Freesurfer

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16 participants
30084 discussions

white/pial surface in lateral ventricle
by Mira Michelle Raman 17 Aug '09

17 Aug '09

Hi, I was looking at some of my data and noticed that the white and pial surfaces occasionally invade the lateral ventricle (see attached picture). I went over to the bert sample dataset and noticed the same thing (coronal slice 87). Is this something I should be correcting or is it something that is ignored during the registration and labeling process? If I don't care about the choroid plexus volume, should I fill the white matter mask throughout the ventricle? Thank you in advance, Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 940305 http://cibsr.stanford.edu

3 3

(no subject)
by caoaize 17 Aug '09

17 Aug '09

Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -all on all my data, the statistical report show that the mean left hippocampus volume is bigger than the right one, while literature shows that the right one should be bigger. This problem continuously appeared in our different studies. I am not sure whether it is r2agui's problem, which changed the oritation of the structural data. Do you have any idea? 2. After autosegmentation, we did a statistical comparison analysis between automatic segmentation and manual segmentation, and the correlation is quite low, less than 80%, which is not acceptable for us. 3. Can I edit the auto segmentation results in Freesurfer if we think the auto segmentation is not good enough in some area? I will be really appreciated for your help. Aize _________________________________________________________________ Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！ http://im.live.cn/safe/

3 6

anatomic better image for Siemens Avanto...
by Gonzalo Rojas 16 Aug '09

16 Aug '09

Hi: Which is the better anatomical sequence for freesurfer that I could get using a Siemens Avanto scanner ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

3 2

registration of gene expression images
by Jared Price 14 Aug '09

14 Aug '09

Hi all, I have some images (2-d (single slice)) from mouse brains which show gene expression data from in-situ hybridization from several different mice. I would like to align each of these images with one another. Does anyone know of a really good tool for that sort of thing? Ideally I am looking to perform a 6-parameter transform of these images to bring them all into the same space. I know mri_robust_register does something similar for structural images of the human brain. Does anyone know of a good tool for this kind of thing? I thought someone in the freesurfer world might know. All the best and thanks for the help, Jared

2 1

mri_label2label
by p.s.bjerkan＠studmed.uio.no 14 Aug '09

14 Aug '09

Hi, Have a question regarding the mri_label2label function. Trying to test it for a subject (called "temp"). It seems to exit on writing the label file in the subject folder. There should not be any problems with the write permissions. Any idea? This is what I get (from command line): ------------------------------------------------------------------ [Cecilie@rossetti ~]$ mri_label2label --srclabel /home/Cecilie/cpi_cortex/old_study/Labels/wais_doss_vs_diff_lh_stg.label --srcsubject avg_hubin --trgsubject temp --trglabel temp/label/wais_doss_vs_diff_lh_stg.label --regmethod surface --srchemi lh --trghemi lh srclabel = /home/Cecilie/cpi_cortex/old_study/Labels/wais_doss_vs_diff_lh_stg.label srcsubject = avg_hubin trgsubject = temp trglabel = temp/label/wais_doss_vs_diff_lh_stg.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 SUBJECTS_DIR is /home/Cecilie/subjects FREESURFER_HOME is /usr/local/freesurfer_3.0.2 Loading source label. Found 21245 points in source label. Starting surface-based mapping Reading source registration /home/Cecilie/subjects/avg_hubin/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/Cecilie/subjects/temp/surf/lh.white Reading target registration /home/Cecilie/subjects/temp/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). INFO: found 21245 nlabel points Performing mapping from target back to the source label Building source registration hash (res=16). Number of reverse mapping hits = 3907 Checking for and removing duplicates Writing label file temp/label/wais_doss_vs_diff_lh_stg.label LabelWrite: saving to temp/label/wais_doss_vs_diff_lh_stg.label mri_label2label: could not open label file temp/label/wais_doss_vs_diff_lh_stg.label No such file or directory ERROR: writing label file mri_label2label: Done ----------------------------------------------------------------- Petr

