Freesurfer February 2022

freesurfer@nmr.mgh.harvard.edu

83 participants
132 discussions

PetSurfer: CORTICAL volume-based analysis
by Jennifer Bramen 16 Feb '22

16 Feb '22

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I am following the steps from the PetSurfer wiki. I see instructions for how to do a cortical surface-based group analysis. I also see how to do a subcortical ROI-based analysis. However, I cannot find detailed instructions for performing a cortical ROI-based analysis. This is how I think I should adapt the instructions from your subcortical ROI-based analysis instructions for cortical gray matter: mri_vol2vol --mov $PET_DIR/$ID/gtmpvc.output/mgx.gm.nii.gz --reg $PET_DIR/$ID/gtmpvc.output/aux/bbpet2anat.lta --tal --talres 2 --o $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz mri_fwhm --smooth-only --i $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz --fwhm 5 --o $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm05.nii.gz --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/brainmask.mgz Can someone confirm or correct these commands? I am especially concerned that I have selected the wrong mask. Thanks you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center

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white matter measurements for labels/annotations
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 16 Feb '22

16 Feb '22

External Email - Use Caution Hi, is it possible to extract white matter volume estimations for labels/annotations? I am specifically wondering about the brodmann atlas and the stanford atlas that is already included in latest FS. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image
by Cristina Pereira Priego 16 Feb '22

16 Feb '22

External Email - Use Caution Hi, My name is Cristina and I'm a PhD Student from Clinical Neurosciences Group in IRB LLEIDA. I downloaded " Freesurfer VirtualBox Image" and I need the paswword to login as the user "developer" in the login menu. I'm waiting for your answer, Best regards, Cristina

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Postdoctoral fellow in multimodal neuroimaging
by Corinna Bauer 16 Feb '22

16 Feb '22

External Email - Use Caution We are seeking a full-time postdoctoral fellow with a strong background in resting state fMRI data analysis to join our team. We aim to better understand the neural correlates of visual perceptual dysfunctions observed in survivors of brain injury. We are actively working on an R01-funded project investigating the potential link between thalamocortical networks and severity of visual impairments. The multimodal project includes structural, diffusion, relaxometry, and functional MRI, in addition to behavioral correlates. We are seeking a candidate with the following qualifications: • Doctoral degree in computer science, neuroscience, or related field • Advanced skills in the processing and analysis of fMRI (resting state and task), particularly focusing on network-based approaches • Strong coding skills in python, MATLAB, bash, etc. • Experience with multimodal neuroimaging datasets is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, and their C.V. to Corinna Bauer (Corinna_Bauer(a)meei.harvard.edu) Additional details can be found at: https://secure-web.cisco.com/1ly1VCBmruOLMT0T7zR9O1yCBITb75_g6M5rEL4v_nj-QP…

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How to measure correlation using FreeSurfer
by Koustav Chatterjee 16 Feb '22

16 Feb '22

External Email - Use Caution Dear FreeSurfer experts, I am trying to find the correlation between the regional cortical thickness and volume with different clinical measures of a neurodegenerative condition. I am using DK atlas to get the cortical measures and establish the correlation using SPSS, a statistical software. But, I would like to get FreeSurfer developed images. I would like to learn how to get the areas through images (the FreeSurfer pipeline generated images showing brain regions associated with clinical measures I am interested in). Looking for your kind help. Regards, KC

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using T2 for recon-all
by Eszter Boros 15 Feb '22

15 Feb '22

External Email - Use Caution Dear FreeSurfer Team, We have collected T1 and T2 images in our study and running recon-all with T2 gives us much better results (it was really good to see it). Our aim is to compare these structural data (in Group A) to another patient group (Group B). The problem is that the data of Group B was collected 10 years ago and we did not have a T2 in that study. I am wondering what would be the best approach? Maybe we should not use T2 in Group A because we do not have a T2 in Group B? Or if we do the manual corrections correctly in Group B, this should not be a problem? I am using Freesufer 7.1.1 Thank you for your answer! I greatly appreciate it. All the best, Eszter Boros

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How to find mean LGI?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 14 Feb '22

14 Feb '22

External Email - Use Caution Hi, I was hoping to extract mean LGI, similar to how there is a mean thickness. But the default LGI output includes the eTIV rather. What would the command be to collect the stats into a csv for this mean LGI? Get Outlook for iOS<https://secure-web.cisco.com/1dRo8XiQnC7RSEfM4uJvu8n55IiY3PyAp4VACtq0qGpKwZ…>

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hippocampal segmentation differences pediatric sample
by Aleksandra Lecei 14 Feb '22

14 Feb '22

External Email - Use Caution Hi, I'm new to this and was wondering if someone could help me out? I used a T1 preprocessed image (fmriprep), normalized to the NIH pediatric cohort 6 (13-18.5 years) template to do recon-all and then used the hippocampal segmentation tool v.7. I have two questions: a) wouldn't one expect the segmentation to be the same for different individuals if the normalized T1's are used (registration seems to be well aligned to the same space when checked in SPM but when looking into the .txt files the volumes are different)? and b) (how) do I need to use the -custom-tal-atlas flag to get the estimates back to the NIH pediatric atlas (cohort 6) and can I make masks from the hippocampal segmentations for ROI analysis in other software for this study population? Thank you!

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DICOM file organization
by krystaly 14 Feb '22

14 Feb '22

External Email - Use Caution Dear Freesurfer experts, There are a bunch of RAW DICOM files in my dataset. I recognize that the name of the images begins with Z, i.e. “Z01”, “Z02”… “Z8568”. After converting them into NIfTI format with mricron, it yields the name in this format: myFolder_MPRAGE_19770703150928_1.nii It’s rather inconvenient to have those names and have been stuck on organizing the images in different categories, i.e. T1, T2, M0, FLAIR and PCASL. I would like to have them named by subject numbers rather than a series of name and digits. For example, T2 DICOM images of a Subject 101 are named 101.nii under a folder called “T2”. Could you please advise if there is anyway categorizing the patients’ data into aforementioned categories automatically with Freesurfer? You help will be highly appreciated! Thanks. Best regards, Krystal

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ventricular volumes - freesurfer 6 vs 7
by Anik Dar 13 Feb '22

13 Feb '22

External Email - Use Caution Hi All, I have some datasets processed with freesurfer 6 and other datasets processed with version 7. Is it ok to combine the ventricular volume results from version 6 and version 7 ? Please advise, Thank you Ani

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Freesurfer February 2022