Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

creating norm.mgz
by Borzello, Mia 31 May '14

31 May '14

Hi all, I'm trying to use tkmedit to pick electrode points for a patient. For the mri, I'm using the average brain provided by freesurfer. I realized that I have no norm.mgz file which tkmedit calls. How do I create this? Thanks, Mia

2 3

Control point error
by Victor Kovac 30 May '14

30 May '14

Hello, I ran recon-all on few subjects but noticed that much of the temporal lobes were excluded from segmentation, so I added control points to missed white matter voxels in this area, and subsequently ran recon-all -autorecon2-cp -autorecon3. The control points fixed much of the segmentation errors in the temporal lobes; however, errors in segmentation of other areas of the brain -- far from where I had placed control points -- were introduced. Attached are images of the same subject and same coronal slice, before and after running -autorecon2-cp -autorecon3, and, as you can see, much of the right superior frontal lobe is now missed. Is there any way to fix this, other than by simply adding more control points to the newly missed areas? One note is that the cores I am running these subjects on have a memory limit of 3.75 GB and I see that the recommended memory per subject is at least 4.0 GB. Could this be the problem? Also attached is the recon-all log. Thank you! Victor

2 1

Re: [Freesurfer] Registration of Functional Data to the Inflated Brain
by Sherryse Corrow 30 May '14

30 May '14

Thanks Bruce. The problem is that the registration itself is not working properly. Recap: The goal is to view the functional data on the inflated brain. We ran recon-all, checked that registration, then attempted to register the functional data to the free surfer anatomical. My understanding is that running reg-feat2anat should create a folder (featdir/reg/freesurfer) with register.dat and anat2exf.register.dat files in (among others). The folder is created and some of the files are created, but those two are not. Although, I should note that there is a file created within this folder called anat2exf.register.dat.init. But I am not sure what the ³init² is for or what it means. The terminal output from running reg-feat2anat is attached. I can see now that there are errors in the output (I am slowly figuring how how to use FreeSurfer!). Any suggestions you have are greatly appreciated! Thanks! Sherryse Date: Tue, 27 May 2014 12:21:30 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Registration of Functional Data to the Inflated Brain Hi Sherryse you only need to register the anatomicals to the funtionals once, then sample the functional data onto the surface using mri_vol2surf. This will create a surface overlay that can be visualized on any of the surfaces for that subject (e.g. lh.white, lh.pial, lh.inflated) cheers Bruce On Tue, 27 May 2014, Sherryse Corrow wrote: >Hi FreeSurfer Team,? >Please help out a FreeSurfer newbie! ?We are having an issue with mapping >our functional data onto the inflated brain. ?When we finish the mapping, >it >seems that much of the data is showing up in white-matter space, and >therefore, cannot be seen on the external surface of the brain. We later >discovered that we were likely using the wrong registration matrix. >However, >it doesn?t seem like the one we are supposed to use is being produced >during >recon-all. ?I am new to FreeSurfer and would greatly appreciate some >assistance! ? >To provide you with more detail.? >Problem: When we run the command line below, and then open the folder >experiment.feat/reg/freesurfer, there is no >anat2exf.register.dat file.??However, there is a file called: >anat2exf.register.dat.init. >Command Line: Reg-feat2anat -feat OurFeatDirectory.feat -subject P143 >Terminal Output: There is no terminal output.??No error of any kind. >Log File: Attached. >Thanks, >Sherryse >P.S. We submitted this issue previously but were not getting a response, >so >we tried again in case our thread wasn?t working properly.? >--? >Sherryse Corrow, Ph.D. / Postdoctoral Fellow >Human Vision and Eye Movement Lab >Department of Ophthalmology & Visual Sciences >UBC/VGH Eye Care Centre >360A-2550 Willow Street >Vancouver, BC, V5Z 3N9 >Tel: 604-875-4111 ext 67672 >Cell: 604-315-6717 >sherryse.corrow(a)eyecarecentre.org > >

2 1

Longitudinal Pipeline for Subjects with only 1 assessment
by Elijah Mak 30 May '14

