Freesurfer August 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
152 discussions

Skull strip t1 in recon-all
by Julie Ottoy 10 Aug '20

10 Aug '20

External Email - Use Caution Dear freesurfer team I'm trying to use my own skull stripped T1 when running recon-all. For this, I'm doing following steps: 1) run recon-all with -autorecon-1 -noskullstrip 2) mri_convert --in_type nii --out_type mgz -rl ./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz ./FreeSurfer/ID/mri/brainmask.mgz 3) run recon-all with -autorecon-2 and autorecon-3 My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore, when transforming to the size of brainmask.mgz (256x256x256), it deforms. I tried nearest, cubic, and interpolate, but none of them gives actually a good result in terms of retaining the contrast. I was wondering if it is important to keep a good contrast for brainmask.mgz , or whether this brainmask.mgz is just used to determine the brain borders for segmentation. (ie.: in which steps of recon-all is the brainmask.mgz actually used and for what?) Any recommendations? Thank you!

1 0

cortical surface area calculation
by Alexopoulos, Dimitrios 10 Aug '20

10 Aug '20

External Email - Use Caution Hi all, Does this command calculate the Cortical Surface Area without the non-cortical Medial Wall?? mris_calc --label ../label/lh.cortex.label lh.area stats 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.

2 1

Hippocampus_substructures_normalization
by Haewon Roh 10 Aug '20

10 Aug '20

External Email - Use Caution Hi. team! Recently, I submitted a paper dealing with volumes of hippocampus and its subfields in epilepsy patients who have significantly reduced hippocampal volume (compared with normal controls) and, in that paper, I used the normalization method using ICV, which was suggested by Jack CR in 1989: normalized volume = volume (observed) – b (ICV – mean ICV), where b is the slope of regression for each ICV. But, one of the reviewers pointed out that I should use the method based on each patient's hippocampus rather than total intracranial volume. Since I've seen that a lot of papers, which dealt about these kinds of issues about hippocampus and subfields, used the same method with me, I am really doubtful that it is more appropriate if I should use the method using individual volume of hippocampus (rather than ICV) in order to normalize its volumes of substructures in the comparison analysis with those of controls. # And, whether this is true or not, could you please recommend to me several literatures that can show which method of normalizing volumes of the hippocampus and its subfields is more appropriate for this kind of issue? # Really sorry for bothering you. Thank you always for your kind and delicate solutions ! : ) -- Hae Won ROH, M.D. H.P: +82-10-4341-8142 E-mail: rofree1st(a)gmail.com

1 0

Directories not populating after recon-all
by Rohin Singh 08 Aug '20

08 Aug '20

External Email - Use Caution Hello, I am a student at the Mayo Clinic trying to do a project with fresurfer. When I run recon-all, it only creates one file “001.mgz” in the MRI directory and the rest of the folders are blank. I am not sure why this is as it completes the process without any errors and I followed the set up instructions exactly. Any help would be greatly appreciated. Thanks, Rohin Singh

2 1

Question regarding Euler number
by Scheffler, F, Mev [fredas＠sun.ac.za] 07 Aug '20

07 Aug '20

External Email - Use Caution Dear FreeSurfer Devs I got a comment about including a SNR variable in my main stats analysis and so came across a Rosen et al 2018 paper which refers to the Euler number. I then checked the archives and came across a thread<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg58748.html> where you say that in version 6.0 the numbers are included in the aseg.stats file, specifically as a global measure called SurfaceHoles. With regards to our QC procedures: We visually inspected all of our scans and then followed ENIGMA’s quality assessment protocols. We excluded scans with motion artefacts or poor-quality images and only included the data from the scans with acceptable or good quality segmentation. Outlier detection and the distribution of our data was also checked prior to analysis of the data. So, my question is, can I include the SurfaceHoles variable in my model as a proxy for SNR? Would that be sensible, or do you have an alternative suggestion? Thanks very much! Kind regards, Freda Scheffler PhD Candidate

3 2

LGI and Global GI
by Alexopoulos, Dimitrios 07 Aug '20

07 Aug '20

External Email - Use Caution HI, I have generated the LGI for a group of pediatric subjects. Is there a way to compute a single Global gyrification index measure for each subject? 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.

