Re: [Freesurfer] fsfast read_surf bug
Hi Joe, that is an overlay for a surface, not a surface itself. It just
has a value for each vertex. A surface has geometry and neighborhood
info. Try using MRIread.m instead.
doug
On 7/14/13 3:57 PM, Joseph Dien wrote:
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: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com//
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[Freesurfer] fsfast read_surf bug
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: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com//
___
Freesurfer mailing list
Freesurfer@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.
Re: [Freesurfer] FreeSurfer: plot activation foci
Dear FreeSurfer team, Firstall, thanks a lot to your great contribution in the neuroscientific and the free software world. I would like to know if is it possible to make a plot activation foci (i.e. example by PySurfer: http://pysurfer.github.io/auto_examples/plot_foci.html) by FreeSurfer directly, and how can it be done? Sincerly, Frédéric Briend CNRS, Archives Husserl Ecole Normale Supérieure, Paris, France ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] integrating another atlas into Freesurfer
Hi Jeff, If you run recon-all on your individual subjects, it would have automatically generate the registration files (?h.sphere.reg) to fsaverage. Doug's reply about mri_surf2surf should work. You just need to apply mri_surf2surf separately for the left and right annots. Cheers, Thomas On Sun, Jul 14, 2013 at 10:27 PM, Jeff Eriksen wrote: > Bruse, > > I apologize, I thought you were answering another question that I had > submitted, which I had foremost in my mind. I will look at mri_label2label > in more detail now in the proper context. > > Thanks, > -Jeff > > On 7/13/13 11:31 AM, "Bruce Fischl" wrote: > > >Hi Jeff > >mri_label2label should do what you want > >Cheers > >Bruce > > > >On Jul 12, 2013, at 6:45 PM, Jeff Eriksen wrote: > > > >> I have the Yeo resting-state fMRI atlases which I downloaded from > >> > >> http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011 > >> > >> They consist of 3 versions, fsaverage being of interest here. The > >> fsaverage folder provided includes the typical FS folders corresponding > >>a > >> recon-all for the average brain for this atlas. I wish to use this high > >> resolution atlas to parcellate my individual subjects. I am unclear how > >>to > >> go about this. I have perused wiki pages on > >> > >> Annotation files > >> FS labels > >> Automatic surface labeling process > >> Surface registration process > >> > >> but still do not find a clear path to my goal. Specifically I would like > >> to end up with a matching set of surface and annot files, as high of > >> resolution as possible, for each of my subjects. Using some specific > >> numbers, the Yeo atlas has around 300,000 vertices when combining the > >> lh.pial and rh.pial surfaces. The matching annot files I believe are > >> l&rh.Yeo2011_17Networks_N1000.annot, which together should also have > >> 300,000 vertices. I suppose what I need to do is align each of my > >>subjects > >> to this atlas and project the atlas onto each subject to get a new > >>surface > >> and annot file for that subject, which will have some unique number of > >> vertices for each subject. > >> > >> Please point me to the right set of documentation that will tell me how > >>to > >> do this. Thanks, > >> > >> -Jeff > >> > >> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@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. > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Measure outer surface area
mris_info should give you surface area On Jul 14, 2013, at 7:37 AM, Irene Altarelli wrote: > 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 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] displaying labels from old session onto new session
Dear Doug & Bruce, It's indeed a confusing situation. What it boils down to is: - I scanned the polar angle session and the eccentricity session on different days - I had defined V1-3 already based on the polar angle session before scanning eccentricity - All data from the polar angle session were lost, apart from the V1-3 labels I made and the anatomical (not inflated) - Since I now didn't have an inflated brain anymore, I inflated the anatomical from the eccentricity - When I tried to overlay the labels onto this newly inflated brain, the labels were not correctly displayed I just tried again by inflating the anatomical from the polar angle session (instead of eccentricity), and when I use tksurfer P2_BK lh inflated -reassign the labels are displayed correctly, so that's great news! However, when I display my eccentricity data, with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are wrong again. Adding -reassign doesn't work in this command (flag not recognised). So at least I could open two terminals, one to display the inflated brain with correct labels, and one to display the eccentricity data. This is of course not ideal if I want to draw labels on the eccentricity screen using the labels displayed in the other screen as a boundary. So if anyone has an idea how to get the labels to be displayed correctly with the tksurfer-sess command please let me know. In any case, thank you all for your help so far! Best, Bianca On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve wrote: > Hi Bianca, I'm still unclear what it is you have done. > > You only need to run freesurfer on one of the anatomicals, it does not > matter which one. > > You should not do anything to the fMRI runs (eg, align with SPM). You > should put your eccen and polar data into a single bold folder under > your session folder. > > Then run preproc-sess. > > I'm not sure how this overlaps with what you have done > > doug > > > On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > > Well the situation is as follows: > > > > I had a polar angle session, of which I only have the labels and the > > anatomical (not inflated) left due to a computer crash. In a different > > session, I scanned both my main experiment and the eccentricity runs. > > Since the eccentricity was in the same session as the main experiment, > > I included those runs in my preprocessing batch in SPM, that is I > > realigned them and coregistered the data to the anatomical of the > > polar angle session. I then inflated the anatomical of this newer > > session (the one with eccentricity) and did my analyses of the > > eccentricity data without using preproc-sess. Apologies if I wasn't > clear. > > > > I thought it should therefore be no problem to overlay the polar angle > > labels onto the newly inflated anatomical, since this one was > > coregistered to the one from the polar angle session. However the > > labels don't look correct. Should I have inflated the 'old' anatomical > > instead? Or would I then nevertheless have needed some kind of > > transformation? > > > > I tried mri_label2label, but when I use a command like this: > > > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK --scrlabel > > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume > > > > then it requires access to the anatomical in mri/orig from the > > srcsubject (the same subject, old session), which I don't have. Well I > > do have the .nii anatomical, but it can't read that header either, it > > probably needs the .mgz one which I don't have. When I try the command > > like this: > > > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel > > lh_V1_v_new.label --regmethod volume > > > > it does create a new label, which however looks exactly the same as > > the previous one. When I change --regmethod to surface, it gives this > > error: > > ERROR: there is a vertex in the label that cannot be matched to the > > surface. This usually occurs when the label and surface are from > > different subjects or hemispheres or the surface has been changed > > since the label was created. > > > > I'm not sure about using bbregister for the labels, what would be the > > movable volume? And do I then use the register.dat file to load the > > labels with? Thanks again for your patience and help. > > > > Best, > > Bianca > > > > > > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > Hi Bianca, I'm a little confused. What do you mean you registered > with > > SPM beforehand? If you're using FSFAST, then the registration is > > done as > > part of preproc-sess. The results for both sessions are on the > > surface, > > so there is no need to do anything to a label created from one > session > > to show it on another session. > > > > doug > > > > > > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > > Hi Bruce, > > > > > > Tha
[Freesurfer] motion dependent resolution: bbr vs flt
Dear freesurfer experts and users, we visualize white matter tracts of anorexia nervosa patients which are characterized by more movements in mri studies. We have the impression that we get worser TRACULA outputs by using bbregister than flt. Could it be possible that bbregister needs a higher resolution than flt? So summarizing it is more sensitive for motion? kind regards Benjamin ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Measure outer surface area
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 ___ Freesurfer mailing list Freesurfer@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.
