Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

RE: [Freesurfer]
by Bagnato, Francesca (NIH/NINDS) [F] 16 Dec '05

16 Dec '05

Hi there: I am trying to lunch the stage1 on a set of IR-SPGRs and I keep having an error saying: Mri_fill: could not find valid seed for the cc. I am not sure how to interpret this. Thanks, -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373

2 1

saving open lines
by Dahlia Sharon 15 Dec '05

15 Dec '05

Hi, Is there a way to save an open line drawn on a subject's surface to load on the surface in a future tksurfer use? Thanks, Dahlia.

1 0

mris_glm tool
by Alexandre DaSilva 15 Dec '05

15 Dec '05

Hello everybody, I am using the mris_glm tool to the test for the effect of a var2 on thickness (see file and command bellow), and I would like to understand the outcome. First, what is the difference in interpretation of the resulting p-value, and the p-value you'd get from a Pearson's or Spearman's correlation test between thickness and frequency. Second, what does the sign of the resulting significance map mean (red vs blue)? Third, is there a way to account for the effect of a regressor of no interest, for example age? Thanks, Alex X.fsgdf GroupDescriptorFile 1 Class MyTitle Variables Dur Freq Age Input subjid1 Class1 10 15 1000 Input subjid2 Class2 20 20 2000 Input subjid3 Class2 20 20 2000 mris_glm –fsgd X.fsdgf --surfmeas thickness --trgsubj brain –nsmooth 250 –gcv 0010 –sight ./thicknessCORfreq-sight-rh.w paint –hemi rh

2 1

Solaris distribution
by Jameson Watkins 15 Dec '05

15 Dec '05

Hi, we're exploring using Freesurfer and wondering if there are plans to release a Solaris distribution. I see in the list archives there was discussion from Nov. 2004 that one was available but was limited in testing. I didn't find any reference to the Solaris distribution on the Freesurfer wiki site. Thanks. Jameson Watkins Director, Internet Development University of Kansas Medical Center http://www.kumc.edu/ 913-588-7387

2 1

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 -----

1 0

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

1 0

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.

4 4

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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Freesurfer