Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

Loading thickness data in python
by Sebastian Urchs 15 Jul '13

15 Jul '13

Hi, I am trying to figure out how to load thickness data into python such that I would be able to identify the thickness at a given mesh node and also identify surrounding nodes. I searched the mailinglist and found this http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07307.html but this unfortunately did not solve my question as I was unable to find a downloadable version of pymgh. Is there some python package that you could point me to and that allows me to load thickness data and do analysis in python? Thanks in advance! Sebastian

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Non-grey matter classified as grey matter
by ye tian 15 Jul '13

15 Jul '13

Dear Freesurfers, Do you think I should delete the extra dura-like structure in the attached case? Thank you very much! Sincerely, Ye

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Delete dura in brainmask.mgz and add voxels to wm.mgz
by ye tian 15 Jul '13

15 Jul '13

Dear Freesurfers, It turns out that I should edit both brainmask.mgz and wm.mgz for a subject. In this case, may I recompile with recon-all -autorecon2 -autorecon3 to save time? Thank you very much! Sincerely, Ye

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Freesufer registration problem
by lijia 15 Jul '13

15 Jul '13

Hi doug, I apologize for the delay. I've verified that the registration to the native anatomical space is correct. I read the processing log. It seems that the registration of volume is implemented from functional to anatomical, then anatomical to mni305 spaces. So I also test the registration of native anatomical space to the MNI305 space via Talairach transformation matrix generated by 'recon-all' is correct. I don't know why the registration of functional space to mni305 is wrong. Thanks Best Regards! Rebecca

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fsfast read_surf bug
by Joseph Dien 14 Jul '13

14 Jul '13

I've been trying to use the read_surf.m Matlab function included in the Matlab folder of 5.3.0 on a Mac under Matlab 2013a. >> [vertex_coords, faces] = read_surf('fmcpr.sm5.fsaverage.lh.nii'); Undefined function or variable "vertex_coords". Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; It looks as though the reason is that the "magic number" evaluates as: 6029568 which does not match either of the numbers it is looking for (which denote triangle and quad files). Does that mean that current surface files have a different format and this function needs to be updated accordingly? Anyway, is there some way I can load surface files into Matlab? I looked through the fsfast Matlab functions but it wasn't clear to me if one of them would do. The best candidate seemed to be fast_read_curv.m but it yielded too many numbers so I'm thinking a curvature file is something different. Thanks! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com//

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Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
by Jeff Eriksen 14 Jul '13

14 Jul '13

Doug, Freeview looks like the best way to get what I want. Still trying to figure out how to mark a point in the 3D viewing window, but at least when I mark them in the 2D windows I get all the coordinates I need. Thanks, -Jeff Message: 5 Date: Fri, 04 Jan 2013 13:36:59 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] FW: FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <50E7214B.6010407(a)nmr.mgh.harvard.edu<mailto:50E7214B.6010407@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed tksurfer may be putting all 0s in the RAS field because the head surface does not match the cortical surface (tksurfer is very inflexible in this way). One way around it is to find the vertex number, then find the RAS for that vertex by converting the surface to ascii. freeview might do a better job than tksurfer. doug On 01/03/2013 10:38 PM, Jeff Eriksen wrote: FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu%3E>> Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu> <mailto:eriksenj@ohsu.edu><mailto:eriksenj@ohsu.edu%3E>> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Can you cc the list so others can answer? Freeview can rotate....

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Measure outer surface area
by Irene Altarelli 14 Jul '13

14 Jul '13

Dear all, how can I measure the surface area of the outer surface computed to calculate lgi? I've tried mris_anatomical_stats subject lh pial-outer-smoothed but that doesn't work (since it doesn't match lh.pial). Any idea would be greatly appreciated. Thank you, Irene

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Re: [Freesurfer] rotated surfs
by Colin Reveley 13 Jul '13

13 Jul '13

actually it would seem (tentatively) a solved problem at this point sorry: wb_command -surface-apply-affine SOURCE.surf.gii FSL_SRC2TARG.mat TARGET.surf.gii -flirt SOURCE_VOL.nii.gz TARGET_VOL.nii.gz where surfaces are made originally in FS from SOURCE_VOL cheers, Colin On 13 July 2013 23:41, Colin Reveley <cmr25(a)sussex.ac.uk> wrote: > I (still) need to rotate some surfaces so that they enclose MR data that > is sliced the same angle as data from the same brain was sliced on a > microtome. > > Transforming surfaces once made is a bit tricky. > > Is there any reliance on the midline being on the y axis past the point of > mri_fill/pretess? > > (for: mris_fix_topology -mgz subject rh -orig orig -inflated inflated > -sphere qsphere -ga -noaseg -noaparc > > mris_make_surfaces -noaseg -noaparc) > > what I'd do is take the results from an ACPC aligned set, and apply a > transform to T1,wm,filled,filled-pretess and so on. > > then run the surface making script as normal. > > the brain's midline is pretty rotated in Z the way I want it. It takes > ages to run this so I'm wondering if there is any issue before I go ahead > and try it. > > best, > > Colin > >

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rotated surfs
by Colin Reveley 13 Jul '13

13 Jul '13

I (still) need to rotate some surfaces so that they enclose MR data that is sliced the same angle as data from the same brain was sliced on a microtome. Transforming surfaces once made is a bit tricky. Is there any reliance on the midline being on the y axis past the point of mri_fill/pretess? (for: mris_fix_topology -mgz subject rh -orig orig -inflated inflated -sphere qsphere -ga -noaseg -noaparc mris_make_surfaces -noaseg -noaparc) what I'd do is take the results from an ACPC aligned set, and apply a transform to T1,wm,filled,filled-pretess and so on. then run the surface making script as normal. the brain's midline is pretty rotated in Z the way I want it. It takes ages to run this so I'm wondering if there is any issue before I go ahead and try it. best, Colin

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Pial surface missing grey matter
by ye tian 13 Jul '13

13 Jul '13

Dear Freesurfers, I would like the pial surface in the circled region in the attachment to extend a little bit more to follow closely the boundary of the grey matter (green line in the second attachment). Is there a way to do so? Thank you very much! Sincerely, Ye

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