Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Implement my own parcellation on aparc+aseg.mgz file
by Das S. 28 Apr '17

28 Apr '17

Hi I have create my own annot file and lookuptable for cortical parcellation. How I can implement my own parcellation in aparc+aseg.mgz file. I am also stuck on how to update the FreeSurferColorLUT.txt file? Please help. Thanks Sarbani

2 4

debug mri_aparc2aseg
by Das S. 28 Apr '17

28 Apr '17

Hi I need to debug the issue I am facing at the moment. So I want to run the program with GDB. I could run it with gdb but no debug information/symbol is present in the current installed form. So I guess I need to recompile the mri_aparc2aseg program with in debug mode. Can you please help me in that? What is the easiest way to recompile with the debug symbols so that I can put a breakpoint in GDB? Also, if there any option to activate more logs/log levels? Thanks a lot for your help. Much appreciated. Regards, Sarbani

2 1

Skull stripping
by John Anderson 28 Apr '17

28 Apr '17

Dear FS experts, I want to inquire if there are any threshold for the flag "gcut " in the command: recon-all -skullstrip -clean-bm -gcut -subjid <subject name> If this not available are there any tools that can help to control how much dura will be cut out Thanks in advance! John

1 0

R: Re: Questions on fsdg file using complex study design
by stdp82＠virgilio.it 27 Apr '17

27 Apr '17

Thanks. I do not know if in the previous mail we well described our case. I repropose my question in more explicative way. In a first step we want assess the differences between 4 groups, considering a single structure (eg. right ROI). We have 4 groups (e.g. Young, Older, MCI, AD). This case is similar to the example reported on the site for Three Groups (One Factor/Three Levels), No Covariates. There you have put Older (OA), MCI, AD. Here we aim at add an other group which is Young (YA). Please could you show me the possible combination of mtx.files? Especially of group.effect and YA-OA+mci-ad.mtx? In the second step we would evaluate the differences between 4 groups in more complex design, including more than a single structure (e.g. right and left ROI1, right and left ROI2, right and left ROI3, right and left ROI4). Many thanks Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 27-apr-2017 17.40 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] Questions on fsdg file using complex study design > > > >On 04/27/2017 09:02 AM, stdp82(a)virgilio.it wrote: >> Dear list, >> >> we have several difficulty to understand how I should build fsdg file >> and we are worried to produce correct results. >> >> On FS site, it is not available an example if we would look for >> differences among 4 different groups (A, B, C, D; 4 Groups - One >> Factor/Three Levels - No Covariates). >> The proposed design with 2 levels and 2 factors is no helpful in our case. >Mathematically, it is the same. >> >> We have 4 groups (1 factor and 4 levels, no covariates) and we our >> hypothesis (in term of impaiment) is A<B<C<D. >This is not a valid linear contrast since it requires an AND operation >(A<B AND B<C AND C<D). You have to use a conjunction analysis in which >you create 3 contrasts then conjunct them (with mri_concat --conjunct) >> >> Which should be the group.effect.mtx? >> How should we look to difference between Group1, Group2, Group3 and >> Group4? >> Should we opt for G1+G3 vs G2+G4 or G1+G2 vs G3+G4? Other option? >> >> Please may you argue a rationale? >> >> e.g. Looking your example on three Groups (One Factor/Three Levels), >> No Covariates, we wonder why if Normals==MCI AND Normals==AD, then it >> MUST be the case that MCI==AD? >> >> We aim at assess differences by using more complex design (4x2x4), >> including >> 4 different structures, looking at right and left structures and >> having 4 levels (4 different groups). >> >> How should we do, please? >> >> Thank you very much. >> >> Best regards >> >> Stefano >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >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 Partners Compliance HelpLine at >http://www.partners.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. > >

1 0

Recon-all error- mri_convert.bin: can't determine type of output volume
by Ariana Marie Stickel 27 Apr '17

27 Apr '17

Dear Freesurfer Developers, I am attempting recon-all on one subject. I immediately get the following error: mri_convert.bin: can't determine type of output volume See recon-all.log (attached). Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: CentOS Linux 7 I have successfully completed recon-all on an older virtualbox (Windows host) version of Freesurfer with the same subject, so I do not think there is an issue with the subject data. Any help would be hugely appreciated. Thank you, Ariana Stickel

2 2

TRACULA anterior/posterior
by Funk, Quentin 27 Apr '17

27 Apr '17

Freesurfer experts: I'm interested in comparing anterior and posterior pieces of a tract generated by TRACULA. Ideally, I'd like to take the probabilistic map (i.e. the path.pd.nii.gz from one of the folders in SUBJECT/dpath) and obtain a "posterior part" and an "anterior part" by masking. Then I'd like to extract stats similar to the stats found in pathstats.overall.txt Is this at all possible? I can produce the poster/anterior mask by hand for each individual subject, (although if there were an automated way to do this that I'm unaware of it would be great) but getting the stats out is something I can't quite figure out from the tutorials I've looked through. Thanks for any help! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

