Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

Subfield parcellation in 1.5 T and 2.6 mm Thickness
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 25 Jun '20

25 Jun '20

? Hi FS developers, We were wondering whether a MRI scan that has 2.6 mm thickness + is 1.5 T would be sufficient for a subfield analysis (amygdala, hippocampus, thalamus). Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Re: [Freesurfer] .IMA to NIFTI conversion using mri_convert
by Vinny K 25 Jun '20

25 Jun '20

External Email - Use Caution Hi, I have diffusion-weighted images (DWI) from a Siemens scanner in the .IMA format. I used the following command in an attempt to convert the DWI series from .IMA to .nii/.nii.gz format.... mri_convert -it siemens_dicom -ot nii NEURO_BRAIN.00034.IMA dwi However, I get an outputted dwi file but it's in a Binary (application/octet-stream) format. Also, the bvecs and bvals files were not outputted. Any help would be appreciated. Thanks, Vinny

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Extracting CRAS from nifti (mri_info)
by Sherin Sugathan 25 Jun '20

25 Jun '20

External Email - Use Caution Dear Freesurfer team, I am a user of freesurfer. The tool mri_info provides me useful information from nifti files. As part of my project, I am using VTK to programmatically extract information like direction matrix, size, origin etc from a nifti file. However, I am unable to extract --cras information from a nifti file. Could you please throw some light on how I can extract the CRAS values from a NIFTI file using matlab or vtk or itk ot nibabel? If the CRAS values are computed, I would like to know how they are computed. Basically, I am trying to understand how I can get the CRAS values without using mri_info tool. Thanks in advance! Regards, Sherin Sugathan

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Re: [Freesurfer] Nifti to gifti conversion
by Glasser, Matthew 25 Jun '20

25 Jun '20

External Email - Use Caution You can use Connectome Workbench’s wb_command -volume-to-surface-mapping (recommend using the -ribbon-constrained option with the white and pial surfaces). You can then use wb_command -cifti-create-dense-timeseries to merge the two hemispheres and subcortical grey matter data into a CIFTI file. If you want a pipeline that does this for you, the ciftify pipeline (https://github.com/edickie/ciftify) might be a good choice if you have already done your preprocessing, or you could use the HCP Pipelines to do all of your preprocessing. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> Reply-To: Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, June 24, 2020 at 7:42 AM To: "freesurfer-bounces(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu>, Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Nifti to gifti conversion External Email - Use Caution Hi Experts, I have a set of resting state data in nifti format. I want to get these data into gifti format, so I can then convert them into cifti format and run melodic ICA. I suspect using mri_vol2surf would do the trick, but I know you need to specify which hemisphere you want the projection to take place on. However, I wondered if it was possible to do this for both hemisphere, or whether there is a command to merge the two hemisphere back together into a single gifti file after running vol2surf separately? The command I am currently running is: Mri_vol2surf –src filtered_func.nii.gz –out resting_surface.gii –srcreg partial-to-struct.lta –hemi lh –projfrac 0.5 –out_type gii Any advice would be great. Thanks, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 ________________________________ 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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Re: [Freesurfer] mesh spatial resolution after mris_expand
by Patricia Pais Roldan 24 Jun '20

24 Jun '20

External Email - Use Caution Dear freesurfer community, I'd like to know if there's any difference between the characteristics of a white or pial surface generated during the standard recon-all and a surface generated through mris_expand (e.g. mris_expand -thickness lh.white 0.2 lh.whitePlus02). In my results, it seems that in some areas the vertices of mris_expand-generated surfaces are more separated from each other (i.e., larger triangles or lower resolution -see original question for details-). Thank you very much. Patricia On 04.05.20 09:20, Patricia Pais wrote: Dear FreeSurfer developers, I'm generating white and pial surfaces using recon-all on an MP2RAGE to later create intermediate surfaces using mris_expand (for example: mris_expand -thickness lh.white_smooth 0.2 lh.layer02, with lh.white_smooth being a smoothed version of lh.white). It all looked fine until I decided to calculate the vertex-to-vertex distance and plotted the distribution of this parameter (something like the "spatial resolution of the mesh") for all the generated surfaces. In the histograms below, you see "distance between vertices" on the X axis and "number of samples" (pairs of vertices) on the Y axis (left/right plots: left/right hemisphere, blue=sulci vertices, red=gyri vertices). The distributions are in agreement with previously published work, but I see a small peak on the left (around 0.25 mm) in intermediate surfaces, like an accumulation of points with a certain vertex-to-vertex distance instead of a gradual decrease towards 0 (pial and white are ok). I traced back the points in these bumps and I confirmed that those vertices in intermediate surfaces correspond to vertices on the left tail of the curve in the pial and white surfaces, so I'm not very worried about it, but I'd like to know whether there's some kind of minimum distance between the vertices of the surfaces generated by mris_expand or any other reason that can explain my results. Thank you very much in advance! [cid:part1.082A4986.CF854785@fz-juelich.de] Best regards, Patricia ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Atlas construction/version information
by TACONNE Marion (INTERN) 24 Jun '20

24 Jun '20

External Email - Use Caution Hello, I would like to know the difference between the available atlas. I find information in your paper (Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature) for ?h.destrieux.simple.2009-07-29.gcs atlas but not for ?h.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs. - Does a paper exist? - Is it built from the same set of manually labeled MRI ? - If not, does the same expert label the new brain surfaces ? And who are the new subjects? - Does the protocol change ? - is it the same change for ?h.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs. ? - and for ?h.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs. ? Thank you in advance for your time and answer. Best regards, Marion Taconné This email and any attachments are intended solely for the use of the individual or entity to whom it is addressed and may be confidential and/or privileged. If you are not one of the named recipients or have received this email in error, (i) you should not read, disclose, or copy it, (ii) please notify sender of your receipt by reply email and delete this email and all attachments, (iii) Dassault Systèmes does not accept or assume any liability or responsibility for any use of or reliance on this email. Please be informed that your personal data are processed according to our data privacy policy as described on our website. Should you have any questions related to personal data protection, please contact 3DS Data Protection Officer at 3DS.compliance-privacy(a)3ds.com<mailto:3DS.compliance-privacy@3ds.com> For other languages, go to https://www.3ds.com/terms/email-disclaimer

