Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

primary auditory cortex ROI
by Ritobrato Datta 10 Mar '14

10 Mar '14

Hi All, My email may have fallen through the cracks over the weekend so I am sending it again. I need to demarcate primary auditory cortex in a group of subjects anatomically and I came across the following papers - https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_a… https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf Is there a script that I can use on my 3T MPRAGE images to get primary auditory cortex ROI ? That will be very helpful. Best, Ri

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version 5.3 bug fix
by Gregory Kirk 10 Mar '14

10 Mar '14

In the release notes for 5.3 i find Stable release version 5.3.0 is a bug fix release to correct the problem with pial and white surface creation affecting thickness and area measures. Is this only related to netative thickness values, which i have never found. I have 150 subjects * 3 timepoints that i ran on a cluster with condor linux and freesurfer version 5.1 i myself inspected time point 1 and did analysis and did not find any unusual problems. i am preparing to do a longitudinal analysis of all 3 timepoints and wondering if i should reprocess and reinspect everything, considering the bug fix and improvements for longitudinal stream. thanks greg

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Looking for cortical thickness procedure
by Saurabh Thakur 10 Mar '14

10 Mar '14

Hello freesurfer Expert, Steps for measuring cortical thickness are in tkmedit : 1. Intensity normalisation, 2. Registration to Talairach space, 3. Skull stripping, 4. Segmentation of white matter, 5. *Tesselation of the WM boundary, * 6. *Smoothing of the tesselated surface and automatic topology correction* Can u help me to step no 5 and 6. How to do this steps. Thanks, Saurabh Thakur,

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fix this error in segmentation
by charujing123 09 Mar '14

09 Mar '14

Hi all, How to fix this problem in segmentation, which can be got in the attachment? Thanks.All the best. Rujing Zha 2014-03-08 charujing123

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cannot sign white matter area by control point and white matter edit
by charujing123 08 Mar '14

08 Mar '14

Hi all. In troubleshooting, I want to sign some area as white matter by control point and wm edit. However neither of them can work. Thanks. the picture can be got in the attachment. All the best. Rujing Zha 2014-03-04 charujing123

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OpenMP and non-OpenMP output is different at mri_ca_register
by Chris Adamson 07 Mar '14

07 Mar '14

I was trying to compile Freesurfer (in a Centos 6.5 VM) with a later gcc to see if the performance improved and noticed that the output gcc 4.4 vs. 4.8 was slightly different. I later compiled with gcc 4.4 *without* openmp support and this version produced the same output as the gcc 4.8 version, as expected. I have attached the recon-all log files, they first differ at line 1664, at iteration 451 of mri_ca_register; after that the differences accumulate. I feel that this shouldn't happen and the outputs should be equivalent. As a side note, I am unable to compile GEMS and dmri_poistats or any of the GUI programs due to vtk undefined symbols errors. Similar to this http://www.vtk.org/pipermail/vtkusers/2010-September/062426.html. This is apparently a known issue with vtk 5.6. How is this resolved? PS. The gcc 4.8 binaries were slower than the 4.4 binaries. Thanks in advance, Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au<http://www.mcri.edu.au/> E chris.adamson(a)mcri.edu.au T 03 9936 6780 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Convert expert segmentation to FreeSurfer space
by Mohamed Oualid Benkarim 07 Mar '14

07 Mar '14

Hi all, I've performed FS subcortical segmentation and my purpose is to use these segmentations as seeds to another method. As FS uses GCA atlas to perform subcortical segmentation, I want to know if the *aseg.mgz* output is in GCA atlas space, or in original space except that the dimensions are 256x256x256, 1mm. On the other hand, I also need to convert expert segmentations in native space to GCA atlas space, that is, the inverse of the process explained in http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I don't know if there is a command to do so, or we have to use a transformation matrix. In the latter case, FreeSurfer creates several tranformation matrices: talairach.lta, talairach.xfm, talairach.m3z....but it's is not clear which one I should use. Thank you in advance!!

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Longitudinal analysis - the effect of FS release?
by Kivisaari Sasa 07 Mar '14

07 Mar '14

Hi, we have a longitudinal data set and have processed all of the baseline data using FS v5.1.0. We are now about to start preprocessing follow-up brains. Can you please give your opinion on whether we had better stick with v5.1.0 for the follow-up data as well or whether it would be safe to switch to v5.3.0? Do you have any updates on the potential time frame of the v6.0 (?) release? Many thanks in advance! Best wishes, Sasa

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Re: [Freesurfer] Surface area in aparc stats
by Douglas Greve 07 Mar '14

07 Mar '14

Hi Zhuangming, please remember to post to the list. Thanks! I don't understand your question. What do you mean by the exterior, anterior, posterior, etc, surfaces? On 3/5/14 11:56 PM, 沈庄明 wrote: > Hi Doug, > Thank you for your prompting response. Do you mean the computation > only calculate exterior surface of the cortical region ? The other > five surface (i.e. anterior, posterior, left, right, interior) are > excluded ? > Thanks! > > Zhuangming > > > -----原始邮件----- > *发件人:* "Douglas Greve" <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > *发送时间:* 2014年3月6日星期四 > *收件人:* freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > *抄送:* > *主题:* Re: [Freesurfer] Surface area in aparc stats > > > By default, the surface area is computed from the white surface > (ie, boundary between WM and GM). It is possible to compute it > from the pial surface (ie, boundary between GM and background) > doug > > > On 3/5/14 9:14 PM, 沈庄明 wrote: >> Hi all, >> I need to know how is the SurfArea in ?h.aparc.stats calculated >> by FreeSurfer? Since each cortical parcellation has its own >> thickness in 3D space, does the surface area computation consider >> both the exterior surface (i.e. the surface separating the gray >> matter and the background) and the interior surface (i.e. the >> surface separating the gray matter and the white matter)? >> Thanks! >> >> Zhuangming Shen >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >

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Large areas of white matter ignored, even with control points
by Andrea Grant 06 Mar '14

06 Mar '14

Hello, I'm working with T1 weighted scans obtained at 7T and have a problem with a subject. I preprocess the images to deal with the B1 inhomogeneity (normalize to PD and mask noisy pixels), and have successfully segmented about 20 scans. I often need to use control points, but they normally work just as I expect. However, I have one subject where large areas of the brain are completely excluded from the segmentation (basically the entire occipital lobe). I added control points and re-ran, to no effect. I'm attaching a screenshot of the brainmask with surfaces, my control points, and the white matter mask. Clearly, the skull stripping wasn't very successful (I adjusted the watershed threshold manually, but at one value I got the current result and at a single integer lower I lost half the brain). I have successfully segmented other subjects with equally poor skull strips, though, so I don't believe this has any bearing on the current issue. Is editing the white matter mask the only way to fix this? If so, do I need to carefully fill in on every slice, or can I just brush in here and there to sort of "goose" the white matter into that region? I can do the slice by slice fix, but if there's a way to avoid the several hours it will take me, I would love to know! Thanks, Andrea ----- Andrea Grant Visual Neuroimaging Technologist Center for Magnetic Resonance Research, University of Minnesota 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 gran0260(a)umn.edu umn.edu/~gran0260 <http://umn.edu/%7Egran0260>

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Freesurfer March 2014