[Freesurfer] bbregister - Are 6 dof enough for MNI305?
Dear Freesurfers, I was wondering if you could help me clarify one question I have re the recommended use of bbregister to register PET data. If I want to register my PET data to MNI305 space used in Freesurfer, is a 6 dof rigid registration enough? I notice that the tailarach function used within autorecon1 is a 12 dof affine, so I'm guessing that bbregister is unlikely to fully register the PET data to the template space in the same way that (eg) brain.mgz is registered. Thank you very much! Best, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] PET analyses in cortical regions
Dear Freesurfers, My goal is to evaluate the cortical thinning patterns in some (cortical aparc) regions, and to relate that to loss of PET activation in the same regions. I would like to clarify the steps of the pipeline in Freesurfer (v5.0.0) for this purpose. From my reading of previous discussions in the mailing list, I can see two possible ways of doing this - but I am not sure and I would like to ask for your feedback on them: First method: 1) Register all PET scans (already in ICBM152 space, enforced with SPM8) to the brain.mgz image of each subject to ensure the PET files are in MNI305 space, to be able to use Freesurfer's atlas, using bbregister or spmregister. 2) Use mri_vol2surf to project the PET data onto the surface of each subject. 3) Use mri_segstats to extract the statistics for each region. Second method: 1) (Same as above). 2) Use mri_annot2label on the relevant aparc regions. 3) Use results from the previous step in mri_label2vol to create the volume masks extracted from the cortical regions. 4) Apply mri_segstats on these (as above). Could you please clarify if I am on the right track, notably which method should be more robust (or correct...)? Also, does mri_segstats also give overall group statistics (mean, std) for each region, or must I use another function/average all subjects together for that? Thank you very much! Best, Joao Pereira Wolfson Brain Imaging Centre University of Cambridge ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
RE: [Freesurfer] Voxel resolution impact / skull stripping and biascorrection replacement
Pedro, Thanks for your reply. By false negatives I mean a lack of detection of atrophic areas which I know are present in this AD cohort, namely the parietal convexities. I'm unable to visualise them with FS. Finally, you've recommended me not to seed anything to recon-all which had been skull stripped. Is there any way of going around this? And what about data which had been previously bias corrected? Thank you very much for all you help! Best, Joao -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Pedro Paulo de Magalhães Oliveira Junior Sent: 03 October 2008 21:25 To: Joao Pereira Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Voxel resolution impact / skull stripping and biascorrection replacement João, Here is my opinion: I have worked on resolutions distinct than 1mm3 isotropic and usually I have no problem. What do you mean by false negatives in your cohort study? I think you should avoid seeding data with skull striped by other program to the pipeline. Best Regards, PPJ 2008/10/3 Joao Pereira [EMAIL PROTECTED] Hello, I have a couple of questions on which I would like to have your opinion. The first is the voxel resolution impact on cortical thickness sensitivity. I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates scans to 1mm - is it possible that the 1.25 mm resolution hinders cortical thickness measurements? I'm asking this because I'm analysing an AD cohort whose result seems full of false negatives (I'm in the process of inspecting the intermediate steps as well - I just wanted to check if resolution was a factor as well). I would also like to know if it is possible (and advisable) to input already optimally skull stripped and bias corrected brains into the recon-all pipeline. If that is possible, I would assume that I need to bypass those steps, and I would like to know which arguments to use in recon-all in order to do so. Thank you very much for all your help! Best, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Voxel resolution impact / skull stripping and bias correction replacement
Hello, I have a couple of questions on which I would like to have your opinion. The first is the voxel resolution impact on cortical thickness sensitivity. I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates scans to 1mm - is it possible that the 1.25 mm resolution hinders cortical thickness measurements? I'm asking this because I'm analysing an AD cohort whose result seems full of false negatives (I'm in the process of inspecting the intermediate steps as well - I just wanted to check if resolution was a factor as well). I would also like to know if it is possible (and advisable) to input already optimally skull stripped and bias corrected brains into the recon-all pipeline. If that is possible, I would assume that I need to bypass those steps, and I would like to know which arguments to use in recon-all in order to do so. Thank you very much for all your help! Best, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Tksurfer rendering problem
Hello, I'm having an issue with tksurfer - whenever I try to load a surface, the display only shows scattered points (with the vaguely recognizable shape of the intended surface). I've noticed the following error that may be related to this: libGL error: open DRM failed (Operation not permitted) libGL error: reverting to indirect rendering I'm using the freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.2 version. Any ideas as to what is going on? Thank you very much for your help. Best, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TIV estimation with FreeSurfer