using mni152reg for hippocampal subfields
by Annie Duchesne 27 Apr '17

27 Apr '17

Hello All, I have successfully ran the recon-all -all -s subject -hippocampal-subfields-T1 using free surfer v.6 on macOS Sierra. In addition to the structural analysis, I want to run resting state functional connectivity analysis using the whole l/r hippocampus as well as specific subfields as structural seeds. I don<t want to generate an average ROI, but generate subject specific HCSF ROIs. My understanding is to perform such analysis I need to: 1)convert the l/rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to mni space (MNI152_T1_2mm_brain.nii.gz). I ran the mni152reg command, however I doubt that the default settings apply to the hippocampal subfields. Is there options I could use to have the subfields register to MNI 2mm space using mni152reg? 2)Generate .nii rois for the whole and subfield regions of the hippocampus. Using mrs_convert I was able to convert the (l/r)h.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to .nii, getting one global hippocampus per hemisphere. Is there a way to automatically generate subfields ROIs? Thank you, Annie

1 0

Last weeks to register for HCP Course 2017
by Jennifer Elam 27 Apr '17

27 Apr '17

It's not too late to register for the 2017 HCP Course: "Exploring the Human Connectome" <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstore.huma…>, to be held June 19-23 at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada! FreeSurfer is a major part of the HCP structural processing pipeline and has been critical to the processing of the project's over 1100 released high quality imaging datasets. Spaces for the course are limited and registration is on a first come, first served basis. May 17, 2017 is the deadline to reserve discounted UBC accommodations within walking distance to the course venue: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A… The 5-day intensive HCP course is a great opportunity to learn directly from HCP investigators and designed for those interested in: - using data collected and distributed from the HCP young adult study - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - using Connectome Workbench tools and sharing data using the BALSA imaging database - learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data - exploring the HCP MMP 1.0 multimodal parcellation brain map and learning about how it can be used in your analyses - positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from HCP development (healthy subjects ages 5-21) and aging (healthy subjects ages 35-90+) and Connectomes Related to Human Disease projects See https://store.humanconnectome.org/courses/2017/exploring-the-human-connecto… for more info. If you have any questions, please contact us at: hcpcourse(a)humanconnectome.org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff

1 0

Questions on fsdg file using complex study design
by stdp82＠virgilio.it 27 Apr '17

27 Apr '17

Dear list, we have several difficulty to understand how I should build fsdg file and we are worried to produce correct results. On FS site, it is not available an example if we would look for differences among 4 different groups (A, B, C, D; 4 Groups - One Factor/Three Levels - No Covariates).The proposed design with 2 levels and 2 factors is no helpful in our case. We have 4 groups (1 factor and 4 levels, no covariates) and we our hypothesis (in term of impaiment) is A<B<C<D. Which should be the group.effect.mtx?How should we look to difference between Group1, Group2, Group3 and Group4? Should we opt for G1+G3 vs G2+G4 or G1+G2 vs G3+G4? Other option? Please may you argue a rationale? e.g. Looking your example on three Groups (One Factor/Three Levels), No Covariates, we wonder why if Normals==MCI AND Normals==AD, then it MUST be the case that MCI==AD? We aim at assess differences by using more complex design (4x2x4), including 4 different structures, looking at right and left structures and having 4 levels (4 different groups). How should we do, please? Thank you very much. Best regards Stefano

2 1

Error when transforming aal.nii to lh.aal.label
by haidong wang 27 Apr '17

27 Apr '17

Hello FS experts, I want to get the thickness of 90 ROIs of AAL using freesurfer. I use the following commands to transform aal.nii to lh.aal.label. 1.bbregister --s sub_con_sub01 --mov ch2.nii --t1 --init-fsl --reg register_vol2surf.dat 2.mri_vol2surf --mov aal.nii --reg register_vol2surf.dat --hemi lh --out_type mgh --o lh.aal.mgh --interp nearest 3.mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf sub_con_sub01 4.mri_label2label --srclabel lh.aal.label --srcsubject fsaverage --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh 5.mris_anatomical_stats -l lh.aal.label -t lh.thickness -b -f sub_con_sub01/stats/lh.aal.stats sub_con_sub01 lh 6.aparcstats2table --hemi lh --subjects sub_con_sub01 --parc aal --meas thickness -t ./aal_thickness.txt The result is that there is no measurement in the produced document named lh.aal.stats. I am also confused about how to set id in mri_cor2label.Could you please give me some suggestions? I am looking forwad for your prompt reply. Yours, Haidong The attachment is the screenshot of my working directory. Here is the error: mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf sub_con_sub01 $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.aal.mgh ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 75659.000; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 6451 label voxels Writing label file ./lh.aal.label LabelWrite: saving to ./lh.aal.label Centroid: -9707.33 -0.50 0.50 mri_cor2label completed SUCCESSFULLY admi@admi:~/Desktop/freesurfer_thickness$ mri_label2label --srclabel lh.aal.label --srcsubject fsaverage --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh srclabel = lh.aal.label srcsubject = fsaverage trgsubject = sub_con_sub01 trglabel = lh.aal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/admi/Desktop/freesurfer_thickness FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6451 points in source label. Starting surface-based mapping Reading source registration /home/admi/Desktop/freesurfer_thickness/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.white Reading target registration /home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. Label point 0: vno = -1, max = 163842

2 2

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