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T1 stats output name confused
by Zeng, Qi 24 Jun '20

24 Jun '20

External Email - Use Caution Hi All, I am a little confused with the stats output. So seg/aparc are cortical white /grey matter and wmparc are subcortical white matter. Is that correct? Best, Qi

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Nifti to gifti conversion
by Mason Wells 24 Jun '20

24 Jun '20

External Email - Use Caution Hi Experts, I have a set of resting state data in nifti format. I want to get these data into gifti format, so I can then convert them into cifti format and run melodic ICA. I suspect using mri_vol2surf would do the trick, but I know you need to specify which hemisphere you want the projection to take place on. However, I wondered if it was possible to do this for both hemisphere, or whether there is a command to merge the two hemisphere back together into a single gifti file after running vol2surf separately? The command I am currently running is: Mri_vol2surf –src filtered_func.nii.gz –out resting_surface.gii –srcreg partial-to-struct.lta –hemi lh –projfrac 0.5 –out_type gii Any advice would be great. Thanks, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)
by Elizabeth Haris 24 Jun '20

24 Jun '20

External Email - Use Caution Thanks for that, Doug and Eugenio. I have two follow up queries: 1. I tried your command (with the appropriate paths) but it didn’t work (error below), however, after adding the flag -at it worked. I wanted to make sure this was still warping the hippocampal/amygdala segmentation using the CVS MNI152 registration. Command you suggested: mri_convert lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z output-in-mni152.mgz Error: mri_convert: extra argument ("output-in-mni152.mgz") Command with flag (which worked): mri_convert lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz -at final_CVSmorph_tocvs_avg35_inMNI152.m3z output-in-mni152.mgz 1. Providing this is correct, I then have a query about the transform into MNI152 space. The original amygdala segmentation gives me 9 areas (attached image: original segmentation), with their relevant labels (7001/3/5-10 and 7015); however, the transformed MNI152 amygdala segmentation doesn’t match these labels (attached imaged: segmentation in MNI). Instead: * For the left hemisphere I get 9 areas, labelled from 7001-9, I am missing the AAA and paraluminar nucleus, but there are labels for the basolateral and centromedial nuclei. * For the right hemisphere I get 10 areas, labelled from 7001-10, I am missing the paraluminar nucleus, and there are still the additional basolateral and centromedial nuclei. Is this somehow correct or has something gone horribly wrong? Thanks so much for all the help. Elizabeth From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 2 June 2020 at 12:35 am To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152) On 5/31/2020 8:48 AM, Elizabeth Haris wrote: External Email - Use Caution Hi Eugenio, Just to double check I understand: 1. If I run segmentHA_T1.sh on the output from recon-all, then the output from segmentHA_T1.sh is also in fsaverage space (not native space)? None of the output is in fsaverage space 1. * If this is correct, then can I just warp this segmentation (from fsaverage space to MNI152 space) using mri_cvs_register? i. How would I specify that mri_cvs_register should run on the registration given by cvs for each subject (in the flagged arguments it only shows how to specify registration to MNI152 space)? OR 1. Did you mean that I can specify segmentHA_T1.sh to run in native space (I couldn’t find anything on how to do this) and then warp this native segmentation to MNI152 space? It always runs in native space. You can use CVS to warp ti to MNI space with mri_convert lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z output-in-mni152.mgz 1. Many thanks for the help and clarification, Elizabeth From: <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu><mailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 28 May 2020 at 10:20 pm To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152) Hi Elizabeth, segment_T1.sh uses a bunch of files in native space for initialization that you’d also have to deform, if you wanted to run it in MNI space. I think the easiest would be to run it in native space, and then warp the segmentation to MNI, using e.g., the registration given by CVS. 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><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Elizabeth Haris <e.haris(a)unsw.edu.au><mailto:e.haris@unsw.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, May 27, 2020 at 23:11 To: "freesurfer(a)nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152) External Email - Use Caution Hi guys, I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are: 1. In recon-all, is there a way to specify registration to MNI152 space, or is it necessary to first run recon-all and then to run mri_cvs_register? 2. Is it possible to run the segmentHA script on the brain registered in MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz (instead of the mri/norm.mgz file). And from what I can see in the script, the parameters set in lines 179/180/181 (below) point to fsaverage brain files, which don’t appear to be the correct targets for the new MNI152 brain; however, there are no corresponding output files in the cvs folder, so I am unsure how to define these parameters. 3. Is there anything I have missed and would also need to do to run the segmentHA script on an MNI152 brain? (I have previously run the script on the average brain and all went well.) 179 set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz"; 180 set ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz"; 181 set LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt"; Thanks in advance, Elizabeth _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FS7.1 CentOS8 build-stamp.txt
by Tyler Ward 23 Jun '20

23 Jun '20

External Email - Use Caution Hello everyone, I just wanted to point out that the build-stamp on the CentOS8 build of FS7.1 includes the text “centos7” which raises some questions among users as to which one we have installed. It’s a tiny detail, but I’m sending this message to document it online in case anyone else sees it and thinks they downloaded the wrong build as I had thought. -Tyler

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Freesurfer June 2020