Dear all, I am posting the questions I made to Bruce without going through the list along with his reply. **I would still like to be sure about question 1)***, as it is central to my conclusions. If anyone has any other ideas, please let me know. There are still a couple of questions in my mind I would really like to understand concerning this TIV estimation though: 1) I first run FS without any visual inspection (-autorecon1 and 2) to get the TIV estimate in the aseg.stats file. I then compared those values to the ones obtained *after* adjusting the affine transf (in some cases using the brain.mgz file, others manually) and the values changed. But is this the correct procedure to adjust the TIV output, or am I looking at an artifact? 2) Is it possible for me to build my own template for TIV estimation purposes? If yes, which file should be replaced? Thank you again for your help (btw, is there any chance I can obtain the eTIV value without running -autorecon1 and 2 all the way?) Reply: (1) We have very little experience with the eTIV, but I guess the answer is yes, that would be the way to do it, and (2) the only way to build your own atlas would be to use the aseg.mgz from a bunch of subjects and mris_ca_train. Although 2) is possible in a practical way (ie, I can build my own atlas), I don't believe it would be valid for TIV estimation with FS, due to the bootstrap method you used to calculate the scale factor. Am I right? Finally, could someone please explain me the point of trying to adjust the talairach output by using the T1.mgz and brain.mgz files? I know this works, but I don't understand why, especially with the brain.mgz: the reference atlas has skull... shouldn't using a skull stripped scan confound the process? Thank you all. Hope to hear from you soon. Joao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TIV estimation using FreeSurfer
Dear all, I have been trying to use the eTIV value FS outputs after the -autorecon1 and -autorecon2 stages, registering it in the aseg.stats file. The purpose would be to see how reliable that value is when compared to our own manual measurements. When reading the Buckner paper, I have noticed that a stringent requirement for optimal perfomance is the usage of an adequate template (i.e., age matched template), and I believe FS uses the MNI 305 template (at least in 2006 versions), which is not adequate for our population. My questions are: 1) Is it possible to build our own template and then introducing it in the FS package? If so, where? (please notice that I am not interested in surface templates) 2) If 1) is possible, is the TIV estimation hindered by such a procedure? I know you have adjusted the calculation of the eTIV using bootstrap, which means that you don't use a pure version of the atlas scale factor (ASF), but you scale it by a fixed number you've obtained with this adjustment. My guess is that this estimate will no longer be valid. 3) I have adjusted the initial transform outputs by using mri_total, T1.mgz, brain.mgz and, in some cases manual adjustments. This affected talairach.xfm. Is this the adequate approach for TIV estimation purposes? I remember reading something about talairach_with_skull.lta... Thank you very much for your patience and assistance! Regards, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] -notalairach error?
Hi, I have just realized I made a mistake when I ran recon-all -s subj -notalairach -autorecon1 -autorecon2, as the -notalairach option is overridden by autorecon1. Nevertheless, when I look at the dates of the files, I see that talairach.xfm is the one I edited, although talairach.log has a posterior date. Moreover, when I look at the transforms with tkregister2, they seem just as I have left them. What am I missing here? Thanks! Joao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Segmentation optimization
Hello again, I've been having some problems with FS segmentation, especially around the temporal lobes, where there is a clear underestimation of the pial surface (and manual edits are not being too successful). The problem is clearly related to the poor resolution of the used images. Are there any parameters to change in order to optimise the segmentation process? Also, in order to evaluate the segmentation I want to use the grey matter segmented volume mask. Is it the ?h.ribbon.mgz files or should I consider something else? Thank you again. Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness difference measurement
Hello again! Firstly, let me thank you for your precious previous advices, which pointed me in the right direction. I have another question for you: I have read your article on Reliability of MRI cortical thickness measurements and its relation with scanner and field, and I would like to know what function did you use to subtract the subjects' average cortical thickness files in order to have a cortical thickness difference layer. I don't know if this is a very basic question, but I can't seem to find how to do it with FS. Thank you! Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Segmentation
Hi, I tried to test FS cortical thickness analysis by using a batch of 10 subjects whose grey matter I manually deleted in the temporal lobes (a significant part at least). When I compared it to the original 10 images, little or none changes were significant! I checked the segmentation and I noticed that the grey/white boundary in the original subjects was too conservative, hence no changes were detected (at least I believe it is the only explanantion). Is it possible to change the segmentation parameters to make it more agressive or am I overlooking something? Thank you! Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all error
I have put my subjects through the recon-all procedure and most ended with no errors. But some ended with an error message, after the command line: mri_diff aseg.auto.mgz aseg.mgz saying: zcat: ~/.../mri/aseg.auto.mgz: unexpected end of file mghRead(~/.../mri/aseg.auto.mgz, -1): read error What is happening? Thanks! Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aseg step bypass
I am using freesurfer for an inter-subject cortical thickness analysis. In order to speed things up, I was considering removing the sub-cortical segmentation step with -noaseg in the recon-all command line. I believe this will not affect my results, but I am not sure if some of the subsequent procedures are affected. Is it OK to do this then? Thank you! Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Skullstripping
Can someone explain me why my the recon-all skull stripping option is writting a file named brainmask.mgz instead of brain.mgz? This is a problem because the subsequent procedures do not recognize the file. Thank you! JP ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] csurf porblem
Hello, I have just installed FreeSurfer and I can't run csurf. The GUI appears but it is useless, giving an error at the beginning saying it can't find the paint file in the bin directory. Even when I select the bert subject, nothing happens, requiring COR files to exist. Could you please help me qith this? Thank you, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
