Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Partial voluming - mri_segstats --pv
by Wu, Paula (NIH/NIMH) [F] 27 Aug '10

27 Aug '10

Hi, I'd like to learn more about how the mri_segstats -pv calculation is done. Could someone send me the source code for this algorithm? Thanks! Paula Wu Summer Intramural Research Training Assistant Laboratory of Brain and Cognition, Section on Functional Imaging Methods, NIMH/NIH/DHHS Building 10, Room 1D80 10 Center Dr MSC 1148 Bethesda MD 20892-1148 wup2(a)mail.nih.gov

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Re: [Freesurfer] MRI Files Doubts
by Nick Schmansky 26 Aug '10

26 Aug '10

the reason, as i understand it, is that the analyze format does not store orientation information. this means there is no way to tell left from right, which can lead to problems in both atlas alignment, and during multimodal (fmri) registration. n. On Thu, 2010-08-26 at 13:32 -0500, Dr. Luis Guillermo Almeida Montes wrote: > Dear Nick: > > Some colleagues asked me some doubts about pre-processing in > FreeSurfer for MRI files. I remember you told me once that MRI files > in analyze format would be inappropiate to pre-process in FreeSurfer > suite. They work with this analyze format since their DICOM files can > ´t be processed because their files are compressed.Can you give > technicals details about the reasons about why analyze files cannot be > used in FreeSurfer for pre-processing? > > Thank you. > > > Best Regards. > Dr. Luis G. Almeida >

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do I have to reprocess my subjects if I install new version of Freesurfer?
by Kevin Head 26 Aug '10

26 Aug '10

Do I have to reprocess my data if I install the new (v5.0.0) version of Freesurfer? If I don't, and process more subjects in the study with v5.0.0 will that be problematic?

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initial G-W contrast is negative
by Hansen, Kathleen (NIH/NIMH) [F] 26 Aug '10

26 Aug '10

Hello, The following command has produced a very wrong registration and a warning: bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat **** WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 **** The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas? Thank you, Kathleen

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scp issue??
by Gennan Chen 26 Aug '10

26 Aug '10

Hi! All, I download and install freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 on my macbook pro yesterday. After that, scp command from terminal is not working anymore. Below is an example: gnchen@mbp:tmp]$ scp -i ~/.ssh/id_dsa.pub sdg.zip macpro:~/tmp -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 -------- It shows freesurfer's version and did not copy file at all. I have no idea why scp command will have something to do with freesurfer. Does anyone know anything about this?? Gen

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ftp server down??
by Gennan Chen 25 Aug '10

25 Aug '10

Hi! I cannot download anything from ftp://surfer.nmr.mgh.harvard.edu/pub. Is it down? Gen

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mri_convert multiple sequences
by Soon Hock Wei 25 Aug '10

25 Aug '10

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How to add volume on pial surface in manual editting the trouble shootings
by 李瑾 25 Aug '10

25 Aug '10

Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin

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CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/volumegpu_impl.hpp'
by DongHye Ye 25 Aug '10

25 Aug '10

Hi. folks. I'm trying to execute new cuda binaries in freeserfer 5.0. When I tried to run it (e.g. mri_em_register_cuda), I got the following error. ============================== ========================================================= Acquiring CUDA device Using default device CUDA device: GeForce 8500 GT aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading '/home/yed/Data/freesurfer_subjects/bert/mri/nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/volumegpu_impl.hpp' on line 104 : invalid argument. ======================================================================================== What am I missing? Please help me out. I appreciate your time. Regards, Dong

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tkmedit and intensity normalisation
by Ali Radaideh 25 Aug '10

25 Aug '10

Dear FreeSurfer experts, I have two question for you please, First, I started recently to get the following message when I try to load the tkmedit GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: IP address And sometimes tkmedit.bin: xcb_io.c:452: _XRead: Assertion `dpy->xcb->reply_data != 0' failed. aborted Second, I have some images that have both intensity normalisation and Geometric distortion due to MS lesions. I followed the tutorial on how to fix these problems. My question is that, I don't want to re-run freesurfer twice (when I fix the intensity normalisation and one when I edit the white matter). Is there any command line I can use after saving changes to do both?. Many thanks in advance Ali This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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