Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

Avoiding or removing overlap when converting surface labels to volume
by Jacob Miller 08 Aug '19

08 Aug '19

External Email - Use Caution Hi Freesurfer team, I am transforming several adjacent surface labels into volume ROIs, using *mri_label2vol*. When doing so, there seems to be some possibly unavoidable overlap in a small number of voxels in the volume ROIs. Is there any way to avoid these labels from overlapping when transformed into the volume? I see that *mri_label2vol* takes an --annot flag, would this help in avoiding overlap in the outputs? Otherwise, I can remove the overlapping voxels int he nifti file outputs, but I was wondering if the algorithm had any options to do this as part of the surface-to-volume transform. Thanks so much! Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/

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TRACULA empty bbr maps after trac-all -prep
by Fred Sampedro 08 Aug '19

08 Aug '19

External Email - Use Caution Dear TRACULA experts, dear Anastasia, I've been successfully using TRACULA for a while with different DTI images from different scanners (siemens, philips...). Now I am working with GE DTI data and whereas the trac-all -prep command went well, and $subject/dmri/dtifit_FA.nii.gz and dtifit_MD.nii.gz look fine, $subject/dmri/mni/dtifit_FA.bbr.nii.gz and all mni-space maps are empty (see pictures attached). I also attach the trac-all.log file. and bvals/bvecs that were generated by trac-all directly from the dicom images. What could have gone wrong?

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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
by Iglesias Gonzalez, Juan E. 08 Aug '19

08 Aug '19

Please try using the 1mm version of the segmentation in FreeSurfer space. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jessica Bourgin <jessica.bourgin(a)univ-smb.fr> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 8 August 2019 at 11:58 To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space External Email - Use Caution Dear Juan Eugenio, Thank you for these precisions. Following the guidelines of FSL, I computed the following sequence on my structural image : bet my_structural my_betted_structural flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural --warp=my_nonlinear_transf --out=my_warped_structural The warped structural image overlapped nicely with the atlas. However, when I compute the following command on the segmentations : applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/lh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_lh applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/rh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_rh The segmentations do not appear on the atlas nor the structural image. Do you know how to solve this problem ? Thanks for your help. PS: I used FSL for registration because I don't know how to do that with Freesurfer. Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
by Jessica Bourgin 08 Aug '19

08 Aug '19

External Email - Use Caution Dear Juan Eugenio, Thank you for these precisions. Following the guidelines of FSL, I computed the following sequence on my structural image : bet my_structural my_betted_structural flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural --warp=my_nonlinear_transf --out=my_warped_structural The warped structural image overlapped nicely with the atlas. However, when I compute the following command on the segmentations : applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/lh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_lh applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/rh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_rh The segmentations do not appear on the atlas nor the structural image. Do you know how to solve this problem ? Thanks for your help. PS: I used FSL for registration because I don't know how to do that with Freesurfer. Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

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SegmentHA_T1.sh hippocampal sub-field issue
by Daniel Callow 08 Aug '19

08 Aug '19

External Email - Use Caution Hello, When using segmentHA_T1.sh on one of my subjects the left hippocampus ROI seems to spill over a lot into white matter and other gray matter regions. See attached picture. Is there a way to fix this or improve the hippocampal segmentation? Or will I have to scrap this subject's data? I have also included the scan log. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Re: [Freesurfer] Help with MRI segstats
by Greve, Douglas N.,Ph.D. 07 Aug '19

07 Aug '19

You should only pass one of --seg, --annot, or --slabel to mri_segstats. I don't understand how you are trying to use this in the context of your permutation. Is this something that you are running on each iteration? If so, it is probably not what you want to do. Probably you want to run mri_surfcluster to get the cluster sizes out. On 8/7/19 1:31 PM, Daliah Ross wrote: > > External Email - Use Caution > > This is the command line: > mri_segstats --seg F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.mgh > --annot lh.aparc.annot lh parc --slabel fsaverage lh cortex --sum > F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.txt > > We are running the permutations within FS, but because our model is a > linear mixed model, and we didn't think that this would be compatible > with fspalm. So, we are running the permutations "manually" (i.e. we > are generating the random permutations, which in our case is just > switching the subject labels for the thickness data. We are then using > mri_surfcluster to extract the maximum cluster size per permutation > and will use the permutation distribution to determine our the > statistical significance of our results). In addition, our analyses > are a bit out of the ordinary in that the thickness data are an > independent variable in our model, for which we have a repeated > non-imaging measure as the outcome. Effectively, we are using the > thickness maps to generate vertex-wise regressors, with a fixed > outcome measure (fixed in the sense that it doesn't vary across the > brain). > > If you have any thoughts about how we could use fspalm in our case, > your advice would be most appreciated. > > Thanks again, > Daliah > > *Daliah Ross* | dross3(a)mail.yu.edu <mailto:dross3@mail.yu.edu> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of > Greve, Douglas N.,Ph.D. > Sent: Tuesday, August 6, 2019 12:56 PM > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Help with MRI segstats > > Can you send command lines? Also, are you using the built-in > permutation tool or trying to do something outside of FS? > > On 8/6/19 8:40 AM, Daliah Ross wrote: > > > > External Email - Use Caution > > > > Hi FreeSurfer experts, > > > > I have a couple of questions regarding mri_segstats tool for an > > analysis on vertex-wise cortical thickness data. We are > attempting to > > compare maximum cluster sizes among permutations. We are having > > trouble figuring out how to get the anatomical label for each > cluster > > using the --slabel argument. We are also wondering if the > difference > > between cluster sizes between mri_surfcluster and mri_segstats > is due > > to partial volumes, and if so, how to correctly use the --pv > argument. > > It suggests in the wiki page that mri/norm.mgz volume is usually > used > > but I believe we need something surface-based since we are using > > thickness data. > > > > Thank you in advance for any help you can provide. > > > > Best, > > Daliah > > > > *Daliah Ross* | dross3(a)mail.yu.edu <mailto:dross3@mail.yu.edu> > <mailto:dross3@mail.yu.edu <mailto:dross3@mail.yu.edu>> > > > > Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf > > Graduate School of Psychology Yeshiva University Albert Einstein > > College of Medicine > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail > > .nmr.mgh.harvard.edu > <http://nmr.mgh.harvard.edu>%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C0 > > 1%7Cmark.wagshul%40einstein.yu.edu > <http://40einstein.yu.edu>%7Cfde693609070412c457808d71a8f16f2% > > > 7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637007074183066654&sd > > ata=ALndUpHJ%2BYhuMzChviSn9ygf8H112mUKvVmJktGoqB4%3D&reserved=0 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… >