2 3

labels in .nii file
by Eleni Nikalexi 07 Aug '20

07 Aug '20

External Email - Use Caution Dear Freesurfer developers,We have a volume that assigns unique numerical labels to each of the ROIs it contains, in NIFTI format. I want to register it to MNI152 (1mm) space, so that I can map it on my subjects and use mris_anatomical_stats.I have tried the following command: 1. tkregisterfv --mov MDROI.nii --s MNI_1mm --regheader --reg registrationMD/MDROI.lta to get : "LTA input is not RAS to RAS...converting...". Then I run: 2. mri_vol2surf --src MDROI.nii --src_type nii --out registrationMD/surf.MDROI.mgh --reg registrationMD/MDROI.lta --hemi lh --surf white --projdist-max 0 1 0.1 3. mri_vol2surf --src MDROI.nii --src_type nii --out registrationMD/surf.MDROI_rh.mgh --reg registrationMD/MDROI.lta --hemi rh --surf white --projdist-max 0 1 0.1The 2 commands above demand the --hemi argument, but I wasn't sure what to put, as the ROIs are mixed and are in both hemispheres. Thus I run the command once for the left and once for the right hemisphere, creating different .mgh files.Last, I continued with: 4. mri_vol2label --i registrationMD/surf.MDROI.mgh --id 1 --l lab.MDROI_lh.label --surf MNI_1mm l which failed, as I get "ERROR: found no voxels matching id 1" Could you please tell me, if the commands make sense, and if I should change something? Thank you so much for your help! Best regards,Eleni

2 3

mri_vol2vol and diffusion issue
by 真我 07 Aug '20

07 Aug '20

External Email - Use Caution Hello! freesurfer experts,I am running dt_recon and mri_vol2vol to obtain FA values of five corpus callosum (CC) sub-regions. command 1, dt_recon --b bvals.dat bvecs.dat --i $TUTORIAL_DIR/$subj/DTI/00001.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon command 2, mri_vol2vol --mov lowb.nii.gz \ --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --reg register.dat --no-save-reg Everything is OK after running the dt_recon command and the registration of all diffusion images with the anatomical data is good. However, some of my subjects show an issue with mri_vol2vol registration. When checking the wmparc2diff.mgz I created, it is apparent that surfaces of lh.white and rh.white are not accurately mismatched with the wmparc2diff.mgz, as showed in the following figure. Is there an error with my command about mri_vol2vol or a problem in other aspects? Any advice with troubleshooting would be greatly appreciated. Best Wishes Bo Tao M.D Student, Department of Radiology / Huaxi MR Research Center (HMRRC）West China Hospital of Sichuan University Chengdu  City, 610041 P.R. China

2 1

MRI_seg stats for multiple subjects
by Sara Lyn 06 Aug '20

06 Aug '20

External Email - Use Caution Hi freesurfer developers, I am trying to run mri segstats for multiple subjects but the following only produces one text file for the first subject. Any idea what I am doing wrong? for subj in $(cat sessid.txt); do mri_segstats --seg /Users/Desktop/AUT/dti/TBSS_FA/FA/${subj}_FA_skeleton_JHU_wmparc_segmentation.nii.gz --in /Users/Desktop/AUT/dti/TBSS_FA/origdata/${subj}.nii.gz --ctab /Users/Desktop/AUT/TBSS_FA/stats/JHU_wmparc_segmentation_ColorLUT.txt --sum /Users/Desktop/AUT/TBSS_FA/roi/FA_${subj}_M.txt done Thank you.

1 0

Needing advises for results in my study.
by Haewon Roh 06 Aug '20

06 Aug '20

External Email - Use Caution Hi. Recently, I analyzed patients who have taken 1.5T MRI ; (Because they had to go in MRI room with some metal materials) and normal controls who took 3.0T MRI. And, after recon and preprocessing of each group of patients and controls in freesurfer v6, I've found that many cortices of patients (1.5T MRI) were significantly reduced, compared with normal age-sex matched controls (3.0T MRI). When I searched in order to know if there is difference between 1.5T vs 3.0T MRI and magnetic field can make a huge difference in calculating volumes or thickness of cortices in Freesurfer, I can find only one article by Heinen and his colleague, reporting there is no big difference and different(1.5 vs 3.0T) magnetic field strength cannot make a significant difference. (Plos ONE, 2016) Furthermore, given that data which is taken in 1.5T MRI is more likely to have more increased volumes or thickness of cerebral cortices than those of 3.0T MRI, I think that reduced cortical volumes which are calculated using 1.5T MRI have more significance than controls of 3.0T MRI... Is it true that different magnetic strengths of MRI cannot change the result significantly in Freesurfer? Thank you always! -- Hae Won ROH, M.D. H.P: +82-10-4341-8142 E-mail: rofree1st(a)gmail.com

3 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2020