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by Maheen Siddiqui 26 Feb '16

26 Feb '16

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missing orientation tag
by Ahearn, T 26 Feb '16

26 Feb '16

Hello, I've a few images that will not process due to a missing orientation tag. I've looked at the header and 0020,0037 is missing. For a similar sagittal image I found the following .. 0020,0037 Image Orientation (Patient): -0.0753529518842\0.99712705612182\0.00771582638844\0.06153532490134\0.01237302832305\-0.9980282187461 ... approximately 0\1\0\0\0\-1 I used dcmodify to insert this tag but it still would'nt process. Is there another tag that I need to look at? Will assuming perfect sagittal alignment make a difference to the freesurfer output? Any thoughts/help appreciated Thanks Trev The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.

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Recon-all error
by m.bahri＠ulg.ac.be 26 Feb '16

26 Feb '16

Dear Experts, I have the following error with recon-all (freesurfer v 5.3) in the orig_nu.log file. Could anyone help to solve the problem? Many thanks, Mohamed -------------------------------------------------------- Iteration 1 Fri Feb 26 14:13:20 CET 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.20504/nu0.mnc ./tmp.mri_nu_correct.mni.20504/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20504/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /usr/local/freesurfer/mni/share/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. ERROR: nu_correct

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Changing coordinate system of surfaces generated by recon-all FS
by Maheen Siddiqui 26 Feb '16

26 Feb '16

Dear FreeSurfer Users, I have a head surface mesh and a pial surface mesh obtained after segmentation of a T1 MRI scan. I am going to importing these into Homer2 Atlas Viewer as subject anatomy. However before I can do this import successfully, I need to bring the two meshes into the same coordinate system. At the moment they are in different coordinate systems (as pictured) and I need to bring the pial surface mesh into the head surface mesh. I am a little unsure how to do this. Does anybody have any experience with this? Or any advice on what I could do possibly? Thanks, Maheen _______________________________________________ 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

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

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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.

2 4

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

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