Freesurfer

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30086 discussions

vertex-wise cortical thickness and whole brain labeling
by Caka 05 May '14

05 May '14

Hi Douglas and all, I have used the ‘recon-all’ command to segment the gray matter of 140 subjects. I have three questions: (1) as the segmentation is done in the individual space, how can I register the results into the template brain? The results includes the surface and the vertex. Is it ‘mri_surf2surf’? (2) If the gray matter is registered into the template brain, then same number of vertex in every region would be obtained. Then what information does the value of each vertex stands? Is it the cortical thickness changes? (3) We know that Freesurfer provides two kinds of brain region labeling, 68 regions and 77 regions in the cerebral cortex respectively. I am wondering whether I can use my own labeling, like 1000 regions? How can I do this? Thank you very much! Qiongmin Ma

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Re: [Freesurfer] LOOK FOR HELP
by 刘东博 05 May '14

05 May '14

Dear Freesurfer: I have some problems with using mri_surf2vol .I'd like to ask if you could help me with this.--volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. And to get this reg I use bbregister. But the result of bbregister is functional to anatomial volume,so I need to inverse the matrix.When I use convert_xfm in fsl I found the register.dat(which is the reslut of bbregister)is not a 4*4 matrix ,it just like dsub1 1.000000 1.000000 0.150000 9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04 1.634627580642700e-02 -3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04 -4.015868902206421e-02 -3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00 -2.181045338511467e-02 0 0 0 1 round Is there a command I can use to inverse the register.dat?Or if I use convert_xfm which part of the register.dat should I use? Thank you ! Yours Dongbo Liu 2014-05-06 10:22 GMT+08:00 刘东博 <lldbuestc(a)gmail.com>: > Dear Freesurfer: > I have some problems with using mri_surf2vol .I'd like to ask if you > could help me with this.--volreg Contains the matrix that maps XYZ in the > reference anatomical to XYZ in the functional volume. And to get this reg > I use bbregister. But the result of bbregister is functional to anatomial > volume,so I need to inverse the matrix.When I use convert_xfm in fsl I > found the register.dat(which is the reslut of bbregister)is not a 4*4 > matrix ,it just like > dsub1 > 1.000000 > 1.000000 > 0.150000 > 9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04 > 1.634627580642700e-02 > -3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04 > -4.015868902206421e-02 > -3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00 > -2.181045338511467e-02 > 0 0 0 1 > round > Is there a command I can use to inverse the register.dat?Or if I use > convert_xfm which part of the register.dat should I use? > Thank you ! > > Yours > Dongbo Liu > >

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Registering functional data to inflated brain
by Sherryse Corrow 05 May '14

05 May '14

Dear FreeSurfer community, We are having some issues registering our functional data (or masks) from FSL to an inflated brain in FreeSurfer. Some of our masks, when registered to the inflated brain and viewed in FreeSurfer, are not showing up on the cortical surface. We have followed web-tutorials for registration but are still having the issue. Any suggestions? Sherryse, University of British Columbia -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre

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comparing two conditions with disproportionate number of trials
by Eryilmaz, Huseyin Hamdi 05 May '14

05 May '14

Dear FS experts, I have a question about the way contrasts work in an event-related design. I am wondering if freesurfer is doing some sort of weighing when it compares two different conditions with incomparable number of trials. For example condition A is represented by 10 trials in the paradigm file, whereas condition B consists of 80 trials. In that case, for the contrast A>B does freesurfer compensate for the small number of trials in condition A? If so, could it lead to inflated activations? We suspected this as in our results, the condition with fewer trials depicted strong activations. Thanks very much for the tips! Best, Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Brain Genomics Laboratory 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462<tel:%2B1%20617%20643%207462>

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Brain Seg Volumes
by Mayer Kristina 05 May '14

05 May '14

Hi there, I am using freesurfer for datas of two year olds. - Is there a special command to run freesurfer on children's data? - When I checked the seg.stats for volumes, I got a higher value for BrainSegVolNotVentSurf (value: 845377 mm3), than for the BrainSegVol (value: 839497) in one patient. The recon-all -all finished without error. How is this possible? Thanks in advance, Kristina

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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

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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

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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 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

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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

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