Freesurfer

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19 participants
30132 discussions

mri_cvs_register for fMRI
by Peter Sperrer 05 Aug '20

05 Aug '20

External Email - Use Caution Dear FreeSurfer experts, My goal is to morph fMRI (data in voxel space) for best possible intersubject GM-overlap. I am using /mri_cvs_register/ as it seemed like a perfect tool for this. I have already run /recon-all /on the anatomical scan (160x239x200 voxels at 1x1x1mm) as well as /mri_cvs_register --mov [anatomical] --mni/. The resulting normalized brain (/final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz/) looks pretty good, maybe except for a remaining piece of skull, which does not seem to have impaired the brain data, though. // Functional data has been ST-corrected, realigned and coregistered to the anatomical data in SPM. Unfortunately, when I try to morph the fMRI images using /mri_vol2vol --mov [PreprocessedFunctional.nii] --o [MorphedPreprocessedFunctional.nii] --m3z cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --targ cvs/final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz/ I end up with a strangely distorted, cropped and ill-oriented image. The file size and resolution is also enormous. First of all, do you have any suggestions on what could have gone wrong? Is there a better way than using mri_cvs_register to normalize fMRI data so gyri and sulci between subjects match? Since I do not need such high resolution for smoothing and analysis, is there a better way than just down-sampling after the morph? Please excuse if any of these questions seem to have obvious answers to you, I am rather new to using FreeSurfer. I have already searched the mailing list archive and did not find a solution to my problem but only a slightly related problem from 2013 (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30673.html) In the solution it was also hinted that morphing fMRI data might be further supported in the future. Is there a tool or function which has been developed since then? I appreciate your advice! Thank you very much! Kind regards Peter Sperrer

3 6

Local GI error
by Alexopoulos, Dimitrios 05 Aug '20

05 Aug '20

External Email - Use Caution We are getting an error running the -localGI utility on a subject. The screen output is below and the output recon-all log file is attached. Any help would be appreciated. Jim . . lGI for vertex number 4101 of the outer mesh is 1.4993 lGI for vertex number 4201 of the outer mesh is 0.6245 lGI for vertex number 4301 of the outer mesh is 0.97077 lGI for vertex number 4401 of the outer mesh is 1.5549 lGI for vertex number 4501 of the outer mesh is 0.57803 lGI for vertex number 4601 of the outer mesh is 5.1163. ... remeasuring lGI value for vertex iV = 4701. It may take a few minutes. WARNING -- Problem for vertex iV = 4701, lGI value is aberrantly high (lGI=23.2391)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/data/shimony/shimony2/neonatal/MOD1467_V1_a/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc' ! Linux linux1 3.10.0-514.10.2.el7.x86_64 #1 SMP Fri Mar 3 00:04:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MOD1467_V1_a exited with ERRORS at Tue Aug 4 11:11:15 CDT 2020 For more details, see the log file /data/shimony/shimony2/neonatal/MOD1467_V1_a/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ________________________________ 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.

1 0

Questions about speed up the longitudinal processing
by Yang Molly 05 Aug '20

05 Aug '20

External Email - Use Caution Hi list, I tried to run some longitudinal data with two time points with the latest version Freesurfer (7.1.0) on the Ubantu 16 system. "recon-all -base" with two time points need 5 hours to complete on my PC, and recon-all -long need 2 hours. I try to use the command "recon-all -long pre009 sub009base -parallel" and it went with errors. I was wondering if I can use other flags to speed up the recon-all -base and recon-all -long for each terminal. Thank you Molly

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Quetion about thalamic nuclei segmentation in freesurfer v7
by Haewon Roh 05 Aug '20

05 Aug '20

External Email - Use Caution Hi. I have a quetion about thalamic nuclei segmentation process in freesurfer v7. Now, I’ve got a large amounts of patients samples which were already pre-processed using “recon -all” pipeline in freesurfer version 6, but I want to know their specific volumes of thalamic nucleis or subsegmentations using freesufer 7. So, due to a quite large number of samples, I feel that it will take a very long time to do preprocessing again in freesurfer 7 and , if possible, without re-pre-processing in freesurfer v7.0, I’d like to do additional subsegmentation of thalamus as well as hippoamygdala. So I’ like to ask if these kinds of thalmic nuclei subsegmentaion or Hippo-amygdala subsegmentation which was newly-introduced in freesurfer 7.0, can be done using data which was pre-processed in freesurfer 6.0 already. (Is it possible to do thalamic segmentaiton using segmentThalamic nuclei pipeline in freesurfer 7 for the data already pre-processed in freesufer 6.0 ? ) and I am also very curious if their results will be different from the results which was made using only freesurfer v7 from pre-precessing? Best, H Roh.

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The input for Petsurfer
by Hengameh Marzbani 05 Aug '20

05 Aug '20

External Email - Use Caution Hello Freesurfer developers, I have PET images for brain and I want to analyze them with Petsurfer. But I don't have T1-weighted MRI of each subject. What should I do? Is it possible? Thank you in advance, Best regards, Hengameh

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Re: [Freesurfer] bad interpreter: No such file or directory error
by fsbuild 05 Aug '20

05 Aug '20

External Email - Use Caution Hello Hengameh, You probably need to install tcsh (and or csh). I would try, $ sudo apt-get install csh tcsh - R.. On Jul 30, 2020, at 09:19, Hengameh Marzbani <marzbani91(a)gmail.com> wrote:        External Email - Use Caution        Hello Freesurfer developers,I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine. Also, freeview works by simply typing the freeview command.However,I have tried to run recon-all. but, I have got the following error message on all PCs:bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directoryalso The build-stamps.txt file contents:freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297bThank you in advance, Best regards, Hengameh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

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

1 0

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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