Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Bad pial surface - continued
by Ed Gronenschild 10 May '10

10 May '10

Hi, I've mailed this once before and tried to solve a persistent problem. Reviewing the results of recon-all I noticed that the derived pial surface chopped away an unacceptable amount of gm voxels. First of all I tried to manually edit some wm voxels, however with no success. Then I tried another solution by combining the FSL-FAST wm segmentation with wm.mgz because I noticed that FSL_FAST produced better results. Although the results did improve, still the pial surface was incorrect. The last option I tried was another set of parameters for nu_correct. Because it concerns 3T scans I used --proto-iters1000 and --distance 50 (see paper of Zheng et al, NeuroImage 48, 73-83 (2009)) and previous e-mails on this subject ("nu-correct parameters", 27 April 2010). Also with these settings the pial surface chopped away too many voxels. I'm desperate, the manuals provide no options on how to fix such problems. The pial surface can be corrected by only REMOVING voxels that are included erroneously but there is no way to extent the pial surface by ADDING voxels. Ed

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Talairach failure
by Antoine Leflon 10 May '10

10 May '10

My files are dicoms and have no extension in the end of their name (IM_0465 for example) . Is it possible to change the format ? thanks , Antoine ________________________________________________________________________________ Talairach is about orientation. What is the format of your file? If it is .hdr and.img, it will fail. On 4 May 2010 11:43, Antoine Leflon <antoine1.leflon(a)etudiant.univ-lille1.fr> wrote: Hi all , I've used data from another Doctor , freesurfer told me the FOV was 330 so I put the flag -cw256 in the command recon-all but the Talairach just failed ... I got this error message . Can someone explain please ? ________________________________________________________________________________ #@# Talairach Failure Detection Tue May 4 12:31:55 IST 2010 /home/cami/freesurfer/subjects/a1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux pride 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Tue May 4 12:31:55 IST 2010 ________________________________________________________________________________ thanks , Antoine _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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tksurfer/tkmedit tcl scripting "could not open display" error
by holmes＠wjh.harvard.edu 10 May '10

10 May '10

All, I have generated a batch script that saves out images from tkmedit and tksurfer which I would like to run on a cluster of workstations across a large dataset. However, when I run the jobs remotely tkmedit/tksurfer opens displays on my local machine. As a consequence, if I do not remain logged in than the tcl script fails with the following error: GLUT: Fatal Error in tkmedit.bin: could not open display: nccwscnl04.ncf.cbs.lsdiv.harvard.edu:12.0 GLUT: Fatal Error in tksurfer.bin: could not open display: nccwscnl04.ncf.cbs.lsdiv.harvard.edu:12.0 GLUT: Fatal Error in tksurfer.bin: could not open display: nccwscnl04.ncf.cbs.lsdiv.harvard.edu:12.0 Is there a way for me to run tkmedit/tksurfer with the display suppressed while still being about to save out *.tiff files of my slices/overlays of interest? Thanks for any help you can offer, Avram Holmes

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small volume correction
by lordowen 10 May '10

10 May '10

Dear freesurfer developers: As I searched wiki, the freesurfer only provided whole-brain FDR and cluster simulation for multiple comparison correction. Is there any way to perform the smell volume correction for the regional cortical thickness in specific regions as it in SPM? Thanks for your kindly answer. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Student Laboratory of Integrated Brain Research Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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tksurfer/tkmedit display color fix in OSX 10.6?
by Fred Dick 09 May '10

09 May '10

Dear all This is a pretty minor issue (except for figure making) - but has anyone experienced and then fixed a display problem in tksurfer/tkmedit in OSX 10.6 (possibly also 10.5) where graphics seem to be drawn only with 256 colors, thereby giving images a kind of contour-plot look? (See attached image below). [Running 10.6.3, i686-apple-darwin10-gcc-4.2.1, tksurfer 1.309 (yes, older), tkmedit v 1.330] I looked around the mail archives but didn't see anyone else commenting on this, but do know someone else having the same issue, so would be happy for any suggestions. Thanks, Fred

2 1

feat registration to standard space
by YUMI MAEDA 07 May '10

07 May '10

HI, I have a question about feat registration to standard space. I used the following line . cd "$featdirectory" flirt -in example_func.nii -ref /autofs/../MNIref/MNI152_T1_1mm_brain.nii -out funcinstd_DUMMY -omat reg/example_func2standard.mat -dof 6 reg-feat2anat --feat "$featdirectory" --subject "$scructural" To check the registration, reg-feat2anat --feat "$featdirectory" --manxfm func2std When I checked the registration of functional and anatomical of the subject, it is very good. But the registration in standard space is not even close but completely wrong. Is there any requirement for the cordination of example_func.nii ? Or other issue? I appreciate any help & advice. YUMI MAEDA

2 1

Using qdec
by John Fredy 07 May '10

07 May '10

Hello All, We are using qdec for the analysis of relation between thickness, two roi: par Opercularis, par triangularis; two test: fmri broca and edinburgo. When I make a design with thickness, one roi and one test in Qdec appears one question like: Does the correlation between X and Y, accounting for Z, differ from zero? And a surface of one hemisphere is colored with hot colors for correlation and cold colors for anticorrelation for a relation between variables defined like X = aY + bZ + intercept. Is that the correct interpretation, thinking in correlation and anticorrelation? Regards

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merge cortical and subcortical labels
by Stefan Brauns 07 May '10

07 May '10

Dear Freesurfer experts, I want to create a medial temporal lobe label. Is it possible to merge subcortical and cortical labels? Do I therefore need to use the --regmethod volume flag of mri_label2label for cortical labels? Many thanks in advance, Stefan

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Talairach x MNI 152
by Tadeu Kubo 07 May '10

07 May '10

Hi, I've been using FS, in which the Talairach transform is applied as a standard space for registration. Instead of the Talairach transformation i would like to use the MNI 152 as it is done in FSL and SPM. Does anybody have some experience with this? What would be the impact on the results of the cortical or subcortical structures? I would appreciate it if somebody could help me out with this. Thanks in advance, Tadeu Kubo

2 1

fsgd file creation
by Rajagopalan, Venkateswaran 07 May '10

07 May '10

Dear All, I am new to freesurfer, i am sorry i am confused so i am posting this message. I have two groups i want to compare cortical thickness values in all the areas reported in aparc.stats file between these two groups. So i started creating my fsgd file the problem i have is with the contrast matrix for instance i have 35 regions where thickness values are reported so i have 2*(35+1)=72 contrasts so do i need to specify each of them individually what i mean iS for instance if i am comparing lh.temporalpole (let us assume this is my first variable) so my contrast is 0 0 1 -1 0 0 0 0 ........(72 numbers) and i name this contrast as group-x-tempole.mtx then my second variable is lh.cuneus then my contrast matrix is 0 0 0 0 1 -1 0 0 0 .....(72 numbers) then i name it as group-x-cuneus.mtx. Is this the way to create or is there a simple way to this. Bottomline is i want to compare the differences in cortical thickness values between two groups in all the regions reported in aparc.stats. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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