Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

SAMSEG thresholds
by Alberto Del Cerro Leon 01 Jul '21

01 Jul '21

External Email - Use Caution Hello FreeSurfer team, I have a question about SAMSEG thresholds. I am analyzing the vascular lessions aplying several thresholds. I would expect that lower thresholds results in lower volumes but dont seems like that. What is the reason?

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NIMH Online Workshop on Naturalistic Stimuli and Individual Differences - August 2021
by Molfese, Peter (NIH/NIMH) [E] 01 Jul '21

01 Jul '21

External Email - Use Caution The Center for Multimodal Neuroimaging (CMN) is thrilled to announce the upcoming workshop on Naturalistic Stimuli and Individual Differences with a range of extramural and intramural speakers presenting cutting-edge work. The workshop seeks to (1) bring together top scientists using naturalistic stimuli and/or the study of individual differences in neuroimaging; (2) showcase theoretical, methodological, and analytical advances in these areas of research; and (3) serve as a catalyst for collaborations between presenters, biomedical NIH researchers, and experts from around the world. Due to the ongoing coronavirus pandemic, the workshop will feature virtual presentations and roundtables in a unique format open to the public. Presentations will be available to stream on-demand starting August 1, 2021. Attendees will be able to view the presentations in their own time, and submit questions to speakers through an online portal. In September, the speakers will again virtually reconvene for a round-table discussion to address some of the attendee questions as well as discuss larger questions in the field moving forward. More information and registration can be found at the link below! https://secure-web.cisco.com/1gUCi1nAb5eIIfmp-e8PHroYHwLS_30qYDB7AOQWmmytxE… Tweets/retweets appreciated: #cmnworkshop2021 -- Peter J. Molfese, Ph.D. [E] Staff Scientist, NIMH Science Lead | Center for Multimodal Neuroimaging Building 10, 1D80 10 Center Dr Bethesda, MD 20892-1148 Email: peter.molfese(a)nih.gov<mailto:peter.molfese@nih.gov> Phone: (301) 402-1350 cmn.nimh.nih.gov<https://secure-web.cisco.com/1jzRlPyc3jjA4x_0RRoeJMH7gad9a3qz5Zqykd5QphbYe8…>

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When GM segmentation is not good enough
by Rosalia Dacosta Aguayo 01 Jul '21

01 Jul '21

External Email - Use Caution Dear Freesurfer team, I was wondering if there is any way to improve GM segmentation with FreeSurfer in cases like this, when all they GM has not been included by FreeSurfer: https://secure-web.cisco.com/1Vs511OuC3LYOAyRmiyTn4sfCMK9fVD-cPX8iYOmw7fzgP… Kind regards, Rosie

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problem with mris_compute_lgi
by Bernardoni, Fabio 30 Jun '21

30 Jun '21

External Email - Use Caution Dear FS experts, when running mris_compute_lgi, the make_outer_surface step produces an error: >> reading filled volume... /bin/bash: /scratch/tp81860215899812157.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp81860215899812157.load_mgh.m.mgh for reading Looking more closer at what produces the error, it is the MRIread function: vol=MRIread('..../surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz') /bin/bash: /scratch/tp81861321896965219.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp81861321896965219.load_mgh.m.mgh for reading ERROR: loading ..../surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz as MGH vol = [] I do not understand where the /scratch/tp81861321896965219.load_mgh.m.mgh is created/located. Is it within the rh.pial.filled.mgz? Even going through the MRIread function I couldn't figure out. Maybe the error is actually in the mri_fill step (that however exits with no error) Thanks in advance for any hint Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1j3t_3Y4iFjkXouNEHQLd1euJWlTzdWEoUG3WoZLDjonBHv…; http://secure-web.cisco.com/1uAkOO7CtOzygpinM5tt9ZZHkhl_HV3HHZnI2wodEWKz8oN… +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1GIWqSkZNuXf_zg2CrESTkx8X0PW_gl1iao4QNgyhxPTCr3… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1GIWqSkZNuXf_zg2CrESTkx8X0PW_gl1iao4QNgyhxPTCr3… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Re: [Freesurfer] mri_glmfit DOSS
by Dr. Cornelius Kronlage 30 Jun '21

30 Jun '21

External Email - Use Caution Dear all, this error seems to be gdfCheckNPerClass in utils/fsgdf.cpp. Using "doss" or "DOSS" as a tag in the FSGD file doesn't help either, strangely. Could it be that it should be strcasecmp() instead of strcmp() in line 1046 of fsgdf.cpp? Cheers, Cornelius Date: Tue, 29 Jun 2021 15:19:20 +0000 From: "Dr. Cornelius Kronlage" <Cornelius.Kronlage(a)med.uni-tuebingen.de> Subject: [Freesurfer] mri_glmfit DOSS To: "'freesurfer(a)nmr.mgh.harvard.edu'" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2a173629cd4540769ec6a07d892ca618(a)med.uni-tuebingen.de> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Dear freesurfers, for a morphometry study, I am comparing a single subject at a time to a group of controls. I would like to include age, gender (as a continuous variable for the sake of simplicity) and eTIV as "nuisance" regressors in the GLM. The FSGD looks like this: GroupDescriptorFile 1 Title SUBJECT1_vs_allControls Class Test Class Controls Variables Age Gender eTIV Input SUBJECT1 Test 50 1 1497422.2500 Input SUBJECT2 Controls 30 0 1709039.536815 Input SUBJECT3 Controls 29 0 1423097.816203 Input SUBJECT4 Controls 31 1 1524690.026713 ... When I try to run mri_glmfit I get the following error even though I specify DOSS: $ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...] gdfRead(): reading SUBJECT1_vs_allControls.fsgd WARNING: variable 1 is "Gender" which is often a discrete factor The proper way to handle discrete factors is to create classes. See https://secure-web.cisco.com/10ThHTirv10OEqbkasMHR-FObJ8JCIIzwnlckPdClcabJk… INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 28.6875 6.36611 1 Gender 0.46875 0.499022 2 eTIV 1.51444e+06 125811 Class Size and Means of each Continuous Variable 1 Test 1 50.0000 1.0000 1497422.2500 2 Controls 31 28.0000 0.4516 1514993.8589 ERROR: Class Test has 1 members. With 3 variables and using DODS, you need at least 4 members How do I get mri_glmfit to use DOSS, or do I have to specify the design matrix by hand in this case? Thank you! Best wishes Cornelius

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mri_seg_overlap error
by Javier Pozo 29 Jun '21

29 Jun '21

External Email - Use Caution Hello, I was trying to use mri_seg_overlap to find the DICE coefficient but, unless having FreeSurfer installed, I receive a "command not found" error when I try to run the tool. I hope you can help me. Regards, Javier.

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Re: [Freesurfer] Masking A Surface Overlay
by Jacoby, John 29 Jun '21

29 Jun '21

The "thresholding" options work well for thresholding a single overlay, but I would like to threshold one overlay using the values of a second overlay.

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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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