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30086 discussions

Converting surface files to ASCII - order of vertices
by Walsh, Shane W. 04 Aug '20

04 Aug '20

Hi FreeSurfer community, I have a set of .mgh patch files that are mapped to the FsAverage4 atlas. I'd like to do some calculations on the xyz coordinates of the vertices that make up a patch. I've been able to get ahold of these xyz coordinates by using mris_convert to convert FsAverage4 surface files to ASCII. I want to ensure the validity of these calculations, and in that process, I've run into two questions: 1. Do the order of vertices in a surface file match that of a mris_convert'ed ASCII surface file? 2. Do the order of vertices in the patches match that of the mris_convert'ed ASCII file? In an attempt to answer to first question, I used Freeview to compare vertex coordinates in lh.inflated with lh.inflated.asc. I'm able to use Freeview to visualize the surface files and click on any vertex to get its xyz coordinates. However, the set of coordinates given in Freeview seems to be completely different than the set of coordinates given in the ASCII version of the surface file. I think this issue is best demonstrated by an example. If I load subjects/fsaverage4/surf/lh.inflated into Freeview, the first vertex (Vertex 0) is listed at [-36.79, -18.60, 64.82]. Not only is this coordinate different from the one on the first line of lh.inflated.asc, it's not contained anywhere in the file. I looked into if the the coordinates differ by a constant if we assume that they're listed in the same order in both files, but I found this not to be the case. Based on this information, I'm unsure of the answer to my first question. My suspicion is that there is some sort of transform applied to the coordinates. I feel like I would need to figure out the first question before I can answer the second. I've hit a dead end and any guidance on either question would be greatly appreciated. Thank you, Shane Walsh

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using own skull stripped t1
by Julie Ottoy 04 Aug '20

04 Aug '20

External Email - Use Caution Dear freesurfer team I'm trying to use my own skull stripped T1 when running recon-all. For this, I'm doing following steps: 1) run recon-all with -autorecon-1 -noskullstrip 2) mri_convert --in_type nii --out_type mgz -rl ./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz ./FreeSurfer/ID/mri/brainmask.mgz 3) run recon-all with -autorecon-2 and autorecon-3 My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore, when transforming to the size of brainmask.mgz (256x256x256), it deforms. I tried nearest, cubic, and interpolate, but none of them gives actually a good result in terms of retaining the contrast. I was wondering if it is important to keep a good contrast for brainmask.mgz , or whether this brainmask.mgz is just used to determine the brain borders for segmentation. (ie.: in which steps of recon-all is the brainmask.mgz actually used?) Any recommendations? Thank you! Julie

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Re: [Freesurfer] How to do permutation for multiple comparison correction?
by Xiaojiang Yang 04 Aug '20

