Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

Resting state fMRI preproc-sess registration error
by Wenzhen Zhao 18 Sep '20

18 Sep '20

External Email - Use Caution Dear freesurfer developers, I am working on preprocessing resting state fMRI and used the following command. $ preproc-sess -s sess01 -fsd rest -stc siemens -surface fsaverage lhrh -surf-fwhm 5 -mni305-2mm -vol-fwhm 0 -per-session When I tried to visualize f.nii.gz with registration file applied and overlaid with aparc+aseg.mgz from structural analysis, they do not overlap. It seems like the orientation is not the same, and the f.nii.gz with registration seems to be 90 degree rotated from apjarc+ aseg. mgz. (I wish I could attach a screenshot, but last time I tried, it says my email exceeded the capacity and sent to the moderator) I also tried bbregister. I was suggested not to use —init-rr, so I tried all the other registration methods, but same problem occurs. $bbregister --mov sess01/rest/001/template.nii.gz --t2 --s subject --lta register.dof6.lta —init-rr does a good job when I checked visually by applying registration on f.nii.gz and checked if it overlaps with structural scan. But, I thought the registration file goes both ways, but when I checked structural scan (orig.mgz or aparc+aseg.mgz) with registration file and overlapped with functional scan (f.nii.gz), it does not overlap. Is there a specific way that I have to apply a registration file to visualize the transformation in the opposite direction? If preprocess registration does not work, is there any other method that I can try to make them aligned? Thank you for your time and help ! Best, Wenzhen

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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

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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

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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

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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

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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

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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

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

18 Sep '20

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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!

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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.

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Freesurfer September 2020