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30099 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 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 MNI 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? Any reply will be highly appreaciated. Thanks All the best. Rujing Zha 2014-05-01 charujing123

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Re: [Freesurfer] using multiple cores
by Lukas.Scheef＠ukb.uni-bonn.de 05 May '14

05 May '14

4 3

Coordinate transformation to average surface space
by ISAAC PEDISICH 05 May '14

05 May '14

Hi All, I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject. By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta reg_avg.lta --iscale --satit and then check and adjust the registration with: tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average These steps work fine, and when I load the average brain in freeview, then load the subject CT with with the registration file reg_avg.lta applied, the two overlap just as they should. However, when I attempt to do the same thing in matlab, some (though not all) of the subjects present a problem. I do the coordinate transformation (as suggested on http://freesurfer.net/fswiki/CoordinateSystems) by applying: inv(Reg_avg) * Tmov * CT_coords with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as reg_avg.lta, and CT_coords as the relevant coordinates in CRS space from the CT (with a vector of ones appended). As I said, some of the scans come out fine, with the coordinates in the correct place on the average surface, while others are very far removed from their correct location. How can I fix this? Thanks, Isaac

3 9

aparc.stats info
by pfotiad＠nmr.mgh.harvard.edu 05 May '14

05 May '14

Hi FS Comminity, I was wondering whether there is a reference that gives the exact definition of the measures reported in the *h.aparc.stats file (i.e. for the measures Integrated Rectified Mean Curvature, Integrated Rectified Gaussian Curvature, Folding Index and Intrinsic Curvature Index). Thank you for your time, Panos

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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

1 0

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

04 May '14

1 0

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

04 May '14

1 0

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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