Freesurfer

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30135 discussions

problems about extracting specific vertex thickness value and getting a average thickness for a specific mask
by charujing123 05 May '14

05 May '14

Hi FS experts and users I have done the each subjects' surface regestration on fsaverage surface, and merge all of them into a *.mgh. Group analysis is also completed. Now I have two questions: 1,I want to extract the VtxMax vertex number thickness for all subjects. The VtxMax vertex number can be got in the *.sig.cluster.summary file. And it represents the most significant vertex in that cluster. I search my question in google and find these scripts which maybe helpful for me: for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh $SUBJECTS_DIR/fsaverage/surf/lh.$i.mgh mris_convert -c $i.mgh $SUBJECTS_DIR/fsaverage/surf/lh.inflated lh.$i.asc done I got the lh.*.asc file and open it. There are five columes in this file. I guess that: first colume is vertex number, the 2nd-4th columes represent MNI305 coordinates in surface, and the 5th colume is thickness of this vertex. If I want to deal with my 1st question, all I need to get the lh.*.asc file and search the specific vertex number in this file. All of above, is there anything wrong? 2, I created a surface mask, and want to extract the average thickness value in this mask for every subject. How can I complete it? Can I extract all vertex thickness in that mask, and average them in each subject? If so, however, it will be a bot of inconvenience. I want to some simple codes to deal with it. Any reply will be highly appreaciated. Thanks All the best. Rujing Zha 2014-05-05 charujing123

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Re: [Freesurfer] When/What to edit?
by Lukas.Scheef＠ukb.uni-bonn.de 04 May '14

04 May '14

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Re: [Freesurfer] using multiple cores
by Lukas.Scheef＠ukb.uni-bonn.de 04 May '14

04 May '14

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Fwd: Optseq2: ntp
by Conchy PF 04 May '14

04 May '14

Dear Douglas, I would like to use optseq2 to set up my experiment sequence. However it is not clear for me what “number of time points” means. I guessed that it was the number a waveform is sampled, but I saw in some mailing lists that it is the time the event is repeated during the run. In case it is the first meaning, how can I get the information about the number a waveform is sampled? Thanks in advance and kind regards. Conchy

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brain.finalsurfs.mgz editing
by Khadka, Sankalpa 02 May '14

02 May '14

Dear freesurfer community, My question is directed to those who have experience with editing brain.finalsurfs.mgz. According to the tutorials, after making edits on brainmask.finalsurfs.mgz (which is normally done when the pial surface is not accurate), we can run, recon-all -autorecon-pial -subjid subj" However, I found an anomaly when I looked at the steps that -autorecon-pial flag goes through. The very first step of autorecon-pial flag is "mri_mask" command. This takes brain.mgz and brainmask.mgz as inputs and gives brain.finalsurfs.mgz as output. Now, if we have made edits on brain.finalsurfs.mgz, it will be overwritten by the new one and hence our edits won't take an effect. I ran few experiments too. First, I made edits on brain.finalsurfs.mgz and ran recon-all with autorecon-pial flag. I ended up with a new brain.finalsurfs.mgz and my edits did not make any changes. Second, I made edits on brain.finalsurfs.mgz and ran with white, smooth2, inflate2, autorecon3 flag (basically starting from mri_make_surfaces command). On doing so, the edits made desirable changes and brain.finalsurfs.mgz remained intact. Third, I made changes on brainmask.mgz and brain.mgz (inputs for mri_mask). It also works as expected. Finally, I also followed the recommended steps from the tutorial by creating brainmask.finalsurfs.manedit.mgz, however, the edits from "manedit" were not carried on to brainmask.finalsurfs.mgz Could anyone please shed some light on this? What would be the best strategy to follow? Thank you, Sankalpa

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brain.finalsurfs.manedit.mgz file edits & longitudinal processing
by Douglas Merkitch 02 May '14

02 May '14

Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525). The problem that I am having is that the edits saved in the brain.finalsurfs.manedit.mgz file do not carry over when processing longitudinally. Previous posts have addressed this topic, but have not (to my knowledge) solved the issue. Please see the threads from the Freesurfer archive below for a brief context: 1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html 2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html Please let me know if more information is needed to understand the issue. Any insight/ideas regarding this issue would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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FSGD and contrast files for group analysis
by Kenza Drissi 02 May '14

02 May '14

Dear Marie,I want to run a group analysis on a set of subjects, correcting for gender(Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus inlh/focus in both h), age and IQ. Should my FSGD file look somewhat like thisbelow:GroupDescriptorFile 2Class NoFocus_MaleClass NoFocus_FemaleClass RhFocus_MaleClass LhFocus_MaleClass BhFocus_MaleClass RhFocus_FemaleClass LhFocus_FemaleClass BhFocus_FemaleVariables age IQIf so, considering that I want to investigate the effect of epilepsy on corticalgyrification, what should my contrast matrix look like?The hypothesis is that the gyrification index is diminished for epilepticpatients, probably more when there is bilateral focus.I know that we need as many number as regressors, so I expect there to be 10numbers, is it so?Thank you so very much for clarifying this point,Kenza

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effect size for conjunction analyses?
by Caspar M. Schwiedrzik 02 May '14

02 May '14

Hi! I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and I was wondering whether anyone can make a recommendation how to display effect sizes for this kind of analyses? Would you show the effect size estimate corresponding to the p-value that is chosen, an average, or anything else? Thanks, Caspar

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MICCAI PC workshop -- May 16 (fwd)
by Bruce Fischl 02 May '14

02 May '14

FYI ---------- Forwarded message ---------- Date: Fri, 2 May 2014 11:28:11 -0400 From: Polina Golland <polina(a)csail.mit.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: MICCAI PC workshop -- May 16 Hi Bruce, Can you please forward this around? Thanks, Polina. MICCAI PC Workshop May 16, 2014, 1-6pm, CSAIL Kiva and Star Conference rooms (32-D463, 32-G449). MICCAI program committee members will present their work in areas of Medical Image Computing and Computer Assisted Interventions. This is a great opportunity to hear about current research of 20 MICCAI groups from all around the world. Open to public; anyone interested in the topics of MICCAI is welcome to attend. Tentative Program can be found here: http://miccai2014.org/pc_workshop.html.

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per voxel regressor in LME toolbox?
by Marnie Shaw 02 May '14

02 May '14

Dear Freesurfers, Is there a way to include a per voxel regressor in an LME model within the matlab LME toolbox? Just like you can do with mri_glmfit? Cheers, Marnie

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