Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Fwd: non-white matter hypointensity
by L 18 Sep '20

18 Sep '20

External Email - Use Caution Dear experts, I am wondering what the non-white matter hypointensity refers to. Does it refer to hypointensity in subcortical regions or all brain regions except white matter? When we do data analysis using volume results from ROI tables, we found a greater volume of non-wm hypointensity in depressed subjects with- than without high vascular risk factors. However, I am not sure where the non-white matter hypointensity ROI covers, and it is possible to visually display the non-wm hypointensity regions in freeview? Appreciate your guidance in advance. Lihong

3 3

Converting Volume ROI to Surface .annot file
by Paul Dhami 18 Sep '20

18 Sep '20

External Email - Use Caution Dear Freesurfer community, apologizes in advance for what may be a simple question. I have a volume region of interest file in .nii format. I would like to do a surface functional connectivity analysis in a MATLAB toolbox, and to do so, I would need to somehow convert this volume ROI to an .annot file. I was wondering if Freesurfer has any tools to do this? Could it be accomplished using a combination of mri_vol2label and then mri_label2annot? Best, Paul

2 1

mri_nu_correct.mni, mri_normalize extremely dark output
by Caspar M. Schwiedrzik 18 Sep '20

18 Sep '20

External Email - Use Caution Hi! I am having some issue at the interface between mri_nu_correct.mni and mri_normalize, using v5.3. Specifically, the output when applying mri_nu_correct to a T1 is quite dark, with white matter in the range of 15. Contrast is ok. When I apply mri_normalize to nu, it does not scale the data to white matter 110. This happens with and without a brain mask, and with various other parameter choices. I am tempted to just add 100 to all voxels. Any advice? Thank you, Caspar

3 3

mri_surf2surf template rh.white to fsaverage5
by 1248742467 18 Sep '20

18 Sep '20

External Email - Use Caution hello,Fs Because I want to build an N*N matrix based on the fixed-point number N of rh.white, but the original rh.white has too many fixed-point numbers, a memory error occurs. I saw a paper, which can be registered to the fsaverage5 space, and then the number of vertices can be reduced to 10242. I learned that the mri_surf2surf command is fine, but how should I use this command? If you can please give me an example Looking forward to your reply

2 1

Recon-all crooked volumes
by Hasimoglu, Yasemin 18 Sep '20

18 Sep '20

Hello, I recently ran recon-all on a group of subjects with FreeSurfer 7.1.0, and for one subject some of the resulting volumes look crooked. The 001.mgz volume looks normal, but every other volume such as orig.mgz, T1.mgz, brainmask.mgz have a severe tilt to them. When we open surfaces on top of volumes, their orientations follow whichever volume is loaded first. I've attached 2 sample screenshots here. We suspected that this could be related to a Talairach registration issue and inspected the volumes using the following command: tkregister2 --mgz --s $sub --fstal --surf orig However, everything seems to be aligned correctly on here, so we're not sure if there's anything we can do. Is this something that needs additional correction, or can we use this data in analysis as is? I've also attached the recon-all.log in case it's helpful. Best, Yasemin

2 1

Prescan normalize and freesurfer
by Mikolas, Pavol 18 Sep '20

18 Sep '20

External Email - Use Caution Dear Freesurfer Developers, I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the 'prescan normalize' option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options: 1. Use the 'prescan normalize' dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without 'prescan normalize' It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner. Thank you, best regards Pavol

2 1

papers that have reported results using FS5.2
by Paul 18 Sep '20

18 Sep '20

3 2

peak MNI coordinates within a masked sig.mgh
by Fred Sampedro 18 Sep '20

18 Sep '20

External Email - Use Caution Dear FS experts, I have a rather simple question: I would like to obtain the MNI coordinates of the most significant vertex in a sig.mgh map but within a specific ROI (for instance the left supramarginal region). Here is my attempt but with practical gaps in terms of command parameters: 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG? --o roimask.mgh 2) fslmaths sig.mgh mult roimask.mgh -o maskedsig.mgh 3) which command could I use to obtain the MNI coordinates of the peak value in maskedsig.mgh? Thanks a lot in advance!

