Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

freesurfer to spm
by 况况 26 Feb '21

26 Feb '21

External Email - Use Caution Dear Community, I want to acquire each amygdala subnuclei volumes' mask to from freesurfer(fsaverage space) to spm(MNI space). what should i do? can you give me some tips? Thank you. student -liangfeng kuang shandong first medical university & shandong academy of medical sciences email: kuangliangfeng123(a)163.com

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Creating a .gcs custom atlas from nifti file for cortical parcellation
by THIBEAU SUTRE Elina 26 Feb '21

26 Feb '21

External Email - Use Caution Hello freesurfer experts, I would like to use freesurfer recon-all to obtain the regional cortical thicknesses of subjects of ADNI dataset. I launched freesurfer recon-all and obtained the parcellations according to Destrieux and Desikan-Killiany atlases. I would like to know how to obtain the same parcellations with another atlas, AICHA (https://secure-web.cisco.com/1st38nLf-34KvmX5j8oNCBRhTI_Ki20PWEfeEACfqaaGqd…) which is only available in nifti format. I understood that I should create a .gcs file from the nifti version but I am not sure how. I saw that mris_ca_train could be used to create such a file from a a manually labelled dataset but I don’t know how to create these labelled subjects from the nifti atlas. If anyone has already this kind of conversion .nii -> .gcs I would be really interested to know how you have done that! Best regards, Elina

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runClustSims.sh error
by Haewon Roh 26 Feb '21

26 Feb '21

External Email - Use Caution Hi, experts. Now, I am doing the process of group analysis between two groups on FS v.7.1.0 Previously, I had used QDEC GUI for that kind of analysis, but, because it is not available since FS 7, I am learning how to do that from video tutorial. But, I’ve got in trouble ; in the process of cluster corrosion, the script of " runClustSims.sh “ doesn’t work. (Please find error message in attached image file). Could you help me out what the problem is ? And I’d like to know whether I can use the function of automated segmentation of hypothalamus in FS v 7.1.0. Thank you! Best, Haewon Roh h.

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mri_glmfit dependent variable
by miracle ozzoude 26 Feb '21

26 Feb '21

External Email - Use Caution Hello Experts, I've a question about mri_glmfit. I want to investigate the association between thickness and neuropsychiatric syndromes, controlling for age and cognition. Which model below is mri_glmfit performing? Model 1 neuropsych syndromes ~ age + cognition + cortical thickness or Model 2 cortical thickness ~ age + cognition + neuropsych syndrome Many thanks, Paul

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WM volume
by Barletta, Valeria 26 Feb '21

26 Feb '21

Dear Freesurfers, In what file inside the patient_name/stats folder do I find the total white matter volume? In the file "aseg.stats" there is something called lh/rh "cortical white matter volume", is that the right value to look at? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823

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Freeview cmmd + F
by Boa Sorte Silva, Narlon 25 Feb '21

25 Feb '21

External Email - Use Caution Hi all, For FreeView version 1 for Mac is there a similar command that can be used to toggle all surfaces, similar to cmmd + F in newest versions of the software? Thanks Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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postdoc opportunity in relaxometry and diffusion MRI
by Corinna Bauer 25 Feb '21

25 Feb '21

External Email - Use Caution We are seeking a full-time postdoctoral fellow with experience in diffusion analysis with an emphasis on network-based approaches, NODDI, DKI, and tract-specific analysis. The NIH-funded project employs structural, diffusion, and relaxometry based MRI methods to target thalamo-cortical changes in morphometry, neural networks, and MRI-based markers of myelin in youths with perinatal brain injury. We are seeking a candidate with the following qualifications: • Doctoral degree with 0-1 years of related work experience • Advanced skills in the processing and analysis of diffusion (including connectivity, DKI, and NODDI approaches) data, particularly focusing on network-based approaches are required • Experience with multicomponent T2 relaxometry • Strong coding skills in python, MATLAB, bash, etc. • Experience working with clinical pediatric populations would be preferred • Experience with psychophysical assessments of functional vision would be advantageous, but not necessary • Experience with fMRI design and analysis is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( Corinna_Bauer(a)meei.harvard.edu) Additional details can be found at: https://secure-web.cisco.com/1suYTWqeXdTkzb6aG2C5Fq7YSTkFJR7uoBAOI8t8wYVZd8…

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Questions related to combining datasets run through different versions
by Lisanne Michelle Jenkins 24 Feb '21

24 Feb '21

External Email - Use Caution Hi experts, We want to combine two large datasets (of patients with different diseases) that have been processed and manually edited using Freesurfer 5.3 and Freesurfer 6.0. From the Freesurfer website and previous posts, we have read that we should re-run the Freesurfer 5.3 data that has been manually edited (both brain masks and pial surfaces) through Freesurfer 6.0 using recon-all and using the -continued flag, and that the manual edits from 5.3 should carry over. However, we have found that around one-third of subjects have skull stripping errors after rerunning through 6.0. Has anyone else found this? Have we missed something? A related question: We have heard it argued that if the data has been manually edited and quality checked, the version of Freesurfer which it is run through should not matter, therefore it is ok to combine data from different versions – what do you think of this argument? An additional argument along those lines that we have heard is: If one were to re-process data with a later version of Freesurfer, using edits from an older version would introduce biases from that version – what are your thoughts on this argument? Thank you. Lisanne

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segmentation is shifted with respect to NIFTI T1W
by Roman Fleysher 24 Feb '21

24 Feb '21

External Email - Use Caution Dear FreeSurfers, I am working with version 6, starting point is T1W image in NIFTI format. I typically transform segmentations back to native space in NIFTI format to be able to use other software (FSL and such). I noticed that segmentation is shifted by 1 pixel in one axis (y-axis). Mapping of segmentation is a two step process based on description in: http://secure-web.cisco.com/1OQ80xn8YGeWjUO2KyO4RDGDpL87LZ0EBpX6Z7_yDHTAQnU… Specific commands are (schematically) : # realign to original MGZ mri_label2vol --seg inputSegmentationInMGZ --temp mri/orig/001.mgz --o outputSegmentationInOrigMGZ --regheader inputSegmentationInMGZ # convert to NIFTI (*.nii.gz) mri_convert --in_type mgz --out_type nii outputSegmentationInOrigMGZ outputSegmentationInOrigNIFTI.nii.gz Are these steps correct? I can shift NIFTI by one pixel using fslroi, but I want to be sure nothing else is happening and that this shift is the correct work around. Thank you, Roman

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rerunning FS 7.1.1 after brainmask.mgz edits
by Alexopoulos, Dimitrios 24 Feb '21

24 Feb '21

External Email - Use Caution Hi, We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the "cloning to T1 method", using the Recon Edit tool in Freeview for adding brain back to the brainmask.mgz. Once the revised brainmask.mgz is re-saved with the same file name, what command needs to be run to regenerated the entire pipeline? We originally ran: recon-all -s -i -hires -all Do we run the same command again or should we use: recon-all -s -make -hires all Thanks. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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