Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] PetSurfer
by Shane Schofield 27 Mar '19

27 Mar '19

External Email - Use Caution Hi Doug, thanks for the explanation. My question is more related to how we might go about knowing what are the high binding regions for any tracer? If I am going to do an FDG-PET study, will the HB region parameters be different from a [11C]-PK11195 study for example? And secondly, might be these be different across subjects? Thanks for your help. Previous email :You should read up on the MRTM2. Basically, when you run MRTM1, it computes a separate k2 for each voxel eventhough the k2 should be the same across the entire brain (since it actually refers to the reference region). With MRTM2, you estimate the single k2 value from high binding regions.

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Thalamic nuclei segmentation
by 郑凤莲 27 Mar '19

27 Mar '19

External Email - Use Caution Hi experts, I have segmented the thalamic nuclei into 25 nuclei using the new FS version. However, when I input "freeview -v nu.mgz -v ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview, just nu.mgz. What's the matter? Please help me. I am looking forward to your reply. Thanks very much. Sincerely, Zheng

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Re: [Freesurfer] Longitudinal Two Stage Model Question
by Arsenije Subotic 26 Mar '19

26 Mar '19

External Email - Use Caution Hi Doug, Thanks for getting back to me so quickly. Just to confirm, I can proceed to use the mri_glmfit analysis as shown on the group level tutorial? I'm not sure I can do the paired analysis since my subjects in one group are not matched with those from the other and one group has more participants than the other. I will however use the the link you gave me to compute the difference within one of my groups. Best, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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Left and right pial surfaces crossing in medial cortex
by Matthieu VANHOUTTE 26 Mar '19

26 Mar '19

External Email - Use Caution Dear FS' experts, Using both T1 and FLAIR in recon-all to improve pial surfaces, I often have the case where pial surfaces from the left and right hemisphere are crossing in medial cortex (see attached images). Is it anormal and bad ? If so, How could I fix it ? Best, Matthieu

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Re: [Freesurfer] Longitudinal Two Stage Model Question
by Arsenije Subotic 26 Mar '19

26 Mar '19

External Email - Use Caution Sorry, I was actually able to compile a FSGD file that has a single line for each subject (containing the fsid base) along with gender and age at baseline. I ran this through the mris_preproc command (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) in order to stack the spc files which were previously cached. I guess my question really is can I now simply continue on and use the mri_glmfit instructions on the group analysis tutorial page or is there a special procedure because I am dealing with longitudinal data? I was planning on simply using contrasts i had designed before for my cross-sectional analysis, controlling for age at baseline and gender. Thanks and my apologies for all the questions! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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PetSurfer
by Shane Schofield 26 Mar '19

26 Mar '19

External Email - Use Caution Hello PetSurfer Developers On the tutorial page, I do not understand this part: --km-hb 11 12 13 50 51 52 specifies the ROIs to use as the high-binding region if using MRTM2. This creates km.hb.tac.nii.gz with the value for the high-binding region for each time point. What exactly is a high-binding region and how do these inputs affect the rest of the estimation? If I do not know what the high binding regions for a tracer are, may I leave this blank? Thank you.

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How to improve recon all on subjets with hight atrophy level like Alzheymer patients?
by Barbara Micaela Duarte Abritta 26 Mar '19

26 Mar '19

External Email - Use Caution Hello everyone, recently I have started to analyze a new sample of subjets which is made up of people with Alzheimer's, due to this pathology several of my subjects have a high level of atrophy in subcortical and temporal areas of the brain, which causes several errors in the pial surface as a wm surface. So to make both surfaces more accurate I tried to put some control points but in many places this solution was not enough due the level of inaccuracy. Is there any solution for this problem? I will appreciate if you could offer any suggestions to solve this problem. Regards Bárbara

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mkanalysis-sess with a customized HRF
by Francesca Strappini 26 Mar '19

26 Mar '19

External Email - Use Caution Dear Freesurfer's experts, I would like to use a customized HRF with mkanalysis-sess. Is there a way to do it? Thanks! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Longitudinal Two Stage Model Question
by Arsenije Subotic 26 Mar '19

26 Mar '19

External Email - Use Caution Hello, I am doing a longitudinal analysis for which I have already qcached my data using the long_mris_slopes command. I am having issues figuring out how to run the mri_glmfit command for my longitudinal two stage model. I'm interested in comparing the spc over time between two groups after controlling for age and gender. The tutorial on the longitudinal two stage model however only shows how to do it for one sample. Am I still expected to use contrasts and make glm directories like the cross-sectional group analysis tutorial suggests? I was just confused because the code is different. I have a longitudinal table so I assumed that would be enough, but do I still need to make a FSGD file that is basically the same as the longitudinal file? Thank you for your help, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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Re: [Freesurfer] mris_fix_topology stuck running
by Soichi Hayashi 26 Mar '19