3 8

Re: [Freesurfer] left-right flip?
by Ellen Ji 18 Sep '20

18 Sep '20

External Email - Use Caution group cc'd - thanks for the reminder. My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all? (Assuming that I can't just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: > Hi Ellen > > Can you cc the list so that others can respond? What was your input data? Did you not have dicoms? > > Cheers > Bruce > > -----Original Message----- > From: Ellen Ji <ellen.ji(a)bli.uzh.ch> > Sent: Tuesday, September 15, 2020 12:38 PM > To: Fischl, Bruce <BFISCHL(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] left-right flip? > > External Email - Use Caution > > Hi Bruce, > > Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again? > > Thanks, > > Ellen > > On 9/15/2020 5:44 PM, Fischl, Bruce wrote: >> And what is your input to recon-all? If it is dicom you should be >> pretty confident that we will get it correct >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve >> Sent: Tuesday, September 15, 2020 10:17 AM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] left-right flip? >> >> How are you checking the LR orientation? >> >> On 9/15/2020 4:10 AM, Ellen Ji wrote: >>> External Email - Use Caution >>> >>> Dear experts, >>> >>> I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts. >>> >>> For example, in our dataset, the lateral ventricle volume is on >>> average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical. >>> >>> In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are. >>> >>> Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake! >>> >>> I found this website on Left-right reversal, and it seems relevant to >>> my issue, but I'm not fully understanding what this means (how would >>> bias occur during segmentation?) - >>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal >>> >>> Many thanks for your input, >>> Ellen >>> >>> --- >>> >>> Ellen Ji, PhD >>> Postdoctoral Research Fellow >>> Psychiatric University Hospital >>> University of Zürich >>> ellen.ji(a)bli.uzh.ch >>> homanlab.github.io/ellen/ >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

4 7

Re: [Freesurfer] Freesurfer Digest, Vol 199, Issue 7
by James Hartzell 17 Sep '20

17 Sep '20

External Email - Use Caution HI Andrew Thanks. I've run autorecon 1, 2, and 3 so far for this one participant. There's an error in autorecon 1 but I see from older list discussion that it can be safely ignored. Even though autorecon 2 claims to finish without error, the error I reported seemed likely significant and I thought probably it should not be ignored--perhaps I am mistaken. I've attached a zip file with all the logs in the scripts folder. Cheers James On Fri, Sep 4, 2020 at 6:01 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: autorecon2, error MRISreadCurvature: (Hoopes, Andrew) > 2. Re: recon-all error (Jie Zhao) > 3. Re: mri_cvs_register with sub-millimeter recons > (Zollei, Lilla,Ph.D.) > 4. Re: recon-all error (Fischl, Bruce) > 5. mri_segstats quetsion (Nasiriavanaki, Zahra) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Sep 2020 20:18:22 +0000 > From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] autorecon2, error MRISreadCurvature: > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <67B3E641-B123-4261-880B-BF3E194A8B87(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi James, > > Can you send the full recon-all.log for this subject? > > Thanks, > Andrew > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of James > Hartzell <james.hartzell(a)gmail.com> > Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> > Date: Thursday, September 3, 2020 at 10:20 AM > To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] autorecon2, error MRISreadCurvature: > > > External Email - Use Caution > Hi > > When running recon-all autorecon2, on a single subject with > (Macbook Pro 10.15.6 (19G2021), > freesurfer-darwin-macOS-7.1.0-20200511-813297b) > > it handles the rh.curv without a problem, but for the lh kicks out this > error: > > /Users...$subj.../surf > \n mris_curvature_stats -m --writeCurvatureFiles -G -o > ../stats/lh.curv.stats -F smoothwm $subj lh curv sulc \n > Toggling save flag on curvature files [ > ok ] > Outputting results using filestem [ > ../stats/lh.curv.stats ] > Toggling save flag on curvature files [ > ok ] > Setting surface [ $subj./lh.smoothwm ] > Reading surface... [ > ok ] > Setting texture [ > curv ] > Reading texture...error: No such file or > directory > error: MRISreadCurvature: could not open /Users/$subj./surf/lh.curv > > ***WARNING!*** > Some error has occurred while reading 'lh.curv'. > This might be due a vertex incompatibility > between the surface 'lh.smoothwm' and curv 'lh.curv'. > > You might be able to correct this by re-running > 'mris_make_surfaces' on this dataset. > > Skipping this (and any remaining) curvature files. > Any measurements / calcuations that depend on the > curvature file will be skipped. > ************* > Note /Users/$subj./surf/lh.curv does exist in the subject's surf folder. > > I ran it twice just to be sure. I don't find an answer for the problem in > the freesurfer list. Any guidance will be much appreciated! > Cheers > James Hartzell, PhD (2x) > Donostia-San Sebati?n, Spain > > >

2 3

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