasViewer, we primarily need the anatomical with 5 tissue segmentation (skin scalp, CSF, WM and GM). Ideally, without (Issue 1) defacing and (Issue 2) transformation into normalized space. As such my specific question is: * How can I run FreeSurfer through the centos7 terminal to acquire the segmentation files without defacing and space-normalization. * Or, if these files are actually generated through recon-all, how/where can I access them? Last words I would greatly appreciate any help with this issue. Although I have some coding experience, my knowledge of Linux is very limited. I tried to find this information on the FreeSurfer webpage but was unable to do so. Many thanks in advance and feel free to provide any support by reaching out to grens(a)uwo.ca<mailto:grens@uwo.ca> [grens AT uwo dot ca]. Best wishes and, again, many thanks Guy Rens

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The differences in stats between BA_exvivo and BA_exvivo.thresh
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 28 Jun '21

28 Jun '21

Hi all, I am wondering to see what the .thresh files mean. I'm assuming its some sort of thresholded value, but there isn't a lot of details in the BA page: https://secure-web.cisco.com/1Os2Q1CROSPpImTp-5xbbZDey2Qg9ZXqjxJDVrM_cYa2Mg… Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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question about partial volume corrections with PETSurfer
by Yu-Wei Chang 27 Jun '21

27 Jun '21

External Email - Use Caution Dear PetSurfer and Freesurfer Developers, I would like to run partial volume corrections on amyloid PET images (from ADNI) with PetSurfer. I have downloaded the amyloid PET images that were intensity normalized to the cerebellar GM. However, I noticed that the PVC analysis in PetSurfer uses the Pons as a reference region. I don't have much experience with PET analyses but I was wondering 1.1 If I should use the same reference region for the PVC? 1.2 If so, how can I change the Pons for the Cerebellar GM in the commands on the website? I found a similar question raised in the forum (https://secure-web.cisco.com/1ZlB3PzPmZnYFpKkL_LMunStJKeDgVzSjzFa3rVWrk5e5O…) and the provided solution is to add ‘--rescale 7 8 46 47’ for left and right cblum wm and gm. 2.1 Does ‘--rescale 7 8 46 47’ suit my question 1? 2.2 If so, where can I find the whole list of ids that specify every brain region in the left and right hemispheres? Thank you. Best, Yu-Wei **************************** Yu-Wei Chang 張育瑋 Doctoral student UNIVERSITY OF GOTHENBURG Department of Physics Gothenburg, Sweden

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(no subject)
by miracle ozzoude 27 Jun '21

27 Jun '21

External Email - Use Caution Hello All, I was wondering if the Right/Left-Cerebral-White-Matter in the aparc+aseg.mgz contains WM hypointensities. mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats --ctab FreeSurferColorLUT.txt Best, Paul

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Re: [Freesurfer] eTIV and FSGD file
by Gallego Angel, Juan 27 Jun '21

27 Jun '21

External Email - Use Caution Hello, I sent the message below a couple of weeks ago but I haven't seen it posted in my freesurfer digest emails. I am wondering if I need to do something different? It's the first time I submit something. Thanks, Juan From: Gallego Angel, Juan Sent: Tuesday, June 8, 2021 4:58 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: eTIV and FSGD file Hi, I am running my first ever FS analysis and just have a couple of questions. I am looking for cortical thickness predictors of response to treatment. I am at the point of running the mri_glmfit command. I'd like to control for the effects of sex, age and eTIV. I already created the contrast and the FSGD files. In the FSGD file I included four classes (male responder, male non-responder, female responder, female non-responder) and added age as a variable and I guess I'd need to add eTIV as well as a variable, and that data could be obtained from the aseg.stats file, right? Let me know if I am missing anything here. Many thanks, Juan Juan A. Gallego, MD, MS Assistant Professor of Psychiatry Zucker School of Medicine at Hofstra/Northwell Assistant Professor The Feinstein Institute for Medical Research Director, Early Phase Schizophrenia Biomarker Laboratory The Zucker Hillside Hospital 75-59 263rd street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: jgallego(a)northwell.edu<mailto:jgallego@northwell.edu> Northwell Health Visit us at Northwell.edu<http://secure-web.cisco.com/1J3nxiTRVud5b64q3yXHIwnCs92SEPdCJwM9b7HGLUligyK…> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Help with LGI pipeline output - Freeview
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 27 Jun '21

27 Jun '21

External Email - Use Caution Dear FreeSurfer experts, Hope that everyone is well and having a great Monday. I am having some trouble opening the outputs for the LGI pipeline via Freeview - could someone please help me with this? I tried using + editing the code available on the website *tksurfer my_subject_id lh inflated -overlay lh.pial_lgi*; however it did not work. Thank you so much, Alex

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Topological and control point errors
by Rosalia Dacosta Aguayo 26 Jun '21

26 Jun '21

External Email - Use Caution Dear Freesurfer experts, I have noticed I have both topological and control point erros in my image. What would you recommend me to do first, topological or the control points? Kind regards, Rosie

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Unable to run recon-all
by Rosalia Dacosta Aguayo 26 Jun '21

26 Jun '21

External Email - Use Caution Dear Freesurfer team, Sorry for posting this question but I have been trying different things and nothing seems to work. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -s sub-001_ses-BSL -i sub-001_ses-BSL_T1w.nii -T2 sub-001_ses-BSL_T2w.nii -T2pial -all *ERROR: cannot find sub-001_ses-BSL_T1w.nii* Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-001_ses-BSL exited with ERRORS at Fri 25 Jun 20:41:02 CEST 2021 For more details, see the log file To report a problem, see http://secure-web.cisco.com/1Jp49SO4XsOvSB6mE6NlUUK8Lo6N1S98h7rexTU7o7iNmF3… rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd ARTICO rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO $ ls sub-001_ses-BSL sub-003_ses-BSL sub-005_ses-BSL sub-002_ses-BSL sub-004_ses-BSL sub-006_ses-BSL rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO $ cd sub-001_ses-BSL/ rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO/sub-001_ses-BSL $ ls sub-001_ses-BSL_T1w.nii sub-001_ses-BSL_T2w.nii rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO/sub-001_ses-BSL $ If I trying to run recon-all inside the subject folder it tells me that this subject has already been run and if that it is a new subject, I should change the name of the folder and the files. I do it, and it keeps giving me the same error. I am out of ideas...

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Freesurfer June 2021