Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30056 discussions

Estimating Quality of Freesurfer Parcellation
by hwier＠uchicago.edu 15 Dec '05

15 Dec '05

Hi, I was wondering if there is any way to determine how good of a parcellation freesurfer is doing on a given brain? Is there something output into the stats directory, or while mris_ca_label is running which I could use to determine this? Thanks, Helen Wier

2 1

(fwd) [Freesurfer] mask_label in script
by Henrik Ormåsen 15 Dec '05

15 Dec '05

I try again: Regards, Henrik ----- Forwarded message from Henrik Ormåsen <henrikor(a)ulrik.uio.no> ----- We use mask_label in the prompt to load this file. How can we load it from a tksurfer tcl script? - Henrik _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ----- End forwarded message -----

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fsl & freesurfer
by cormorent 14 Dec '05

14 Dec '05

Dear all, I am new user of those two softwares, FSL & Freesurfer. I am trying to DISPLAY FEAT STATISTICS ON SURFACE (http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html) But in the first step, I met a big problem (attached files 1 and 2): the T1 image converted from ${SUBJECTS_DIR}/subjID/mri/T1 was different with ${FEAT_DIR}/example_func image in xyz position and orientation. Then I ran "flirt -in example_func.hdr -ref struc_fs_T1.hdr -out func2struc.hdr -omat func2struc.mat -bins 256 -cost corratio -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -dof 12 -interp trilinear", but I got a failed cogistered results (attached files 3). Did I make some misunderstanding? By the Way, the freesurfer website told me some command lines that transform fsl to freesurfer, but I couldn't find them, such as "reg-feat", "feat2surf". Any suggestions? hope your helps! best wish! cormorent

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autorecon2-wm
by Sasha Wolosin 14 Dec '05

14 Dec '05

Dear all, When we run autorecon2-wm it doesn't seem to be reading the editing done in the Edit WM With ASeg step. Looking at wm.mgz, none of the filling that we see after autorecon2 is present after autorecon2-wm. What's going wrong? Thanks, Marin Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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mris_glm and beta file formats
by Marie Schaer 13 Dec '05

13 Dec '05

Hello everybody, I have some trouble reading bfloat format, as given by the --beta output of mris_glm. I tried load overlay in tksurfer but a register.dat file seems to be necessary, can someone help me about how I can visualize the regression coefficient on the inflate surface? Thank you very much, Marie Schaer

2 1

Dev vs Beta versions
by Katherine Perdue 13 Dec '05

13 Dec '05

Hello- What are the differences between the Freesurfer surfaces created with the development version and the surfaces created with the standard version? I am trying to use the new annotation files from the dev version and map them into SUMA to form ROIs. I think there are some problems with the alignment though- when I looking at the annotation files made with the development version on an average brain made with the standard version, the annotation files were shifted (which leads me to believe there are differences in the surface files that the SUMA command I was using was not taking into account). It would be really great if I could use the dev annotation files, but it has taken a lot of work to get the functional and structural data in line with each other, and I'd rather not throw that away. Is there a way to to this? Thanks for any suggestions, Katherine

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talairach
by Sasha Wolosin 12 Dec '05

12 Dec '05

Dear all, We are having some difficulties getting accurate talairach.xfm files. After running recon-all, the final objective function value for most of our brains was above .2 We then regenerated the transform using brain.mgz. This helped, but our final objective function values are still above .1, some are above 1.5 There don't seem to be any bright neck regions left in the brain volumes, so we don't think bright neck regions are causing the problem. Manual inspection shows that the fuzzy talairach brain is slightly smaller than the subjects' brains, but seems to be in the correct orientation. Is there anything else we should try before manually adjusting the xform? Is there any objective way to evaluate a manually adjusted xform? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

1 0

Normalization of mris_anatomical_stats
by Glenn Lawyer 10 Dec '05

10 Dec '05

Hi, We want to compare grey matter volumes from specific labels. Is the output of mris_anatomical_stats normalized in any way? It doesn't appear to be. Thanks! +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

3 4

fieldsign broken with new surfaces
by Don Hagler 10 Dec '05

10 Dec '05

I tried to run fieldsign calculation using surfaces created with the new recon-all but the results look wrong, with some vertices that have a salt-and-peppery look to them. The code I'm using is ripped out of an older version of tksurfer and works fine on old surfaces. It seems that there is a lack of correspondence between vertex numbers in the flattened surface and orig or something. Another odd thing is that the ripflag is set for all vertices in the flat patch, but that is probably unrelated. We noticed that the file size of the different surfaces (e.g. orig, smoothwm, inflated) varies. In the older version, the surfaces all had an identical size. This suggests that the different surfaces have different number of vertices now, or you've changed the file format somewhat. Can you tell me what's going on there? My current work-around is to use recon-all up to the point of fill, taking advantage of the new aseg, but then I'm using the old programs to generate surfaces compatible with my fieldsign code.

2 1

talairach
by Sasha Wolosin 09 Dec '05

09 Dec '05

Dear all, I am trying to improve talairach registration and I noticed the following suggestion in the freesurfer wiki: "If you suspect that the bad transform is the result of a bright neck region, edit the volume to erase the neck and run mritotal on the edited volume. This can be accomplished through simple volume editing: set all the regions to zero where y is greater than a certain value (around 170). This generally works better than using the brain volume. Check your transform using tkmedit" I would like to try this, but I don't know which command to use. Could someone please fill me in? Also, after fixing the talairach registration, is it necessary to re-run -autorecon2? Or is it sufficient to over-write the header files and talairach.xfm? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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