Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

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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make other atlases compatible with freesurfer
by Roxana Namiranian 26 Jun '21

26 Jun '21

External Email - Use Caution Dear Friends, I want to use neonatal atlas in freesurfer which is compatible with brainVisa (available: https://secure-web.cisco.com/1xxPZ7hbZXB7YNzBLH04kH_oyg98giX78BB7hKRwAwIw9I…) How Can I use this atlas in freesurfer? (available files of this atlas are: label_?h.gii, template_?h.gii, template_?h.mesh, template_head.mesh, T1.nii, T2.nii, labeltable.csv) I am trying to do this using mris_ca_train, but it is challenging to provide suitable files needed for this function from the available files. Is there any other way to use this atlas in freesurfer? Thank you very much, best regards, Namiranian

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Changing script from tksurfer to freeview
by Marlene Staginnus 25 Jun '21

25 Jun '21

External Email - Use Caution Dear FreeSurfer Team, As part of the ENIGMA consortium, research groups that contribute data need to run certain standardized scripts to pre-process their data and create outputs for subsequent quality control using FreeSurfer. One issue that has recently occurred is that Mac users with a recent MacOS are no longer able to run one of the scripts that uses tksurfer to generate lateral and medial screenshots of the pial surface reconstructions. Reading previous posts in the mail archive, this seems to be due to recent versions of MacOS being unable to run 32-bit programmes like tksurfer and that users should either use Freeview for visualisation or revert to an older operating system. As the latter is not possible for some groups, we’ve been trying to edit the script by altering which programme it calls (e.g., freeview or tksurferfv instead of tksurfer) as well as other aspects of the script (e.g., -cmd instead of -tcl). However, so far, we have been unable to successfully amend the script. Would you have any pointers for us as to how to alter the script to call freesurfer whilst arriving at the same output (i.e., multiple screenshots of the external view of a subject’s brain)? Is there a way to script Freeview similar to using tcl in tksurfer? I have also attached the script in question to this email. The FreeSurfer versions used by the contributing research groups are 5.3 or 6.0. Thank you in advance for any advice you might have on this. Best wishes, Marlene

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Edits to White Matter (wm.mgz)
by Boa Sorte Silva, Narlon 25 Jun '21

25 Jun '21

External Email - Use Caution Dear FreeSurfer experts: I am working on a manual for my lab and I would like to clarify the two points below (to which I couldn’t find answers in the online FS content available): * When editing the wm.mgz fails, can control points (CPs) be used to correct pial errors cause by lesions (e.g., perivascular spaces, microbleeds, WMH). I understand the FS tutorial recommends against this, however at times it seems that only editing the wm.mgz will not be sufficient (Figure 1 below) * Should white matter voxels with 0 intensity in the wm.mgz (inside the white surface) be filled in, even when these voxels do not affect white matter surface segmentation whatsoever? (Figure 2 below). * Would the cerebral white matter volumetric data (wmparc.stats) be affected by these 0 intensity voxels? Thanks so much for you help! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon [cid:0757C5B4-5E01-42A4-8BE6-6C5779C2D024][cid:E4FD3068-0778-4057-850B-40E9EB3318C8]

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Differences in FLAIR assisted pial segmentation from FS6.0 to FS7.1
by Fredrik Magnussen 25 Jun '21

25 Jun '21

External Email - Use Caution Dear FreeSurfer experts, We have processed UKB data with FLAIR assisted pial segmentation using FS7.1. The results differs quite a lot from using FLAIR assisted pial segmentation in FS6.0. For details please see the reported issue on the freesurfer github page: https://secure-web.cisco.com/1BsLOtOMPefP19V4jaUIGxvB6cloD65XJYgob0S0aurJu0…. Might be related to another issue reported here (though this is T2w assisted pial segmentation): https://secure-web.cisco.com/1ZD-HjicZD5y6JRb7Rg-7byCuNf0LNbmLLvFu37e46JHBZ…. The FS pial segmentation for UKB data is prone to include dura if only T1w data is used, so assisting with FLAIR is quite detrimental. Best regards, Fredrik Magnussen

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