04 Aug '20

External Email - Use Caution Thank you! Now I see how permutation works. So given about 100-200 subjects in the normal group, doing 1000 permutations is of no help. In fact, in my cortical thickness abnormality test, no matter how many times of permutations I take, the original non-permutated data is the only one arrangement I can observe that has a "big" cluster area - all permutated data has no cluster of big continuous area (given the vertex-wise threshold). So, permutations cannot give me a reasonable probabulity distribution of the sampling data, which means I cannot rely on it to reduce False Positives. Very frustrated here. If you have more comments here, please let me know. Thanks. Best Regards, Xiao Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Tue, 04 Aug 2020 08:27:47 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> There are actually only N-1 permutations that you can make: Real matrix: 1 0 0 1 0 1 0 1 0 1 Permutation 1: 0 1 1 0 0 1 0 1 0 1 Permutation 2: 0 1 0 1 1 0 0 1 0 1 On 8/4/2020 10:41 AM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, I am still uncertain how to permutate the data for multiple comparisons. Please help me with a little more details on this. For example, could you give me 2-3 examples of the permutations for the matrix you gave to me? In addition, if you can explain to me in a non-design-matrix way, that would be great. For example, suppose I have 1 subject to be compared to n subjects in a normal group. The number of comparisons is m. So I have m x (1+n) data in total: V_10 V_11 , V_12 , V_13 , … V_1n V_20 V_21 , V_22 , V_23 , … V_2n …… …… …… …… V_m0 V_m1 , V_m2 , V_m3 , … V_mn _ _Could you please explain to me how data should be permutated? Or give me 2-3 examples of the permutations of the above data that could be? _Thank you a lot! Xiao Douglas N. Greve < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from… >Thu, 23 Jul 2020 10:54:17 -0700 < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date… > You would have a design matrix with two columns and rows equal to n+1, eg 1 0 0 1 0 1 0 1 0 1 ... n times you would then permute the design matrix On 7/23/2020 12:06 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, For the first question, you answered "It is unusual, though it should work". Could you please briefly describe the way FS used to permute (based on my notation v0, v1, ... vn)? Or, the usual way to permute?The way I described seems to be the only way I can think of. Looking forward to your help here. Thanks a lot! Xiao Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…>Thu, 23 Jul 2020 07:37:13 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> On 7/21/2020 11:45 AM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, For your questions: 1. "Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space." By "In the ROI", I mean for all vertices listed in the label file. Here, I am talking about a test subject and n control subjects, they are all considered in the same reference subject space - fsaverage. A ROI is defined by a label file for the subject fsaverage. So, I am comparing the test subject and control group on the same ROI region, vertex by vertex. I want to permute points in the test subject and points in all subjects in control groups. I am not talking about permuting vertex locations; I am talking about permuting values (thickness in my case) from subjects on each vertex. For example, for vertex i, I have one value (v0) from test subject, and n values (v1, v2,...vn) from control subjects: test subject control subjects v0 v1, v2, ...... vn One way of permutation would be: test subject control subjects v1 v0, v2, ...... vn Is this a reasonable way to do permutation? It is unusual, though it should work. 2. "Not sure. You cannot discriminate between the groups when you are doing permutation" By doing the permutation many (say 1000) times, I want to get the probability distribution of the sampling (observed or test) data inside the ROI area, so that I can decide if I should reject or accept null hypothesis based on cluster-wise significance level. What problems do you think I have in this idea? That should work. I'm not sure what my original concern was Thanks a lot! On 7/21/2020 1:12 AM, Xiaojiang Yang wrote: External Email - Use Caution Dear FS experts, Instead of using mri_glmfit-sim, I am trying to implement a customized multiple comparison correction algorithm using permutation. Before I implement my own, I want to make sure my permutation idea is correct. So I was looking at how mri_glmfit-sim does the permutation. The link here http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has < http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm%C2%A0has > < http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm%C2%A0has > <http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm%C2%A0has> a simple description for how to do permutation, but I don't quite understand the 1st step: Permute the design matrix. To me, permute the design matrix means permute the matrix rows here, but still hard to understand why permuting matrix rows does the trick. This is pretty standard in permutation. I think Tom Nichols has some basic tutorials on how permutations work. Anyway, I will not use any design matrix in my customized implementation, so it does not matter for now. My problem can be described as follows: if I have a ROI (a label file) on fsaverage, and I have a test subject and a group of control subjects whose thickness values on every vertex in this label are all known. (The test subject and control subjects are all using fsaverage reference space). I want to compare this test subject's thickness within the ROI to a control group of subjects (within the same ROI). This is a multiple-comparison problem, so I want to use permutation to get less FP rate. My question is: How do I permute the test subject's points and control subjects' points in ROI? Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space. My understanding is that: for each point in the label, I randomly re-assign all (1+n) values from (1+n) subjects to these (n+1) subjects (where n is the number of subjects in control group). And when all points in the label are done, this is only 1 permutation. I will need at least 1000 times of permutation to get the comparison statistics. Is my understanding right? Not sure. You cannot discriminate between the groups when you are doing permutation Thank you! Xiao _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] How to do permutation for multiple comparison correction?
by Xiaojiang Yang 04 Aug '20

04 Aug '20

External Email - Use Caution Hi Doug, I am still uncertain how to permutate the data for multiple comparisons. Please help me with a little more details on this. For example, could you give me 2-3 examples of the permutations for the matrix you gave to me? In addition, if you can explain to me in a non-design-matrix way, that would be great. For example, suppose I have 1 subject to be compared to n subjects in a normal group. The number of comparisons is m. So I have m x (1+n) data in total: V10 V11, V12, V13, … V1n V20 V21, V22, V23, … V2n …… …… …… …… Vm0 Vm1, Vm2, Vm3, … Vmn Could you please explain to me how data should be permutated? Or give me 2-3 examples of the permutations of the above data that could be? Thank you a lot! Xiao Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Thu, 23 Jul 2020 10:54:17 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> You would have a design matrix with two columns and rows equal to n+1, eg 1 0 0 1 0 1 0 1 0 1 ... n times you would then permute the design matrix On 7/23/2020 12:06 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, For the first question, you answered "It is unusual, though it should work". Could you please briefly describe the way FS used to permute (based on my notation v0, v1, ... vn)? Or, the usual way to permute? The way I described seems to be the only way I can think of. Looking forward to your help here. Thanks a lot! Xiao Douglas N. Greve < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from… >Thu, 23 Jul 2020 07:37:13 -0700 < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date… > On 7/21/2020 11:45 AM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, For your questions: 1. "Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space." By "In the ROI", I mean for all vertices listed in the label file. Here, I am talking about a test subject and n control subjects, they are all considered in the same reference subject space - fsaverage. A ROI is defined by a label file for the subject fsaverage. So, I am comparing the test subject and control group on the same ROI region, vertex by vertex. I want to permute points in the test subject and points in all subjects in control groups. I am not talking about permuting vertex locations; I am talking about permuting values (thickness in my case) from subjects on each vertex. For example, for vertex i, I have one value (v0) from test subject, and n values (v1, v2,...vn) from control subjects: test subject control subjects v0 v1, v2, ...... vn One way of permutation would be: test subject control subjects v1 v0, v2, ...... vn Is this a reasonable way to do permutation? It is unusual, though it should work. 2. "Not sure. You cannot discriminate between the groups when you are doing permutation" By doing the permutation many (say 1000) times, I want to get the probability distribution of the sampling (observed or test) data inside the ROI area, so that I can decide if I should reject or accept null hypothesis based on cluster-wise significance level. What problems do you think I have in this idea? That should work. I'm not sure what my original concern was Thanks a lot! On 7/21/2020 1:12 AM, Xiaojiang Yang wrote: External Email - Use Caution Dear FS experts, Instead of using mri_glmfit-sim, I am trying to implement a customized multiple comparison correction algorithm using permutation. Before I implement my own, I want to make sure my permutation idea is correct. So I was looking at how mri_glmfit-sim does the permutation. The link here http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has <http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm%C2%A0has> < http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm%C2%A0has > a simple description for how to do permutation, but I don't quite understand the 1st step: Permute the design matrix. To me, permute the design matrix means permute the matrix rows here, but still hard to understand why permuting matrix rows does the trick. This is pretty standard in permutation. I think Tom Nichols has some basic tutorials on how permutations work. Anyway, I will not use any design matrix in my customized implementation, so it does not matter for now. My problem can be described as follows: if I have a ROI (a label file) on fsaverage, and I have a test subject and a group of control subjects whose thickness values on every vertex in this label are all known. (The test subject and control subjects are all using fsaverage reference space). I want to compare this test subject's thickness within the ROI to a control group of subjects (within the same ROI). This is a multiple-comparison problem, so I want to use permutation to get less FP rate. My question is: How do I permute the test subject's points and control subjects' points in ROI? Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space. My understanding is that: for each point in the label, I randomly re-assign all (1+n) values from (1+n) subjects to these (n+1) subjects (where n is the number of subjects in control group). And when all points in the label are done, this is only 1 permutation. I will need at least 1000 times of permutation to get the comparison statistics. Is my understanding right? Not sure. You cannot discriminate between the groups when you are doing permutation Thank you! Xiao _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Change in volume driven by SA or CT?
by Meike Hettwer 04 Aug '20

