Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

segmentation region export
by vin 10 Nov '08

10 Nov '08

hi, I am trying to export segmented regions as NIFTI, and it works for the regions like Thalamus whole. But when freesurfer finished autorecon, than it showed lot of sub regions for example : Thalamic sub regions and also CC_Posterior, CC_Mid_Posterior, CC_central (CC= Corpus Callosum) and...Mid anterior and Anterior. How I can get these sub regions. In which files they are stored, and How I can extract them as NIFTI format. any suggestion would be great !! thank you very much , vin

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analysis
by b9403208 10 Nov '08

10 Nov '08

Hi, I have some problem about analysis with QDEC. 1) How can I get the information about analysis, like T value, cluster threshold, and so on? 2) What threshold setting (uncorrected or corrected) is Freesurfer used? Thanks a lot! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

2 1

analysis
by b9403208 10 Nov '08

10 Nov '08

Hi, I have some problem about analysis. 1) How can I get the information about analysis, like T value? 2) What threshold setting (uncorrected or corrected) is Freesurfer used? Thanks a lot! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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scan of 2.6 mm thicknes with overlap of 50-70 %
by asaf achiron 09 Nov '08

09 Nov '08

Dear Group we have acquired some MRI scan with an axial 3dfspgr with 2.6 mm thickness and an overlap of 50-70 %. thus the r reconstructed thickness is 1.3 mm. is the reconstructed scan suitable for analyses in freesurfer? can we use the scan with the 2.6 thickness and overlap also? thank you Asaf

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inflated surface
by Nurunisa Neyzi 08 Nov '08

08 Nov '08

Hello, I just wanted to ask what you think makes this inflated surface look somewhat wrong in the occipital lobe? (Or is it OK?) I attached the figure. Thanks a lot ! -Nurunisa-

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fslcalc.fsl
by Akram Bakkour 07 Nov '08

07 Nov '08

Hello, Thanks for adapting fslcal.fsl to work on surfaces Doug. This is very helpful. It was working for me until today. I'm working on thigpen. setenv SUBJECTS_DIR /space/brich_004/users/akram/HRDEV_processing mri_surf2surf --srcsubject 03222007_4TT_clindem47 --sval \ 03222007_4TT_clindem47/surf/rh.thickness --trgsubject HRDEV197_1mm \ --tval 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.mgh --hemi rh mri_surf2surf --s HRDEV197_1mm --sval \ 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.mgh --tval \ 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.fwhm15.mgh --fwhm 15 \ --hemi r mri_surf2surf --s HRDEV197_1mm --sval HRDEV197_1mm/surf/rh.thickness --tval HRDEV197_1mm/surf/rh.thickness.fwhm15.mgh --fwhm 15 --hemi rh fscalc.fsl HRDEV197_1mm/surf/rh.thickness.fwhm15.mgh -sub \ 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.fwhm15.mgh \ HRDEV197_1mm/surf/tp1_min_tp2.thickness.mgh --surf HRDEV197_1mm rh I get the following error: ** ERROR: nifti_convert_nhdr2nim: bad dim[1] ** ERROR (nifti_image_read): cannot create nifti image from header 'HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1.nii.gz' ** ERROR: nifti_image_open(HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1): bad header info Error: failed to open file HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1 Cannot open volume HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1 for reading! It's weird, because I did exactly the same thing with a different subject tp1 and tp2 two days ago and it worked great! Thanks for the help! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

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availability of freesurfer version 4.0.1
by Burmicz, Ryzarda 07 Nov '08

07 Nov '08

Hello, I have some data which was recon-all'd using 4.0.1 and I have since lost this version of the software. Would it be possible to get hold of 4.0.1 in order to rerun some corrected brains? Thanks, Rysia

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DEALING WITH INTENSITY NORMALIZATION PROBLEMS
by david felps 07 Nov '08

07 Nov '08

Hi Bruce, hi Susan, i was trying to solve the intensity normalization problem using the methods proposed in "How-to Guide for Cortical Inflation using FreeSurfer by Susan Mosher Updated May 25, 2005 " . I was able to add the necessary control points which created, as mentioned in the guide, the "control.dat" file in the right directory. Now i can not erase or remove the selected control points from my wm.mgz in the tkmedit and the following command: % mri_normalize –f $SUBJECT/tmp/control.dat is not working. i ll be thankfull for any hint. _________________________________________________________________ Messenger Online Treff: Spontan chatten, über Hobbies reden, sofort Spass haben? Jetzt klicken! http://redirect.gimas.net/?n=M0811xMOTDE

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mri_binarize download
by Dominic Dwyer 06 Nov '08

06 Nov '08

Hi all, Where I can find a copy of the mri_binarize file? It doesn't seem to be included with 4.0.5, and based on a post from 2007 I looked in ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/ to no avail. I've also checked the site. Since this is my first post I'd also like to send my thanks to the developers for a great program and ongoing support! Dom ------------------------------------------ Dominic Dwyer, PhD candidate Melbourne Neuropsychiatry Centre The University of Melbourne

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Single subj v. group analysis in qdec with covariates-- impossible?
by Laluz, Victor 06 Nov '08

06 Nov '08

Hello, When trying to do a single-subject vs. group qdec study with covariates, I always get errors, such as: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. This error seems quite sensible to me, and I understand why the GLM is unable to deal with it, but is there any way I can "force" it to use the covariates on the single subject, such as is possible in SPM5? Doing uncontrolled analyses are fine (I wouldn't trust the controlled data very much anyway) but it would, in theory anyway, eliminate the hassle of coming up with a well-matched control group for these kinds of analyses. Any help would be appreciated; thanks as always. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center

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Freesurfer