Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

wm.mgz edits
by marco mcsweeney 15 Jun '16

15 Jun '16

Dear all, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip errors, intensity normalization errors and pial errors, but I am a bit stuck when it comes to fixing topological defects. My question relates to what should or should not be included in the wm.mgz. Apart from the optic chiasm, which I have removed, is it normal to have, what appear to be, multiple specs included in the wm.mgz which when the aseg is loaded turn out to be parts of the amygdala and hippocampus. When I view the smoothwm.nofix these appear as jagged shard like shapes protruding out from the surface. In one publication I saw recently it was suggested that these should be removed but should this be done if they are parts of the amygdala and hippocampus. I am worried about this as these are the 2 main subcortical areas I will be focusing on. Also, is it normal for the wm.mgz to include parts of the cerebral cortex (labelled as such in the aseg). Also, most of the scans I am working with have numerous holes and handles and this is taking a very long time to fix. I have tried to run the automatic topology fixer again. This has helped a bit but the scans still require a lot of edits. Could this be down to the quality of the scans or could it be that I have edited too much - control points for example. I have followed the advice given and have tried not to make too many edits, but having said that it has taken me a very long time. Any advice in relation to any of these questions would be very very very much appreciated. Best wishes Marco

1 0

selxavg3-sess error
by Francesca Strappini 15 Jun '16

15 Jun '16

Hi Freesurfer experts, I'm re-posting this message because I think it got lost. I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2 -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous and I got this error message: Found 122573/130829 (93.7) voxels in mask Creating Design Matrix ... creation time = 0.019 sec DoMCFit = 1 ntptot = 875, nX = 80, DOF = 795 Saving X matrix to /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); Thanks! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

3 5

Fwd: Getting the pial surface to cover the entire medial temporal lobe structures
by David Groppe 15 Jun '16

15 Jun '16

Dear Free Surfers, I am using FreeSurfer's pial surface to map ECoG electrodes onto the FreeSurfer average brain for group analyses via these two methods: Dykstra, A. R., Chan, A. M., Quinn, B. T., Zepeda, R., Keller, C. J., Cormier, J., et al. (2011). Individualized localization and cortical surface-based registration of intracranial electrodes. *NeuroImage*, 1–42. http://doi.org/10.1016/j.neuroimage.2011.11.046 Yang, A. I., Wang, X., Doyle, W. K., Halgren, E., Carlson, C., Belcher, T. L., et al. (2012). Localization of dense intracranial electrode arrays using magnetic resonance imaging. *NeuroImage*, *63*(1), 157–165. http://doi.org/10.1016/j.neuroimage.2012.06.039 The methods work great. However, we've noticed that the pial surface typically underestimates the extent of the amygdala and hippocampus (see attached example images from FreeSurfer's demo Bert subject) where we often have electrodes. I understand that FreeSurfer does this by design, since the amygdala and hippocampus are not neocortex. However, is there a way to force the pial surface to include those medial temporal lobe structures for our purposes? I tried "mris_make_surfaces -fix_mtl" but that did the opposite of what we need (i.e., it withdrew the pial surface so that it included none of the amygdala or hippocampus). much appreciated, -David P.S. Thanks for creating and maintaining such an amazing suite of freeware.

3 2

Convert ascii to .mgh
by Robby De Pauw 15 Jun '16

15 Jun '16

Dear Doug Thank you for your answer. I however encounter an error: >> F.vol = fast_mat2vol(lfdr,F.volsize) ERROR: szvol inconsistent with mat2d I have attached the final output (.mgh) and the .asc file. (As the files are too large, I added them here: https://we.tl/MKhhmeT5Zn) Thank you Robby From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve <greve(a)nmr.mgh.harvard.edu> Reply-To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday 15 June 2016 at 17:43 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Convert ascii to .mgh I would do it in matlab, eg, F = MRIread('F.mgh'); % This is to get the proper header information lfdr = load('lfdr.asc'); F.vol = fast_mat2vol(lfdr,F.volsize); MRIwrite(F,'lfdr.mgh'); On 6/15/16 4:45 AM, Robby De Pauw wrote: Dear FreeSurfer users, To address the problem of multiple comparison, I wanted to apply the localfdr-method. For this purpose, I need the F-statistic (which I can extract from the F.mgh scalar overlay I presume?). I converted this to an ascii-file, which I was able to load into R, using the following chink of code: mris_convert -c /Users/robbydepauw/Desktop/FreeSurfer/GLM/lh.Group.volume.glmdir/Groupeffect/F.mgh $SUBJECTS_DIR/fsaverage/surf/lh.white F.asc After performing an local fdr analysis in R, I want to create a scalar overlay “lfdr.mgh”, but I fail at converting the asci file into an “.mgh”-overlay file. Any idea how I could approach this conversion (from asci back to .mgh)? Many thanks, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email Robby.DePauw(a)Ugent.be<mailto:Robby.DePauw@ugent.be> Ghent University | Rehabilitation Sciences and Physiotherapy Campus Heymans 3B3 (022) De Pintelaan 185 BE-9000 Ghent Route to my office<https://soleway.ugent.be/routes/1090> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] SIENAX
by Hassan bakhshi 15 Jun '16