04 Aug '20

External Email - Use Caution Dear Freesurfer Experts I am trying to get more information about a cluster indicating a change in cortical volume as a function of a continuous variable. I am currently considering different approaches to find out if this change in volume is primarily explained by a change in surface area or cortical thickness. Is there a standard procedure that freesurfer users go for to do this? (Otherwise I would probably extract volume, SA and CT values from the cluster and run an external analysis.) Thanks a lot, Doro

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Recon-all error when refining pial surfaces with T2 FLAIR
by Pankush Kumar 04 Aug '20

04 Aug '20

External Email - Use Caution Hello, I am a student using freesurfer 7.1.0 having some trouble with recon-all on some subjects. I am trying to calculate pial surfaces by adding FLAIR images to my T1 (already processed on recon-all beforehand), but encounter the following error: Starting loop over 121584 vertices vno = 0, t = 1.21632 vno = 20000, t = 3.38757 vno = 40000, t = 8.77043 vno = 60000, t = 11.8685 vno = 80000, t = 14.6273 error: Numerical result out of range error: MRIhistogramLabelRegion: constant image Log is attached. Other subjects get stuck on the vno = 80000 step and run for days without progress. No artifacts in any of the images, but some have obvious structural variation such as enlarged and misshapen ventricles. Thank you, any help would be greatly appreciated! Sincerely, Pankush Kumar

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Local GI vs. Folding Index
by Alexopoulos, Dimitrios 03 Aug '20

03 Aug '20

External Email - Use Caution The aparc.stats file contains a Folding Index measure for each cortical parcellation. How is this measure determined and how is it different from the one calculated using the -localGI flag after precessing a subject? Jim Get Outlook for Android<https://aka.ms/ghei36> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Converting sulc files
by Alexopoulos, Dimitrios 03 Aug '20

03 Aug '20

External Email - Use Caution Is there a command that will convert the ?h.sulc to ascii, i.e. depth at each vertex? Get Outlook for Android<https://aka.ms/ghei36> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mrisurf note for bevin?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 03 Aug '20

03 Aug '20

Hi all, I am using a freesurfer 6 dev version of tkmedit and opening one of my brain scans that was processed through 7.1 (I copy the ?h.pial.T1 -> ?h.pial to accept the -surfs command). I get the note mrisurf.c:4077 trial: 0 nextPendingSIze:2 BEVIN IS LOOKING FOR AN EXAMPLE THAT DOES THIS after one of the pial loads. Is this a subject that the FS devs would like for debugging? Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

Labels from thalamic parcellation
by Jason Smucny 03 Aug '20

03 Aug '20

External Email - Use Caution Hello Freesurfer Team, I am running thalamic parcellation using freesurfer 7.1 and the program (http://freesurfer.net/fswiki/ThalamicNuclei) is outputting thalamic labels e.g. 8108, 8109, 8208 etc. I was wondering if you might point me towards a dictionary so I know which thalamic subregion corresponds to each numbered label. Thank you, Jason

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