Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

Downloading OVA
by Tellis, Wyatt 16 Nov '23

16 Nov '23

External Email - Use Caution Hi, I'd like to download the OVA to run in VirtualBox, but the wiki article (https://secure-web.cisco.com/14mYPNciAyjJLQ-z9NWag-roFmGKjbtQeqtDD8X-3yq9rT…) says its being updated: As of 09/11/2023 he (sic) VM image is currently being updated and the link to it will be restored when the update is complete. Is there an estimate for when the new OVA will be released? Thanks, Wyatt

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Question about lesions output
by reza razmara 16 Nov '23

16 Nov '23

External Email - Use Caution Hi freesurfer I did an experiment about lesions about the output of samseg. And the results are as follows: The volume of lesions in label 99 in seg.mgz result is 745 mm^3. The samseg output for lesions in samseg.stats is 633 mm^3. Is it ok? Why are they different? Thanks for your help

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Problem with brainstem overlap after BBR
by Spapens, Jeltje (NP) 16 Nov '23

16 Nov '23

External Email - Use Caution Hello Freesurfer Developers, I have performed a boundary-based registration followed by a mri_vol2vol on a Neuromelanin sensitive MRI scan (partial FoV) with a T1 structural scan. I used this code: Boundary-based registration in Freesurfer Set the environment in the terminal. bbregister --s MRS_203_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz --reg MRS_203_NM2mp2rage.dat --T1 --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_regt1.nii.gz --reg MRS_203_NM2mp2rage.dat –cubic I performed the analysis on two participants, but the brainstem does not overlap very nicely. I attached the screenshots of Freeview of the two participants with the T1 scan and the NM scan after the BBR. Our analysis focuses on the Substantia Nigra. I also attached the full script that we use including the pre analysis. Do you have a tip how to improve the BBR to reach better overlap. Kind regards, Jeltje Spapens

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Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer
by Xinjie Chen 16 Nov '23

16 Nov '23

External Email - Use Caution Dear FreeSurfer Team, I am writing to report a significant issue I have encountered while using the PALS_B12_Brodmann.annot files in FreeSurfer. I have noticed a critical error concerning labeling certain Brodmann areas. Specifically, in the left hemisphere, labels such as Brodmann area 33, CON_deeper_than_WS_t_2', and ASP deeper' appear to share the same label ID. Similarly, in the right hemisphere, the label for Brodmann area 3 seems to be merged with Brodmann area 33. This overlap of labels and the lack of unique IDs for distinct Brodmann areas like Brodmann 3 and Brodmann 33 are causing significant confusion and potential errors in analysis. For instance, this issue complicates tasks such as calculating variables for individual Brodmann areas, leading to inaccurate results. I am keenly interested in any solutions or methods you could suggest for resolving this problem. Thank you in advance for your assistance and I am looking forward to a resolution. Best regards, Xinjie

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Create an lta or xfm file for mri_vol2vol
by Peled, Noam,PhD 15 Nov '23

15 Nov '23

Dear group, I have 2 images (preop t1 and postop CT), and a 4x4 registration matrix (as a text file). Is there an easy way to create an lta or xfm file to use it with mri_vol2vol? Thanks! Noam

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Does Synthseg include longitudinal processing?
by STACEY M SCHAEFER 15 Nov '23

15 Nov '23

External Email - Use Caution Hello, We are in the midst of longitudinal data collection. Before diving into our first longitudinal structural processing, have a few questions: Does Synthseg include a longitudinal processing stream? If so, how does it compare to the Freesurfer Longitudinal Processing stream? In the past, including both a T1 and T2 has been recommended for optimal segmentations. I don't see any mention of including a T2 in the longitudinal workflow (https://secure-web.cisco.com/1Hs2Tl_vnSro2vTkaUDdxTgiD9pw3XNueD_u5Drjxzqa7l…) Would it be worth including T2 scans if they are available? Thank you for your thoughts and guidance! Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project & Co-Leader of the MIDUS Admin Core Institute on Aging 2245C Medical Sciences Center University of Wisconsin-Madison 1300 University Ave Madison, WI 53706 USA 608-265-3486

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[WARNING: ATTACHMENT UNSCANNED]mri_label2label with Gifti file
by P Pieperhoff 15 Nov '23

