Freesurfer July 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
160 discussions

area.pial files for fsaverage
by Xiaojiang Yang 23 Jul '20

23 Jul '20

External Email - Use Caution Dear FS developers, I have noticed that for each subject, there are ?h.area and ?h.area.pial files under the $SUBJECT_DIR/$subject/surf sub-directory. According to Bruce's words from here https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23751.html, they are for white surfaces and pial surfaces respectively. But for the fsaverage subject, I only find file ?h.area; there are no ?h.area.pial files existing. Could you tell me why? and where can I get those files? Thanks! Xiao

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Subcortical Structure Pial Line Exclusion
by Angel Hammond 23 Jul '20

23 Jul '20

External Email - Use Caution Hello Freesurfer Experts, I think I may already know the answer to this, but just wanted to check in to be sure. I know that in general when checking the recon for a subject for pial and wm line correctness, that subcortical structure segmentation within those lines is not that important to correct. I was looking at a subject that looks to be be omitting subcortical structures from the pial line and persists for many slices. Is this something that needs to be corrected with wm edits or is this not to be worried about? I included some screenshots of the area. Thanks! Angel Hammond Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Anatomical cluster description table from mri_glmfit-sim?
by Fred Sampedro 23 Jul '20

23 Jul '20

External Email - Use Caution Dear FS experts, From an statistical map obtained by mri_glmfit-sim, say a cache.th13.abs.sig.masked.mgh map, I would like to list all the significant regions from all clusters in the following intuitive way, for instance: Supramarginal gyrus: X vertices, X mm^2, peak T-value=X Superior frontal gyrus: Y vertices, Y mm^2, peak T-value=Y ... That is, the % of significant vertices in the statistical map belonging to each region of the default FS atlas. I know that the cache.th13.abs.sig.cluster.summary file "summarizes" each cluster by a label, but clearly large clusters are made of several different anatomical regions that I would like to report. In other words, I wonder if there's an easy way to obtain a cluster description report similar to the one provided by the xjview toolbox for voxelbased maps in MNI space. I know I could probably achieve it by scripting, i.e. but looping through each ROI extracted from an atlas in fsaverage space and applying a mask with the glmfit map and then computing the overlap and such. But probably there's an easir way, or someone has already thought about it. I tried to search about this topic in the archive but failed to find a clear solution, probably I was not searching by the appropriate words. Thanks a lot in advance,

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outlier detection and remove
by Zeng, Qi 23 Jul '20

23 Jul '20

External Email - Use Caution Hi, I have a question about how to handle outliers in aparc, aseg and tracula results? Usually, each subject has one result regarding one measurement and I detect and remove outliers using barplot. However, for results in freesurfer, we have multiple outcomes for each region in terms of measurements of aparc, aseg and tracula. Do we detect outliers for specific regions or tracts and remove the outliers? Or detect which subjects have outliers consistently for all the regions, and then we remove the subjects? Thank you so much ! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Re: [Freesurfer] How to do permutation for multiple comparison correction?
by Xiaojiang Yang 23 Jul '20

23 Jul '20

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? 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? 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 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

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Motor Cortex Label/Mask
by Anja Samardzija 23 Jul '20

23 Jul '20

External Email - Use Caution Hi, I was wondering if there is a way to extract the whole motor cortex (not the separate regions of the motor cortex, but all of these regions together) of a subject following running recon-all on the subject. Thank you, Anja

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tksurfer - failed to calloc
by Nasr, Shahin,Ph.D. 22 Jul '20

22 Jul '20

Hi Surfers, I get the following error when I use tksurfer for one of our subjects: znzTAGskip: tag=1830834290, failed to calloc 1834378240 bytes! To clarify, this error is only limited to freesurfer version 6.0 and 7. But version 5.3 works fine with the same subject. Regards

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Join the final round of the IronTract Challenge
by Yendiki, Anastasia 22 Jul '20

22 Jul '20

Dear all - This is your chance to enter the final round of the IronTract Challenge. First, make sure to check out the results of round 1 of the challenge, along with other great work in the ISMRM Orientation Modelling & Fibre Tractography oral session, and join us for the Q&A: https://ww5.aievolution.com/ism2001/index.cfm?do=ev.viewEv&ev=3702 Then join us for round 2! This round requires less work by participants, as we have fixed the pre- and post-processing based on the results of round 1, and those steps will be provided. All you have to do is add your favorite orientation reconstruction and tractography method, stir, and serve chilled. Participants will have further opportunities to participate in publications that will result from the challenge. As in the previous round, the challenge is hosted on the QMENTA platform. Detailed instructions are provided here: http://irontract.mgh.harvard.edu/compete-round2/ See you at ISMRM! On behalf of the organizers, Anastasia Yendiki. | Anastasia Yendiki, Ph.D. | Associate Professor, Harvard Medical School | Associate Investigator, Massachusetts General Hospital | Martinos Center for Biomedical Imaging | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 | Web: http://scholar.harvard.edu/a-y

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Postdoc opportunity (2 years), C-Lab, Krakow (Poland)
by Renate Rutiku 22 Jul '20

