Freesurfer

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30132 discussions

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 5.3.0 recon-all failure
by Ian 23 Jun '20

23 Jun '20

External Email - Use Caution Hey guys. I have need to run recon-all from freesurfer 5.3.0. When I do I get this error: INFO: SUBJECTS_DIR is /execute Actual FREESURFER_HOME /usr/local/freesurfer Linux ca9b4aef337a 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 GNU/Linux Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/x86_64-linux-gnu/perl5/5.28 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.28 /usr/share/perl/5.28 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. Could you advise please? Thanks, Ian -- *Ian Hardingham*

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PhD Position - Early MRI and childhood outcomes - Liggins Institute, Auckland
by Eleanor Kennedy 22 Jun '20

22 Jun '20

External Email - Use Caution Hello, We are seeking a PhD candidate at the Liggins Institute, University of Auckland with Prof Jane Harding. Research at the Liggins Institute focuses on early life determinants of long-term health and covers a broad range of disciplines from basic science through to clinical trials and translational research. Project Description: MRI is increasingly being used in preterm newborns to assess early brain injury and brain maturation, but its relationship to later development is unclear. We plan to determine the relationship between early MRI and later development in children who as babies took part in clinical trials of additional nutrition, or of magnesium sulphate administration to prevent cerebral palsy. If early MRI is predictive of particular problems such as cerebral palsy, it could be used in the future to identify babies at risk and allow early intervention. The project will involve neonatal MRI (DTI, fMRI and structural scans). Assessments of children at two years of age for cognitive, language, motor and executive function. We are looking for candidates with a degree in a health, psychology or education-related discipline and some experience with MRI analysis. For more information, see the Find a Thesis entry here: https://www.findathesis.auckland.ac.nz/research-entry/10464530 Thanks, Eleanor Kennedy Research Fellow Liggins Institute DDI +64 9 923 6701 Ext 86701 E eleanor.kennedy(a)auckland.ac.nz<mailto:eleanor.kennedy@auckland.ac.nz> W www.liggins.auckland.ac.nz<http://www.liggins.auckland.ac.nz/> A The University of Auckland, Building 503, Level 2, 85 Park Road, Auckland P Private Bag 92019, Auckland 1142, NZ [Liggins Logo Colour_small]

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Re: [Freesurfer] How to make surface cuts / flatmaps. Alternative for tksurfer in 2020?
by Chris Klink 22 Jun '20

22 Jun '20

External Email - Use Caution Someone messaged me that in the latsest FS7 we can now do this in Freeview. Awesome! I don't think a lot of people know about this. Spread the word! -- Chris Klink (sent from a phone)

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Re: [Freesurfer] QDEC analyses
by xunzhang_hmrrc 22 Jun '20

22 Jun '20

External Email - Use Caution Thanks for your timely response. To assess the two group differences in cortical thickness, whole-brain vertex-wise analyses were performed using the graphical user interface of FreeSurfer known as QDEC. We used a general linear model to compare the thickness between the patients and healthy controls with age and sex as covariates. The Monte Carlo Null-Z Simulation was conducted to control for multiple comparisons (cluster-wise corrected P< 0.05). But, as we all know, QDEC analyses have always be done for the two hemispheres separately, so the multiple comparisons are also conducted for two hemispheres separately, which, the reviewer assumed, is different from multiple comparisons for the whole brain? So, could you please provide some perspective and citation about the validation for such design of QDEC (i.e., the right and left hemisphere were tested separately)? ------------------ Original ------------------ From: "Douglas N. Greve"<dgreve(a)mgh.harvard.edu>; Date: Mon, Jun 22, 2020 10:17 AM To: "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu>; Subject: Re: [Freesurfer] QDEC analyses How you did you do your analysis? As an exploratory/map-based analysis? Or as an ROI analysis? How did you correct for multiple comparisons? Generally, in a map-based analysis, the correction for multiple comparisons incorporates the fact that there are two hemispheres being tested. On 6/20/2020 10:04 PM, xunzhang_hmrrc wrote:         External Email - Use Caution        Hello Freesurfer developers, Recently, I have used QDEC of freesurfer 6.0.0 to examine the cortical thickness differences between two groups, and the manuscript has been submitted to a journal. One reviewer raised a question -"The manuscript stated that the right and left hemisphere were tested separately. Could the authors provide an explanation for this? I assume that testing over 68 (all ROIs) vs testing separately left and right (34 ROIs) would have an effect?" Unfornately, I don't know how to responde to this reviewer, so I would like to ask for your help. I just followed the tutorials of QDEC (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0) and I found QDEC analyses have always be done for the two hemispheres separately. So, could you please provide some perspective and citation about the validation for such design of QDEC? Thank you in advance for your assistance, Best regards, Xun _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all for macaque brain
by Minqing Jiang 22 Jun '20

22 Jun '20

External Email - Use Caution Dear Chris and Douglas, Thank you for the help! I would try the hires and precon_all. One more quesion, now I have a much better recon result from adult macaque brain. But when I performed MRI in 1 years old macaque. Recon-all barely can generate result, either with error or very bad segmentation. We are using TI 1100ms, TR3000/TE3.29 and FOV 128*128. Is there any way to segment young monkeys better? Thanks again. bests, Minqing Hi Minqing Jiang, Getting a macaque brain through Freesurfer requires a bit of manual tinkering. We have a description of how we do it on GitHub: https://github.com/VisionandCognition/NHP-Freesurfer There's also precon_all (https://github.com/recoveringyank/precon_all) which I haven't personally used yet, but I've seen results and it looks very promising! ?Good luck! Chris

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