Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 17
by McMains, Stephanie 06 Jun '13

06 Jun '13

Here is the original thread (to at least most of it). Maybe I am just an idiot, but I cant' figure out how to easily reply from the web to an entire thread, and pulling it out of the digests I get is a pain!! They wanted to take an ROI from SPM and put it into free surfer to extract cortical thickness. I thought going through fsaverage was a good way to do this. But as I said, looking at the surface, I have some concerns. I am more confused by when you tell them to run the MNI template through recon-all to get a surface, because I thought fsaverage was a kind of MNI space that has already been run through? Thanks, Stephanie what space is your VBM map in? doug On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote: > Hi Doug, > > Thank you for your response! I am still a bit confused about the vol2surf > command. I have a volumetric mask with voxels of interest based on a VBM > analysis in SPM. I would like to extract the cortical thickness measurements > based on these voxels. I am not clear what specifications I need to include > when using vol2surf. For example, what do I use as my registration matrix? > > Thank you for your help! > Ola > > Ola Ozranov-Palchik M.S. > Research Coordinator, Gaab Lab > Laboratories of Cognitive Neuroscience > Children's Hospital Boston > 1 Autumn Street, Mailbox # 713 > Boston, MA 02115 > olga.ozra...(a)childrens.harvard.edu<http://childrens.harvard.edu> > phone: (617) 334-5046 > main lab: (617) 355-0400 > fax: (617) 730-0518 > http://www.childrenshospital.org/research/gaablab > > > -----Original Message----- > From: freesurfer-boun...(a)nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, June 04, 2013 1:48 PM > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness > > > Make sure that your SPM volume is registered to the anatomical, then use > mri_vol2surf to map the volume to the surface, then mri_segstats to extract > the mean of the thickness > > doug > > > > > On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote: >> main lab: (617) 355-0400 > Dear FreeSurfer Experts, > > I was wondering if anyone can advise on the best way to use an ROI mask > created in SPM (XjView) to extract cortical thickness values in freesurfer. > > Thank you in advance for your help! > > Ola > > Ola Ozranov-Palchik M.S. > Research Coordinator, Gaab Lab > Laboratories of Cognitive Neuroscience > > Children's Hospital Boston > 1 Autumn Street, Mailbox # 713 > Boston, MA 02115 > olga.ozra...(a)childrens.harvard.edu<http://childrens.harvard.edu> > <mailto:olga.ozra...@childrens.harvard.edu> > phone: (617) 334-5046 > main lab: (617) 355-0400 > fax: (617) 730-0518 > http://www.childrenshospital.org/research/gaablab > Then it goes on: Hi Ola, this probably will not work. The tal coordinate is notoriously inaccurate in cortex. You are verylikely to totally miss the area you are looking for. A better way is to run the MNI template through recon-all, map your VBM result to the surface of that, then use mri_surf2surf to map the effect to each individual. doug On 06/05/2013 02:58 PM, Ozranov-Palchik, Ola wrote: > Hi Doug, > > Thank you, again! I decided to try to use the Talairach coordinates from my > analysis for ROI extraction. I created an average subject and preprocessed > the data (mris_preproc). I obtained the vertex index based on the coordinates > from the average subject. Any ideas on how I can now find the corresponding > vertices in all my subjects? > > Thanks very much! > Ola > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422

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The feasibility of this procedure
by 淼 06 Jun '13

06 Jun '13

Dear FS, I want to do an analysis with freesurfer but this is relatively complicated. I would like to know whether this is doable by freesurfer. I first want to create a custom template based on my subjects and I have seen the SurfaceRegAndTemplate page and this should be the place where I should start. Then I should use mris_register to register all my subjects to the new template. Then I want to export volume data of each region of interest and total intracranial volume of subjects to SPSS for further analysis and I don't have a clue on how to do that yet. Do you think this is feasible? Any problems there? Thanks for any help in advance. Miao Sent from my iPhone

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averaging tracts?
by Hoptman, Matthew 06 Jun '13

06 Jun '13

Hi all, Thanks for tracula , which I think is a terrific tool. Is there any way to average tracts across subjects for viewing purposes? I have in mind somehting along the line of a group average merged_avg33_mni_bbi.mgz. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Enquire about running FreeSurfer {Disarmed}
by pablo najt 06 Jun '13

06 Jun '13

Hello I have a question regarding the installation/running FreeSurfer.I have just completed the installation and got the confirmation that Free surfer was installed. Please see snapshot.However when I follow the steps for testing (https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer) I always get "command not found". I was wondering if you would be able to help me.Thanks,Pablo