22 Jul '20

External Email - Use Caution Dear all we are hiring a postdoc with strong experience in MRI data acquisition and analysis to collaborate on a large-scale international project ( https://skuldnet.org/) aimed at exploring the neural architecture of consciousness. For more information see: https://c-lab.pl/news/2020/07/09/post-doc-position.html Application deadline is August 9, starting date flexible this fall. If interested, please contact Prof. Michał Wierzchoń (michal.wierzchon at uj.edu.pl). Job ad in Polish: https://ncn.gov.pl/baza-ofert/?akcja=wyswietl&id=183286

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Re: [Freesurfer] mri_fieldsign error
by Douglas N. Greve 21 Jul '20

21 Jul '20

No, it does not. The only other problem I can think of is that it has something to do with WSL. Do you have a real linux box you can try it on? On 7/17/2020 5:24 PM, Xiaomin Yue wrote: > > External Email - Use Caution > > HI Doug, > > Sorry for the slow response. I got the same “segmentation fault (core > dumped)” error when running the left hemi. I tested it multiple > times. Does this function create a detailed log I can send to you? > > Thanks, > > Xiaomin > > *From: *Douglas N. Greve <mailto:dgreve@mgh.harvard.edu> > *Sent: *Friday, July 17, 2020 1:07 PM > *To: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] mri_fieldsign error > > I was not able to replicate this on my CentOS7 linux box. You sent me > left hemi data, so I ran the command below > > mri_fieldsign --fs fieldsign.71.nii.gz --polar > LOO.wedge.polar.lh.real.nii.gz LOO.wedge.polar.lh.imag.nii.gz --eccen > LOO.ring.eccen.lh.real.nii.gz LOO.ring.eccen.lh.imag.nii.gz --s LOO > --hemi lh --sphere > > But I also noticed that the command that you gave below is for the > right hemi. Do you know if the left hemi works? > > > On 7/11/2020 1:43 PM, Xiaomin Yue wrote: > > * External Email - Use Caution * > > Hi Doug, > > I used FS 7.1 under WSL to analyze retinotopy data. Since the > ring and wedge were presented at a different frequency, the data > had to be analyzed separately for each condition. To get the > field sign, I had to use the mri_fieldsign function to combine > polar and eccen data. However, an error happened with running > mri_fieldsign: “Segmentation fault (core dumped)”. The > following is the command-line output. > > Thanks for your help! > > Xiaomin > > cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala > > cmdline mri_fieldsign --fs > LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar > LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz > LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz > --s LOO --hemi rh --sphere > > sysname Linux > > hostname DESKTOP-SVDQE4Q > > machine x86_64 > > user xiaominyue > > eccen real > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz > > eccen imag > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz > > polar real LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz > > polar imag LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz > > patch (null) > > subject LOO > > hemi rh > > fwhm -1.000000 > > nsmooth -1 > > fieldsign LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz > > usenew 1 > > Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere > > Using spherical coordinates > > Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot > > reading colortable from annotation file... > > colortable with 36 entries read (originally > /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) > > Complex > > Ripping Zeros > > Rot (rad): 0 0 > > surfer: compute_fieldsign2() > > dthresh = 1.5 > > shape = 1 > > nvertices = 153801 > > 0 0 45452 0.03 33.2224 > > 1018 1000 39160 21.33 -18.3959 > > 2055 2000 44734 43.26 33.0783 > > 3148 3000 49793 65.38 0.653687 > > 4344 4000 38626 88.16 16.7555 > > 5529 5000 54149 110.12 -4.90118 > > 6706 6000 61599 133.36 -5.74607 > > 7971 7000 50134 155.88 -17.5589 > > 9165 8000 34182 178.05 -18.9387 > > 10591 9000 59682 200.70 -4.60514 > > 12034 10000 63856 223.18 -4.4884 > > 13297 11000 41007 245.62 27.3489 > > 14938 12000 27365 267.70 -1.40077 > > 16684 13000 23615 289.10 -0.518007 > > 18048 14000 47088 309.37 18.7017 > > 19798 15000 21060 330.11 15.9458 > > 21681 16000 33067 350.27 -11.1953 > > 23173 17000 28744 371.48 -6.18747 > > 25112 18000 27738 392.41 -6.93845 > > 26953 19000 20538 414.47 2.99349 > > 28903 20000 80583 435.98 -0.338512 > > 30319 21000 16251 459.83 -45.2313 > > 32174 22000 17139 483.36 -2.31642 > > 34093 23000 13307 507.02 19.1461 > > 36170 24000 17826 530.65 -10.7575 > > 37683 25000 69324 555.78 -6.17011 > > 39666 26000 14043 583.29 -10.5151 > > 41746 27000 76017 609.92 -0.0112556 > > 43986 28000 84646 636.28 1.24722 > > 46088 29000 9763 664.26 12.7035 > > 48326 30000 92161 694.30 2.03416 > > 50431 31000 99884 724.91 1.20525 > > ./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation > fault (core dumped) mri_fieldsign --fs > $line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz > --polar $line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz > $line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen > ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz > ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz > --s $subjname --hemi $hemi --sphere > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Freesurfer July 2020