Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Tadeu Takao Almodovar Kubo has invited you to Dropbox
by Dropbox 11 May '10

11 May '10

We're excited to let you know that Tadeu Takao Almodovar Kubo has invited you to Dropbox! Tadeu Takao Almodovar Kubo has been using Dropbox to sync and share files online and across computers, and thought you might want it too. Visit http://www.dropbox.com/link/20.dR8lfOqJiy/NjE3MTczNDAyNw to get started. - The Dropbox Team ____________________________________________________ To stop receiving invites from Dropbox, please go to http://www.dropbox.com/bl/0bbe861e473f/freesurfer%40nmr.mgh.harvard.edu

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Contrast Problem
by Andrés Camarena 11 May '10

11 May '10

I am having an issue where the sig.nii file created after running mkanalysis and slxavg sets the value in a high contrast region to zero. Any idea what could be the problem. I've attached an image of the problem. -- Department of Aeronautics and Astronautics Massachusetts Institute of Technology Class of 2010

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after mri_glmfit whats next
by Samantha Clark 11 May '10

11 May '10

Hi Doug, I did the first level analysis for my DTI data per the tutorial mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir groupanadir Not sure how to proceed from here to view the regions that are statistically signifiant. Can you help? Thanks Samantha

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QDEC discrete covariate question
by Dominic Brendon Dwyer 11 May '10

11 May '10

Hi all, We're using QDEC DODS to compare the average thickness maps of patients V. controls using sex and age as covariates. The results are identical for "Does the average thickness differ between patientsVscontrols with sex and age as covariates" and "Does the average thickness differ between sex with patientsVscontrols and age as covariates". This doesn't seem to make sense (with my limited statistical knowledge) because the criterion variable has changed. Also it is not the case that the groups contain only one sex. Could anyone shed light on this? Also, we tried to check the contrasts but weren't able to find the categories for each of the columns in the vector. Where can this be found? Thanks very much in advance, Dominic Melbourne Neuropsychiatry Centre

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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

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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

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