30 May '14

Dear FS Experts, I am running a longitudinal analyses, and I'd like to use the Linear Mixed Effect framework as even subjects with only 1 time-point can be included into the model. How do I create the base for a subject with only 1 TP? Is this the correct approach? recon-all -base *[basename]* -tp [*subjectid] *-all ? I tried that, but I was met with the following error: ... mghRead(*subjectid*/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -436, rheno = -396 orig.nofix lhholes = 219, rhholes = 199 Loading mri/aseg.mgz Getting Brain Volume Statistics Darwin pspc112 12.5.0 Darwin Kernel Version 12.5.0: Sun Sep 29 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64 x86_64 recon-all -s [*subjectid]* exited with ERRORS at Fri May 30 04:43:50 BST 2014 Thank you all. Best Regards, Elijah -- Elijah Mak, B.A. Doctoral Candidate *|* Psychiatry University of Cambridge *| *Department of Psychiatry Trinity College, Cambridge, CB2 1TQ

2 1

Extract peak voxel (vertex) coordinates from surfaces
by Milde, Christopher 30 May '14

30 May '14

Dear Freesurfers, I would be interested in figuring out the peak vertex of clusters based on coregistered functional FEAT data with the reconstructed anatomical surfaces. The FEAT preprocessing was run without smoothing and smoothing was applied after the feat2surf Does anyone know how to obtain the peak coordinate (preferentially on smoothwm surface) ? I need exact vertex indices for running mris_pmake Kindly regards, Christopher

1 0

Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing
by Knut J Bjuland 30 May '14

30 May '14

Hi Due to aberrantly high for a few of the subjects, I ran recon-all -autorecon2-wm -randomness -autorecon3 –hemi ?h before, calculating the localGI index. However, I intended to use these data in a longitudinal stream. These subject that were reprocessed using recon-all -autorecon2-wm -randomness -autorecon3 , and should I rerun the longitudinal stream for these subjects before doing I use recon-all –long id base_id –localGI? What are the optimal smoothing when using the linear mixed models? Best regards Knut J Bjuland

2 3

FDR correction in Matlab
by Nandita Vijayakumar 29 May '14

29 May '14

Hi FS team, I was wondering if you could help me with FDR correction for linear mixed models within Matlab. I have run FDR2 correction using the following command: *dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); *However, dvtx was empty, so I would like to try lme_mass_FDR instead. Could you please help me with the command for FDR correction, as well as how to visualise the corrected significance map in FreeSurfer? Thank you, Nandi Vijayakumar MPsych (Clinical Neuropsychology) / PhD Candidate ADAPT | Adolescent Development and Psychopathology Team Melbourne School of Psychological Sciences University of Melbourne Email: *n.vijayakumar(a)student.unimelb.edu.au <n.vijayakumar(a)student.unimelb.edu.au>*

2 1

Surface Label to Nifti File
by MCLAREN, Donald 29 May '14

29 May '14

I'm trying to convert a surface label to a nifti file to use with functional surface data that is already in nifti format. The ultimate goal is to be able to use the converted surface label as a seed in gPPI analyses that is run in MATLAB. I've been able to use volume based seeds for the MNI305 subcortical stream and carryout the analysis on the surfaces already. I'm just wanting to use cortical surface seeds now. I think I've got the code correct, but wanted to double check that I am using the correct command: mri_label2label -srclabel mylabel --s fsaverage --trglabel tmplabel --outmask test.nii --regmethod surface --hemi lh In this case, does the target surface matter? It seems to default to white? Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

1 0

Tracula with multi-shell data
by Chris Watson 29 May '14

29 May '14

Dear Anastasia et al. I have data DTI that has multiple b-values. I worked around this by skipping '-tensor', and sym linking 'mean_fsumsamples.nii.gz' to 'dtifit_FA.nii.gz'. However, at the end of 'trac-path', there is an error thrown. Specifically when 'dmri_pathstats' is called, because it is looking for dtifit_{L1, L2, L3, V1, ...}. Do you have a workaround for this? Should I just run dtifit on the data? Also, merged_avg33_mni_bbr.nii.gz wasn't created, but I was able to create it (I copied the code from around line 400 of 'trac-paths'). When I view it with freeview, though, there is a light blue/greenish background. I assume those voxels are supposed to be 0's, but for some reason aren't here? Thanks, Chris

1 0

URGENT: Error in analyse
by Saloni Sharma 29 May '14

29 May '14

Dear Freesurfers, So I have followed all the instructions given on your website in order to use qdec. When i analyse the images only using a file group.levels that defines the two groups I'm comparing the analysis runs fine and gives me results, but when I add gender, for instance, as a discrete factor, it loads the data successfully but when I click analyse it shows the following error: Error in Analyze: Couldn't open file /tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/lh.thickness.fwhm10.fsaverage.mgh Please guide me as to what is going wrong and what I can do to fix it. I would appreciate a quick response as my thesis submission is due in two weeks and I cannot proceed until this problem is sorted. Thanks and regards, Saloni

6 13

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