Freesurfer May 2014

freesurfer@nmr.mgh.harvard.edu

139 participants
206 discussions

When/What to edit?
by O'Shea,Andrew 05 May '14

05 May '14

Hello FS experts, I have had a continuing curiosity regarding when/what to edit in FS cortical reconstructions. The wiki does a good job at showing how to deal with large scale problems, (i.e. invalid tal transformation, white matter not being recognized, large portions of the skull included in the surface) however I have yet to come across much that guides edits besides a "trained eye". How do we know when a problem is "big enough" that it needs attention? Are there any tool boxes/ quantitative guidelines that may help someone determine which scans need edits? I know QA tools outputs info on SNR/white matter intensity and I have looked for outliers here. However, I was wondering how else to automate/guide the decision process. Much of the discussion I have seen on this topic in manuscripts is either vague or nonexistent. Does anyone know of any manuscripts that have compared "raw" FS datasets to "selectively edited" datasets? What sort of effects do edits make in the grand scheme of a study? One could imagine problems with someone editing the data when they are knowledgable of the study's hypotheses and groups. Any additional info or guidance on this topic would be much appreciated. -Andrew

3 2

Fwd: Fwd: Optseq2: ntp
by Conchy PF 05 May '14

05 May '14

Hi everybody, I have a question about optseq2. In order to calculate ntp, I need to know the total time that my run lasts. Thus, I do not know whether I have to include in the total trial time the fixation cross time (500 ms) + event (1000 ms) + variable ISI average (1 s, ranging from 500 to 4000 ms), or not to include the variable ISI, increasing the total run time by 50% at the end. On the other hand, I have the same dilema about the event command (ev) and the duration of the stimulus that I should set. Also, if I use the fixation cross plus event duration, they would add together 1.5 ms, while the tr is 2. According to the program's instructions, the stimulus duration must be a multiple of tr. Then, I guess that I should use to calculate the whole thing the fixation cross (500 ms) + the event (1000) + the variable ISI average (1 s). Am I right? Thank you very much and kind regards, C

2 1

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

2 2

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

2 2

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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Freesurfer May 2014