26 Mar '19

External Email - Use Caution Bruce, I am still going through the wiki, but I found the mri/brainmask.mgz contains a lot of non brain voxels like these.. [image: Screenshot from 2019-03-26 11-56-48.png] Could this be the cause of the problem? Maybe Freesurfer had a problem generating a good brainmask? Does this create the high number of vertices that needs to be corrected? Soichi On Tue, Mar 26, 2019 at 10:46 AM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Soichi > > look at the inflated.nofix in the 3D view, not the orig.nofix. You can > check out our tutorial here: > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_free… > > > although there may be a better one (hopefully someone else will chime in > if > so) > > cheers > Bruce > > > > On Tue, 26 Mar 2019, Soichi Hayashi wrote: > > > > > External Email - Use Caution > > > > Bruce, > > Thank you for your help. I'd very much appreciate it. > > > > I've looked at rh.orig.nofix / rh.inflated.nofix, but I couldn't really > find anything out of > > ordinary.. from my layman's eyes. > > > > Screenshot from 2019-03-26 10-35-42.png > > > > Could you point me to the wiki you mentioned? > > > > Soichi > > > > On Sun, Mar 24, 2019 at 4:37 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > Hi Soichi > > > > that is too big a defect to expect it to fix - more than half the > number > > of vertices in a typical hemisphere. It means something is badly > wrong > > that you need to correct prior to the topo fixer. You can look at > our > > wiki for this kind of thing, but I would start by looking at the > > rh.orig.nofix and the rh.inflated.nofix. Something big is wrong, > like large > > parts of the skull attached to the surface or something like that > > > > cheers > > Bruce > > > > > > On Sun, 24 Mar 2019, Soichi Hayashi wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello. > > > I am trying to troubleshoot an issue where recon_all is not > finishing after >24 hours. > > It's getting > > > stuck when it tries to run the following command. > > > > > > $ mris_fix_topology -rusage > ./output/touch/rusage.mris_fix_topology.rh.dat -mgz > > -sphere > > > qsphere.nofix -ga -seed 1234 output rh > > > INFO: assuming .mgz format > > > reading spherical homeomorphism from 'qsphere.nofix' > > > using genetic algorithm with optimized parameters > > > setting seed for random number genererator to 1234 > > > > > > ************************************************************* > > > Topology Correction Parameters > > > retessellation mode: genetic search > > > number of patches/generation : 10 > > > number of generations : 10 > > > surface mri loglikelihood coefficient : 1.0 > > > volume mri loglikelihood coefficient : 10.0 > > > normal dot loglikelihood coefficient : 1.0 > > > quadratic curvature loglikelihood coefficient : 1.0 > > > volume resolution : 2 > > > eliminate vertices during search : 1 > > > initial patch selection : 1 > > > select all defect vertices : 0 > > > ordering dependant retessellation: 0 > > > use precomputed edge table : 0 > > > smooth retessellated patch : 2 > > > match retessellated patch : 1 > > > verbose mode : 0 > > > > > > ************************************************************* > > > $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman > Exp $ > > > $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ > > > reading input surface > /home/hayashis/Downloads/output/surf/rh.qsphere.nofix... > > > before topology correction, eno=-696 (nv=191488, nf=384368, > ne=576552, g=349) > > > reading brain volume from brain... > > > reading wm segmentation from wm... > > > using quasi-homeomorphic spherical map to tessellate cortical > surface... > > > > > > Correction of the Topology > > > Finding true center and radius of Spherical Surface...done > > > Surface centered at (0,0,0) with radius 100.0 in 9 iterations > > > marking ambiguous vertices... > > > 133741 ambiguous faces found in tessellation > > > segmenting defects... > > > 63 defects found, arbitrating ambiguous regions... > > > analyzing neighboring defects... > > > -merging segment 16 into 0 > > > -merging segment 23 into 0 > > > -merging segment 48 into 0 > > > -merging segment 32 into 22 > > > -merging segment 49 into 47 > > > -merging segment 54 into 51 > > > 57 defects to be corrected > > > 0 vertices coincident > > > Computing Initial Surface Statistics > > > -face loglikelihood: -9.3123 (-4.6561) > > > -vertex loglikelihood: -6.5427 (-3.2713) > > > -normal dot loglikelihood: -3.5794 (-3.5794) > > > -quad curv loglikelihood: -6.0564 (-3.0282) > > > Total Loglikelihood : -25.4907 > > > > > > CORRECTING DEFECT 0 (vertices=65141, convex hull=8287, v0=517) > > > > > > --------------- > > > > > > After displaying the last line, the process seems to be stuck > running with 100% > > cpu (single core) > > > for >24 hours until our batch scheduler kills it. I think the > issue is with my input > > data, but it > > > looks clean and well ACPC aligned, and I don't know what's wrong > with it. The input > > image dimensions > > > are 182 x 218 x 182. > > > > > > Does anyone have any suggestion on how to troubleshoot this > problem? > > > > > > Thank you, > > > > > > Soichi Hayashi > > > Indiana University > > > > > > > > > > > >

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