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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
by Jessica Bourgin 07 Aug '19

07 Aug '19

External Email - Use Caution Dear Juan Eugenio, Thanks a lot for your quick response. I don't understand what you mean exactly by "propagate the hard segmentations". And when you say to register the subjects to the Brainnetome, do you mean replace the atlas used by recon-all to do that ? (sorry, I am currently a PhD student with little experience in neuroimaging). You also mention that the transformation is not trivial. But do you think this is "correct" to make it ? Thanks for your help ! Cheers, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

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Fwd: Recon-all output space and .annot file registration
by Rachel S 07 Aug '19

07 Aug '19

External Email - Use Caution Hello freesurfer developers, I am trying to get the user defined segmentation for a subject generated in here (https://github.com/mattcieslak/easy_lausanne) . After recon-all, I have the pial surface with ~250k vertices. My first question is about the recon-all space. I thought the output of recon-all is already registered with the fsaverage space since it uses bucker40 as the template for segmentation. But some mentioned it is in the individual native space. Which one is true? My second question is about the procedure to generate the segmentation for downsampled surface. I have the .annot file and .label file for that subject and also for fsaverage. Reading the .annot file can give me the region mapping for ~250k matrix. I want to map the subject to fsaverage5 space and also downsample the vertices for the cortical surface to ~20k. And I want to get the region mapping for this ~20k vertices from the ~250k vertice .annot file. I looked into the documentation and email archive, here is a few things I tried. I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 1. Try to map to fsaverage in the recon-all step by using recon-all -i 0000.dcm -s p6_fs5 -all -qcache -target fsaverage5 And here is the error: --------------------------------------------------- #@# 1/1 p6_fs5 Wed 07 Aug 2019 04:49:09 AM EDT -------------- ----------------------- mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness --sfmt curv --noreshape --cortex MRISread(/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg): could not open file Source registration surface changed to fsaverage5.sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/rachelsun/Software/freesurfer/subjects cd /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname rachel-pc machine x86_64 user rachelsun srcsubject = p6_fs5 srcval = /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness srctype = curv trgsubject = fsaverage5 trgval = ./tmp.mris_preproc.7614/p6_fs5.1.mgh trgtype = srcsurfreg = fsaverage5.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg No such file or directory mri_surf2surf: could not read surface /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg No such file or directory Linux rachel-pc 4.19.62-1-MANJARO #1 SMP PREEMPT Sun Jul 28 09:14:58 UTC 2019 x86_64 GNU/Linux 2. Use the basic recon-all step recon-all -i 0000.dcm -s p6 -all, and run mri_surf2surf --srcsubject p6 --sval-xyz pial --trgsubject fsaverage5 --tval-xyz --tval lh.pial.p6 --hemi lh And I can get the surface mapped to fsaverage space, but I am not sure how to get the region segmentation for this new surface. From what I learned, mri_surf2surf is to map .annot between subjects. Sorry for the long email and thank you for your time. I would really appreciate it your input. Best regards, Rachel

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Help us help you learn methods in Advanced Statistics in Neuroimaging and Genetics
by ROBERT CARY WELSH 07 Aug '19

07 Aug '19

External Email - Use Caution Hi, We are in the midst of designing a short course on Advanced Statistics in Neuroimaging and Genetics. We would like to get a sense of the interest. If you don’t mind, please take a moment to fill out this short survey. https://csbsutah.co1.qualtrics.com/jfe/form/SV_eLqjkjI8ikjY0TP Much appreciated, Robert Welsh ------------------------------ Robert Welsh, PhD Associate Professor Department of Psychiatry University of Utah robert.c.welsh(a)utah.edu

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Transform hippocampal/amygdala segmentation to another space
by Jessica Bourgin 07 Aug '19

07 Aug '19

External Email - Use Caution Dear all, I would like to use the Hippocampal Subfields and Nuclei Of Amygdala tool concomitantly with the Brainnetome Atlas for a resting-state analysis. For this purpose, I need the hippocampal/amygdala nuclei to be in the same space as the Brainnetome. Can you advise me on the method to use to transform the segmentation to another space ? Thank you in advance for your help. Best regards, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

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