Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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

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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

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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)

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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

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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?

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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

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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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any SurfStat users on this list
by Siddharth Srivastava 14 Aug '09

14 Aug '09

Hi All, I got introduced to SurfStat through this list, and i have been using it of late to try some alternatives to the surface based GLM analysis on my data, already processed by freesurfer. The results are a perfect match, except for the x,y,x coordinates reported by SurfStat (same data set). I do not want to misuse this list, but i wanted to know if there any active users of SurfStat on this list whom i can contact to discuss this issue, and get some help/advice? I have tried all the usual means of contact as mentioned on the SurfStat website, and i have not recd. any response as yet. thanks, and sorry for a bit off topic mail. sid. --------------------------------------------------------------------------------------------------------------------------------------------------

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thickness map
by Feng-Xian Yan 14 Aug '09

14 Aug '09

Hi, I have some problems want to understand. (1) I want to analysis the cortical thickness difference of three groups. But, three groups (one factor/three levels) of Freesurfer is not satisfied with our demand. Because we want to get a thickness difference map that satisfied with the many voxels containing A group > B group > C group and A group < B group < C group, Freesurfer can’t do that. So, we want to get this map by myself and use Matlab or other tool to obtain that. And, now I want to obtain a file that containing the Tal coordinate and the thickness value of this coordinate for all subjects. Would you tell me how to get the file that containing the Tal coordinate and the thickness value of this coordinate? (2) Before, I want to use the following command to get the thickness value. The command line is "mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --sfmt surface --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt surface --hemi lh --sval-tal-xyz orig --tval-xyz", and then i type “mris_convert lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”. But, the result file(lh.thickness.asc) does not contain the thickness value of this coordinate. So, I think these commands have some error. (3) Use the command “mris_convert –c lh.thickness lh.white lh.thickness.asc” to obtain the thickness value of the RAS coordinates. But, I’m confused about that if I change lh.white to lh.pail or lh.inflated. What’s difference for the three? (4) And, I ask some problem before. Everyone said the result file(lh.thickness.asc) is using RAS coordinates through “mris_convert –c lh.thickness lh.white lh.thickness.asc”. But, I have confused about this. When I open this subject by tksurfer, I look at the coordinate of the vertex RAS in the tksurfer tool box, and the coordinate is difference from the coordinates that obtain from the command “mris_convert –c lh.thickness lh.white lh.thickness.asc”. So, which one is right? Thank you in advance! Feng-Xian

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reinstalling
by Ahmed, F, Me <fahmed＠sun.ac.za> 14 Aug '09

14 Aug '09

Hello, I just have a quick question, when reinstalling FS, is it ok to use the license that I initially received when first installing it? Or must I register for a new license? Thank you and Kind regards, Fatima

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