Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Annotation file's LUT
by Faeze Vedaei 25 Feb '16

25 Feb '16

Hi Freesurfer experts, I want to have all the label files extracted from the annotation file base on Destrieux atlas. I used the command mri_annotaion2label to do this. The result is just 75 labels. Are these all the regions included in annotation file? Can you let me know how I can access to all the regions (structure name) contained in annotation file? Thanks, Faezeh Vedaei

2 1

Minor adjustment to RB_all_2008-03-26.gca
by Kok, JG (neuro) 25 Feb '16

25 Feb '16

Hi, I wish to split the putamen in an anterior part and a posterior part in >60 subjects which have been analyzed by the recon-all stream (FS version 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the coronal plane through the anterior commissure) and apply this "new" atlas to all subjects, one of the advantages being the bias that would be introduced by splitting the putamena manually in all subjects would be avoided. After some time trying to make this happen, I now think this could be achieved by adjusting RB_all_2008-03-26.gca and applying something like "mri_ca_label -align subject_norm.mgz subject_talairach.m3z RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz". The problem is that till now I wasn't able to figure out how to correctly read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB function load_gca.m, but that seems to only work up to version 4 of the .gca file format (as GCA_VERSION is set to 4 in the function), and RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the file anyway in MATLAB using the code written for version 4 and below (by setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is already way too large, although I suspect the error occurs earlier). My questions: 1. Do you think I am following the right track to achieve a sensible splitting of the putamena this way? Or should I try something else? 2. Is there a newer load_gca.m file around which is able to read a version 5 .gca file? Or could you point me to the difference in the design of the version 5 .gca file compared to that of the version 4 file so that I can rewrite load_gca.m? Cheers, Jelmer ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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How to invoke skullstrip adjustments and wm control points
by Gronenschild Ed (NP) 25 Feb '16

25 Feb '16

Hi, I have made some manual skullstrip adjustments and added a number of control points in the white matter. How should I proceed with recon-all to incorporate both adjustments? Cheers, Ed

3 2

Problem with brainstem substructures segmentation
by Riccardo Gubellini 25 Feb '16

25 Feb '16

Dear Freesurfer users, We have downloaded the Freesurfer 6.0 version since we are really interested in the brainstem segmentation. We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM. We installed freesurfer6.0 on a virtual machine Linux (CentOs 6.7) enabling 4vcpu 11Gb of RAM. Disk space was 50 GB and after installation we have 15 GB free for data. We have launched recon-all –all for some cases and everything went right. Then we have tried to launch recon-all –all –s nameofsunbject –brainstem-structures and the process, after about 6 hours, stacks, during the SegmentSubject process and after having computing hyperparameters for estimation of Gaussian parameters. Do you have any ideas of what is happening? Thank you for your help! Riccardo Gubellini

1 0

Fwd: Creare Annot File in Freesurface
by Faeze Vedaei 24 Feb '16

24 Feb '16

Hil Freesurfer experts, I am trying to create annot file in freesurface using mris_label2annot command. In this process, I got an error : cannot find or read 'labelfile'sname.label'. I want to help me and explain what is the problem I have such this error for every label file I practice? Here is the command line I used : mris_label2annot --s 002_S_0295 --h lh --ctab 002_S_0295/LABELS/aparc.annot.a2009s.ctab --a myaparc --l lh.G_orbital.label ERROR: cannot find or read lh.G_orbital.label. I'd appreciate it if you clarify me about this process and how I can solve this. Regards, Faezeh Vedaei

2 1

bbregister problems
by Pradeep 24 Feb '16

24 Feb '16

Hello All, I am trying to map pet scans to MRI using bbregister and quite a few subjects were improperly registered. Here are my steps: bbregister --s $fs --mov ${pet_ext}_LIA.nii --init-fsl --t1 --lta output.lta tkregister2 --mov summed_LIA.nii --reg output.dat --surf [ mri]$ more output.dat.mincost 0.860663 0.000513 0.000492 -11.863233 The first value is quite close to 1 so its bad I have attached a screen shot of the image and the log file generated after bbregister. Please let me know if there are any parameters that I could tweak to make the registration better. Thank you for your help, -Pradeep

2 2

Re: [Freesurfer] [Fsdev] [PATCH] fix ups for DESTDIR
by Z K 23 Feb '16

23 Feb '16

Hello Yaroslav, It the case when "some subdirs makefiles do not care about DESTDIR, which is generally respected by autotools" an autotools version issue? Or related to something else completely? I see that making the change on my end does not produce any ill effects, but I would like to observe the behavior before committing the "fix". -Zeke On 02/22/2016 11:33 PM, Yaroslav Halchenko wrote: > Dear FS Developers, > > Per ZK's blessing I am moving my "whining"... khe khe... dialogue over > to fsdev mailing list. And would like to begin with this patch which > have got buried in the users' mailing list: > > I have got into a problem that currently some subdirs makefiles do not > care about DESTDIR, which is generally respected by autotools... > attached patch should help to make FS 'installable' e.g. via > > make install DESTDIR=$PWD/INSTALL-DIR/ > > NB in the future, it would be a nice "test" to add to .travis.yml > upon successful build, without system wide installation with sudo ;) > > Please review/adopt/accept. > > With best regards, > > > > _______________________________________________ > 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. > > > > _______________________________________________ > Fsdev mailing list > Fsdev(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev >

1 0

FreeSurfer group analysis: mri_glmfit-sim
by Silas 23 Feb '16

23 Feb '16

Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> FsTutorial/GroupAnalysisDng - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> surfer.nmr.mgh.harvard.edu Introduction. This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including ... 1) I would like to do a surface based analysis where i'm only investigating a certain area or label - instead of doing a whole brain analysis. This can be done by introducing --label surface_area_of_interest.label when running mri_glmfit. Would this give me different results from doing a whole brain analysis - or would it just exclude the results from outside the label? And how about after clusterwise correction for multiple comparisons? -> is there a better way to do this than following the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when configuring the overlay? Best, Silas

2 5

Convert spm volume to fresurfer surface
by Daniel Baena Pérez 23 Feb '16

23 Feb '16

Dear Fresurfer users, I would like to analyze group differences in cortical thickness in fresurfer by using as a mask a volumetric SPM activity image. Which command should be used for this purpose? Thanks a lot and best wishes, Sofia

3 2

Still age corrected?
by Daniel Baena Pérez 23 Feb '16

23 Feb '16

Dear Freesurfer user, We have performed group contrasts on cortical thickness correcting by age. Now we want to use the mean cortical thickness of one of the significant clusters as a regressor in other analysis, but we do not know whether the mean cortical thickness value for each subject within this ROI is corrected by age or not. Best regards and thank you

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