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(no subject)
by David Dalton 06 Jun '13

06 Jun '13

Hello, I am currently attempting to download the freesurfer software onto my mac device from the website, but I am having trouble. None of the links will open, and when I tried typing the wget (curl-O for me) command into my command line, nothing happened. Any suggestions? Thanks, David

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problem about file format
by huang bs 06 Jun '13

06 Jun '13

Hi All, Sorry to take up your time. My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: *tkregister2 --mgz --s linziyi --fstal --surf orig* The terminal then reports: *ERROR: /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm does not start as 'MNI Transform File* This file *talairach.xfm* does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as "executable file". That's quite strange because I did not make such change to it. These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either. For the cases I just re-con, since they are not moved to elsewhere, everything seems OK. Have you guys had such problem before and how to fix it? Thanks! -- Best Regards, B Huang

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Saving subjects
by Garikoitz Lerma-Usabiaga 06 Jun '13

06 Jun '13

Hi list, we have some subjects with acquisition problems. Do you think it is possible to save this two subjects, and if so, how? They have been run with: recon-all -i (file) -s (subject) -qcache -hippo-subfields -all They have been acquired with 3T, MPRAGE (but I didn't add the flags). I've read in the list about -washu-mprage , but I don't know how to use, couldn't find the documentation. Should it be enough adding wm control points? Many thanks in advance! Gari (sorry to post that many images, they belong to only two different subjects) [image: Inline image 5][image: Inline image 4][image: Inline image 3][image: Inline image 2][image: Inline image 1]

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maximum thickness value?
by Colin Reveley 06 Jun '13

06 Jun '13

I'm using data that's 0.35mm isotropic (and lower, but I've just noticed this). to do that I alter the header so that the voxels claim to be 1mm. it's a small brain so this works. Everything in general is fine. the only thing is I'm having touble with the cortical thickness output of mris_make_surfaces. I can't remember if this is a new problem, or has just never mattered to me before. when I run mris_make_surfaces, the ?h.thickness data seems to top out at 5. So that most of the brain has a thickness of 5. I wonder does freesurfer top out the thickness metric data at 5mm, since humans (or monkeys) don't normally have GM that is more than 5mm thick? if that's the case, can I change the behavior? I hope it is my error, and the thickness is topping at 5 for some reason I can control. attahced: pial surface with metric on it and scale bar sagittal slice with little measurements drawn to estimate thickness. if you multiply the meaurements by 0.35 they are roughly what you'd expect. but many are >5mm before scaling. they all report as 5mm. I really need just anyway to calculate the thickness. that would be great. It needs to be quite accurate. maybe I could change the volume back to 0.35 conformed, then scale the surfaces as well, and use mris-refine or something like that? the data would be the same but freesurfer would now know the true dimensions when it ran mris_refine. or anything that generates ?h.thickness. many thanks, Colin

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Group analysis
by Tudor Popescu 06 Jun '13

06 Jun '13

> > Under fsaverage/surf there is both an lh.white and an lh.white_avg file, >> while under average/surf there's only lh.white_avg. I repeated the >> mri_surf2surf command above with "--s fsaverage" instead of "--s average" >> (since I understand in this case it's the same thing), and then it ran to >> completion. >> > It should be close but probably not exact. So if I want to use the study-specific "average" subject surface with mri_surf2surf, rather than the generic "fsaverage" one, how can this be done given that the required ls.white file only exists in the latter but not in the former? Can I just rename (or duplicate) ls.white into ls.white_avg? Also, 1) Doesn't mri_surf2surf also need to be applied to surface of individual study subjects, or only to the (fs)average subject? 2) Shouldn't the input to mri_glmfit be the output of mri_surf2surf? In the group tutorial<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#GLMAnalys…>, the former is "lh.gender_age.thickness.*10*.mgh" while the latter is "lh.gender_age.thickness.*10B*.mgh". Or should it just be the unsmoothed output of mris_preproc? 3) Assuming the label files (corresponding to my ROI, and extracted from the Destrieux atlas) are different for each subject, and given mri_glmfit is called just once, for all subjects, which label file (corresponding to what subject) should I point it to? Thanks!

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Re: [Freesurfer] max thickness value
by Colin Reveley 06 Jun '13

06 Jun '13

I just found mris_thickness. which has a setting to override the default 5mm. you just run it. whoops. I'm very tired. apologies. I just assumed it would be hard.

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