15 Jun '16

We have some cases which we want to process , I searched about SIENAX and as you are more expert in this area, I wanted to know Freesurfer preferences on SIENAX!!!! ??? The other thing is process time in these two software. Kind Regards,

2 1

Memory
by Fu, Jason (NIH/NINDS) [F] 15 Jun '16

15 Jun '16

Is there any way to check how many autorecon processes I can run at the same time? I am using a linux with 16gb ram.

1 0

-hippocampal-subfields-T1T2
by Daniele Orlandi 15 Jun '16

15 Jun '16

Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): can't open file >No such file or directory >ERROR: Reading transform from file /media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta Do you have any suggestion? thank you all for your collaboration Daniele _______________________________________________________________________________ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorlandi(a)fatebenefratelli.it; daniele.orlandi.psy(a)gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php)

3 2

Convert ascii to .mgh
by Robby De Pauw 15 Jun '16

15 Jun '16

Dear FreeSurfer users, To address the problem of multiple comparison, I wanted to apply the localfdr-method. For this purpose, I need the F-statistic (which I can extract from the F.mgh scalar overlay I presume?). I converted this to an ascii-file, which I was able to load into R, using the following chink of code: mris_convert -c /Users/robbydepauw/Desktop/FreeSurfer/GLM/lh.Group.volume.glmdir/Groupeffect/F.mgh $SUBJECTS_DIR/fsaverage/surf/lh.white F.asc After performing an local fdr analysis in R, I want to create a scalar overlay “lfdr.mgh”, but I fail at converting the asci file into an “.mgh”-overlay file. Any idea how I could approach this conversion (from asci back to .mgh)? Many thanks, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email Robby.DePauw(a)Ugent.be<mailto:Robby.DePauw@ugent.be> Ghent University | Rehabilitation Sciences and Physiotherapy Campus Heymans 3B3 (022) De Pintelaan 185 BE-9000 Ghent Route to my office<https://soleway.ugent.be/routes/1090>

2 1

Coregister the CT image and MRI image
by HARI GURAGAIN 15 Jun '16

15 Jun '16

Dear Freesurfer community, I am relatively new to this community. I was trying to register the CT image and the MRI images (MRI as a the target volume and CT as the movable volume). I used the mri_robust_register to to do the registration as below: mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit The problem is that: after register, the new image (v1to2.nii) is not exactly aligned with the original MRI image (vol2.nii). It gives a very different output. I wonder if I am missing anything here or I need to do some extra steps after the above command in order to get the correct alignment of the two images. I was hoping to get the resultant image should be well orient with the target volume image (vol2.nii image in my case). I really appreciate any help here. Hari Guragain

4 9

GLM: Define the design matrix by myself
by Hao wen 15 Jun '16

15 Jun '16

Hello, Freesurfer experts: I want to define the design matrix by myself in GLM, I know that in FS, when we deal with the categorized factors, we treat them as classes, So basically, I want to make a design matrix like this: 1) formula_EffectOnGroupWithAgeGenderCovariates = 1 + TermGroup + TermAge + TermGender and 2) formula_EffectOnGroupWithAgeGenderInterectionCovariates = 1 + TermAge + TermGender * TermGroup Here, TermGroup and TermGender are categorized factors, so I know that we can make the design matrix like 2) in FS, cuz here we define it as intersection, but my question is that if wen can define a matrix like the first one? I know in SurfStat, we can define it like 1) Hope to hear from you soon:) thank you in advance!

2 9

← Newer
1
...
10
11
12
13
14
15
16
...
22
Older →

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 June 2016