Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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. --------------------------------------------------------------------------------------------------------------------------------------------------

2 1

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

2 1

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

3 2

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

14 Aug '09

Hello, I am trying to reinstall FS, and I am having some difficulties. When I type in the following command: cd /usr/local tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz (replacing the -<platform>-<release> with my Linux variant which is freesurfer-Linux-centos4-stable-pub-v4.3.1) I get the following error: tar: freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar: Cannot open: No such file or directory tar: Error is not recoverable: exiting now tar: Child returned status 2 tar: Error exit delayed from previous errors Please can you advise me on how to correct this? Thank you kindly Fatima

2 7

tksurfer problem
by sina zarei 13 Aug '09

13 Aug '09

Hello I am not able to see the surface by running "tksurfer bert lh pial". I receive the error "surfer: ### redraw failed: no gl window open". I have tried "export doublebufferflag=1". Mesa is installed and updated. Linux ATI drivers is installed. Os: Fedora 11 Graphics: ATI RV515 X1300. I have tried rh9 and CentOS4 versions of the freesurfer on separate Fedora 11 and CentOS 5. On CentOS I see only a small part of the image. I have tried NVIDIA graphic cards too. 3D games work fine. I am very grateful if you may assist me. Sina

1 0

FreeSurfer: fornix segmentation
by Judit Haasz 13 Aug '09

13 Aug '09

Hi, I have run mri_cc -fornix. In some cases I encountered the following problem. Although fornix.mgz was created, and it seems the program has run properly, the file (same size as those who contain fornix) turns to be empty. Looking at the input volume, I could identify fornix. Could you help finding a solution for my problem? Thank you for help! Judit Haasz mri_cc -fornix -aseg aseg.auto_noCCseg.mgz -o fornix.mgz *SES including fornix in segmentation reading input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to fornix.mgz reading aseg from /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/aseg.auto_noCCseg.mgz reading norm from /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/norm.mgz 11261 voxels in left wm, 26612 in right wm, xrange [125, 132] global minimum found at slice 128.0, rotations (0.25, -1.50) final transformation (x=128.0, yr=0.250, zr=-1.500): 1.000 0.026 0.004 -3.864; -0.026 1.000 -0.000 3.409; -0.004 0.000 1.000 0.560; 0.000 0.000 0.000 1.000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 120 96 eigenvectors: -0.001 0.001 1.000; -0.192 -0.981 0.001; 0.981 -0.192 0.001; error in mid anterior detected - correcting... writing aseg with callosum to to /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/fornix.mgz... writing fornix to to /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/fornix.mgz... corpus callosum matter segmentation took 0.6 minutes

2 1

manually edit segmentation
by Fischi Gomez Elda 13 Aug '09

13 Aug '09

Dear all, I'm trying to manually edit the -segmentation step in the recon -all -autorecon2 command. Actually, my problem is that I need a cortex parcelisation of a newborn brain and, as far as I know, I cannot run directly the -recon all as it s based on a adult brain template. My idea was, inf act, to reedit the -segmentation step, as I have a manually segmented template of a newborn brain, and then, run this modified recon -all to obtain the parcelisation. Is it possible? Does exist any way to obtain this cortex parcellisation for a newborn brain using FreeSurfer? Thanks

2 1

subject-inflation-sphere
by Zhong Jidan 13 Aug '09

13 Aug '09

Hi Freesurfer experts, I have a question about the sphere transformation from the inflated surface. In the paper "cortical surface-based analysis II", you mentioned that each vertex is put in a normal vector field which is from the center of the sphere to the vertex, then you project the inflated surface onto a unit sphere. The question is, how do you choose the center of the sphere? If you choose a different location as the center of the sphere, the new sphere you get will be different. So how do you make sure that the center you choose is the one you want? Thanks a lot. -- Regards, Jidan

2 1

reinstalling freesurfer
by Ahmed, F, Me <fahmed＠sun.ac.za> 13 Aug '09

13 Aug '09

Hello Experts, I apologise for the stupidity of this question, but I am not used to using Linux at all, but I need to uninstall my Freesurfer and then reinstall it, however, I have no idea how to uninstall in Linux. Can someone possibly assist me in this problem? I'd be extremely grateful. Thank you and Kind regards, Fatima

3 6

Extending Pial Volume
by Derek Huffman 12 Aug '09

12 Aug '09

Hello FreeSurfer Team, I am wondering how to add cortex to the pial volume that is already present in the brainmask volume. When I look at the brainmask volume, there is visible cortex located outside the red "pial" line. I have already added white matter control points and corrected all white matter defects. I am wondering if you have any tips for me. I apologize if this is a repeat question but I couldn't find anything in the wiki about correcting this type of error. Thank you, Derek

2 1

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