15 Nov '23

External Email - Use Caution Hi FreeSurfer developers, I want to transform a label file in Gifti-format from the fsaverage space into the native space of a subject (CON01a). The FreeSurfer reconstruction pipeline was completely executed before for this subject. The label file lh.JulichBrainAtlas_3.0.3.label.gii is in freeview correctly visualized on the surface of fsaverage. But when I call mri_label2label as below, it seems that the Gifti-format is not recognized: mri_label2label --srcsubject fsaverage --srclabel ../atlas/lh.JulichBrainAtlas_3.0.3.label.gii --trgsubject CON01a --trglabel CON01a/label/lh.JulichBrainAtlas_3.0.3.label.gii --hemi lh --trgsurf white --regmethod surface *Output:* srclabel = ../atlas/lh.JulichBrainAtlas_3.0.3.label.gii srcsubject = fsaverage trgsubject = CON01a trglabel = CON01a/label/lh.JulichBrainAtlas_3.0.3.label.gii regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 Loading source label. <!DOCTYPE GIFTI SYSTEM "http://secure-web.cisco.com/10pJypOCaxCr0cVxOqUZEEwUWnA-a8JBJInZZrsmFvbBpZc…"> error: mri_label2label: could not scan # of lines from label file The Gifti-file contains a LabelTable (including a RGB-color for each label), and a DataArray of Labels (for each vertex), but not the vertex coordinates. Please, could you tell me how I can transform this file into the native space of each subject? I have attached the compressed label file to this mail. Best regards, Peter

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Re: [Freesurfer] mri_cvs_register failure
by Antonín Škoch 15 Nov '23

15 Nov '23

External Email - Use Caution Dear Doug, thanks for the response. Talairach registration seems OK. I am not sure, how to check surface-based registration. I have tried to look at subject's ?h.sphere.reg (with ?h.curv loaded) and ?h.sphere of fsaverage overlaid. But I am not sure if it is a correct way to do it: the spheres even do not spatially coincide (screenshot). Regards, Antonin I'm not sure what happened. Have you checked the surface-based registration? Also check the talairach reg. On 10/19/2023 11:35 AM, Anton?n ?koch wrote: > > ????????External Email - Use Caution > > Dear experts, > > I have encountered an failure of > > mri_cvs_register --mov my_subject --mni > > The resulting output file > > final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz > > looks like in the attachment. > > Could you please give me a hint, where could be a problem, or how to > troubleshoot the mri_cvs_register routine? > > Regards, > > Antonin Skoch >

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Aseg fail, pathology affecting anatomy
by Konstantinos Chiotis 15 Nov '23

15 Nov '23

External Email - Use Caution Dear all, I am reaching out regarding a challenging issue I've encountered in the segmentation of an extreme case. This particular case involves a history of a traumatic brain injury in the left lateral frontal lobe, resulting in gliosis in that specific area. My efforts included running recon-all on the case, incorporating T1 + FLAIR imaging. The segmentation of the cortex appears reasonably accurate overall, except for a notable challenge in the segmentation of the medial frontal surface. Notably, in the anterior areas of the brain, the lateral ventricles were not successfully segmented during aseg (aseg value of 0). This omission has notably impacted the parcellation process, particularly concerning the medial surfaces of the medial frontal cortex. Moreover, the aseg also encountered difficulties in parcellating the anterior subcortical areas, specifically the caudate nucleus and portions of the putamen. I am attempting to provide an image for better context. I acknowledge that this case, due to substantial gliosis, presents suboptimal conditions for segmentation. Nevertheless, I am open to any suggestions or insights you might offer to approach and potentially address this challenging issue. Thank you for your time and consideration. Kind regards, Konstantinos [A brain scan with a colorful design Description automatically generated with medium confidence] N?r du skickar e-post till Karolinska Institutet (KI) inneb?r detta att KI kommer att behandla dina personuppgifter. H?r finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/1LbGLriTgQNgdXYvDMiuX7zjOnHuhicCi76lawI86XHhG5…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1D7D6_w_SWvPD8r_TkEtei0MyFxzuaSVWLR_BuiIK69eM_…>.

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Doubts about GLM contrasts
by Laura Willers de Souza 15 Nov '23

15 Nov '23

External Email - Use Caution Hello FreeSurfer Developers, Following the FSGD examples on the website, I built the following test: Question: Is there an association between cortisol and cortical thickness regressing out the effect of sex, age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles), abeta, ptau, diagnosis (CU and CI)? Regressors: 2 factors (sex, diagnosis) with 2 levels each, 5 covariates (age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles), abeta, ptau, cortisol) >> 24 regressors Contrast: 0 0 0 0 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 FSGD: GroupDescriptorFile 1 Title CSF_semgrupos Class MaleCU Class MaleCI Class FemaleCU Class FemaleCI Variables Cortisol Age ABETA ptau APOE4_carrier Input 098_S_4003_I224603 MaleCI 11 81.3 741.5 22.83 1 Does this feel right to you? I am having difficulty understanding how to construct the contrast to answer the following question "Is the interaction between group (CU/CI) and cortisol significant regressing out the effect of sex, age, APOE_carrier, abeta and ptau?" It seems like the contrast would be the same as before.. Can you guys help me with this? Thanks in advance! Laura Willers de Souza PhD Student in Pharmacology and Therapeutics Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Freesurfer November 2023