2 1

mris_anatomical_stats error
by Rutvik Desai 14 Aug '09

14 Aug '09

We get the following error on one subject when running mris_anatomical_stats. The same command workson other subjects who were generated the same way. Using freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5, also tried freesurfer-Linux-rh9-stable-pub-v3.0.5. No heavy processes were running on the machine that would prevent memory allocation. thanks, Rutvik --------------------- % mris_anatomical_stats -a ep.1071/label/lh.aparc.annot -b -i 0.5 8 -f ep.1071.lh.stats ep.1071 lh computing statistics for each annotation in ep.1071/label/lh.aparc.annot. only considering thicknesses in the range [0.5,8.0]. reading volume /usr/home/possing/pub/Epilepsy/ep.1071/mri/wm.mgz... Talairach transform /home/mgolovin/fs_subjects/ep.1071/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /usr/home/possing/pub/Epilepsy/ep.1071/mri/transforms/talairach.xfm reading input surface /usr/home/possing/pub/Epilepsy/ep.1071/surf/lh.white... reading input surface /usr/home/possing/pub/Epilepsy/ep.1071/surf/lh.pial... reading input surface /usr/home/possing/pub/Epilepsy/ep.1071/surf/lh.white... done. computing second fundamental form...reading colortable from annotation file... CTABreadFrom: could not allocate -2 bin table Cannot allocate memory Segmentation fault (core dumped)

2 3

Hippocampus segmentation problem
by caoaize 14 Aug '09

14 Aug '09

Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -all on all my data, the statistical report show that the mean left hippocampus volume is bigger than the right one, while literature shows that the right one should be bigger. This problem continuously appeared in our different studies. I am not sure whether it is r2agui's problem, which changed the oritation of the structural data. Do you have any idea? 2. After autosegmentation, we did a statistical comparison analysis between automatic segmentation and manual segmentation, and the correlation is quite low, less than 80%, which is not acceptable for us. 3. Can I edit the auto segmentation results in Freesurfer if we think the auto segmen! tation is not good enough in some area? I will be really appreciated for your help. Aize _________________________________________________________________ 上Windows Live 中国首页，下载最新版Messenger！ http://www.windowslive.cn

1 0

frontal gray and white matter volumes
by Jared Price 14 Aug '09

14 Aug '09

Hi all, I am interested in obtain a total gray matter volume and a total white matter volume specific to the frontal lobes. How can this be done in freesurfer?

1 0

f.nii & f.nii.gz compatibility
by Garth Coombs 14 Aug '09

14 Aug '09

Hi, I am going to be running some new analyses on an old data set from another lab group that was collected in 2005/2006. Their group unpacked and analyzed using the f.nii.gz format; however, our lab unpacks and anayzes the f.nii format. Since I will be comparing the group from their lab with the group from our lab, do I need to re- unpack into f.nii or convert the already existing f.nii.gz files into f.nii ones, or are the two versions essentially the same and can be compared directly? What about if we want to combine some of their subjects with our subjects for a group analysis? Any advice would be greatly appreciated. Thanks! -Garth

2 1

Clusterwise correction
by Dankner, Nathan (NIH/NIMH) [F] 14 Aug '09

14 Aug '09

Hello all, I have a couple of questions regarding the way the cluster correction simulation in freesurfer works. I've read the wiki pages on the subject, but if I've missed something and any of this is answered elsewhere please let me know. My technical knowledge of these things is not great so I am just trying to get some background. First of all, how does smoothing the data prior to running the simulation affect the results? I've run corrections on the same data smoothed with a 10mm FWHM, and also on completely unsmoothed data, and the cluster results were different. Secondly, what determines whether vertices are neighbors or not? Is there an option to tinker with this or is it predetermined? Lastly, how do the p values of individual vertices factor into the simulation? Are they taken into account when the determination of the max cluster size under the null hypothesis is performed? Thanks in advance, Nate

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