Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

mkanalysis-sess and mkcontrast-sess scripts for FIR analysis
by Fang, Angela,Ph.D. 19 Oct '20

19 Oct '20

Hello Freesurfer community, I am trying to configure first level FIR analyses and contrasts for an event related task based on the design in the attached paper. I have 3 conditions (self, other, case) plus fixation. I believe the time window is 30 sec with 11 frames, 12 time points and the TR = 2.5 sec: Timecourse: -5 -2.5 0 2.5 5 7.5 10 12.5 15 17.5 20 25 Timepoint: 0 1 2 3 4 5 6 7 8 9 10 11 The paradigm file for 1 of my 3 runs (attached) was developed using Optseq with Doug’s help, and I believe the TER in this case would be 2.5 sec. Do the following commands look correct? mkanalysis-sess -analysis selfotherfir.lh -TR 2.5 -refeventdur 2.5 -paradigm self.other.par -event-related -fsd bold -surface fsaverage lh -nconditions 3 -timewindow 30 -fir 5 30 -TER 2.5 -per-run mkcontrast-sess -analysis selfotherfir.lh -contrast self-v-other -a 1 -c 3 -no-sumdelays -rmprestim I want to be able to view timecourses at each time point (hence the -no-sumdelays flag) in tksurfer (or freeview) but I am not sure about using the -rmprestim flag. Is there any instance when I would not want to remove baseline shifts? Thanks for your help! Angela Angela Fang, Ph.D. Assistant Professor of Psychology, Harvard Medical School Department of Psychiatry, Massachusetts General Hospital OCD and Related Disorders Program 185 Cambridge Street, Suite 2000 Boston, MA 02114 Email: afang(a)mgh.harvard.edu<mailto:afang@mgh.harvard.edu> Phone: (617) 643-7717 Fax: (617) 643-3080

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fwhm values for gyrification index analysis
by vittal korann 19 Oct '20

19 Oct '20

External Email - Use Caution Hi Doug I'm analyzing the gyrification values between schizophrenia and healthy volunteers. While performing group analysis in QDEC, I encountered an error when setting the smoothing (fwhm) parameter to 25. Here is the error message from the terminal output > fwhm.dat: 66.612034, rounded to 67 > ERROR: fwhm out-of-range (< 1 or > 30)! > Error in Monte Carlo simulation: Error running mri_surfcluster! The same error persists for all smoothing values i.e. 5,10,15,20,25. QDEC works when I set fwhm to zero units. Why it is like this? And what is the ideal value of smoothing kernel (fwhm) for gyrification analysis? With thanks Korann

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Problem of the Mapping Label to the Subject
by 李梦君 19 Oct '20

19 Oct '20

External Email - Use Caution Dear FreeSurfer Developers: My name is Mengjun Li, I am a MD in the Second Xiangya Hospital, Central South University. I compared the cortex, area, volume in the mild traumatic brain injury patients with health control by the FreeSurFer and found the problem when mapping label to the single subjects. There is statistic difference in the area and volume between the mild traumatic brain injury patients and the health control, I defined the statistic difference region as a label on the fsaverage and mapped this label to subjects by the Qdec. Although the label defined on the fsaverage was mapped onto all subjects successfully,the label in the subjects did not match well with the inflated cortex of the subjects. At the same time, the volume and area value of the label have been extracted in every subject and I found that there is no statistic difference between the mild traumatic brain injury patients and health control. I have checked the segmentation of every subjects and it was a good job done by FreeSurFer. Attached figures illustrated the label mapping results. Figure 1: the label defined on the fsaverage Figure 2: the lateral view of the label in the subjects Figure 3: the inferior view of the label in the subjects FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra I am sending this email for help since I am not sure how to fix this problem. Looking forward to hearing your reply! Thank you very much! Best wishes Mengjun Li Second Xiangya Hospital Central South University.

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Creating ROI from sig.mgh
by Basavaraju, Rakshathi 19 Oct '20

19 Oct '20

External Email - Use Caution I have run a vertex based gyrification index analysis. Now I want to create a mask/ROI from the cluster of vertices which are above the threshold of 3 in sig.mgh file (p<0.001). Which command should I use for this purpose? Is it mri_mask? or mri_vol2roi? Next how do I extract the GI value (a numeric) from the above obtained ROI from individual scans? If anyone has done anything similar with thickness or volume (which I am sure many would have done), it would be helpful if you guided me. Eagerly waiting for your response. Thanks, Dr. Rakshathi Basavaraju (MD Psychiatry) Postdoctoral Research Scientist Taub Institute for Research on Alzheimer's Disease and the Aging Brain Columbia University Medical Centre 622 West, 168th Street, New York - 10032 E-Mail: rb3419(a)cumc.columbia.edu<mailto:rb3419@cumc.columbia.edu> https://indiaalliance.org/fellow/rakshathi-basavaraju

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Re: [Freesurfer] Error sending tcl command
by Kothapalli, Satya 19 Oct '20

19 Oct '20

External Email - Use Caution Hi Expert, I am trying to render the surface maps using tksurfer command in the freesurfer VDI. The data was rendered on the brainmask , however the options for this maps are not appeared (as shown in the figure). [cid:image004.jpg@01D6A27B.5A1522A0] Further I found the error message on the command window that related to tcl command as shown here. I would appreciate if you can provide the possible solution to this issue. [cid:image001.png@01D6A279.F78D6670] Thanks, Satya. ________________________________ 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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Help with creating contrast matrix - 6 classes and 3 variables
by Paul Dhami 19 Oct '20

19 Oct '20

External Email - Use Caution Dear Freesurfer community, I am having trouble with my contrast matrix, and would greatly appreciate any help with this. I have 2 categorical variables, sex (2 levels) and training type (3 levels). I also have three (continuous) variables: Age, percentage reduction in depression scores, and number of sessions. I would like to assess the correlation between cortical thickness and % reduction in depression scores, while accounting for the effects of sex, training type, age, and number of sessions as nuisance variables. Below is 1) my command line, 2) the FSGD fiile, and 3) the design matrix 1. mri_glmfit.bin --y MDD-lh-thickness.mgh --fsgd Reduction_Correlation.fsgd.txt --C ME_ReductionCorrelation_Contrast.txt --fwhm 20 --surf fsaverage lh --glmdir /Users/prabhjotdhami/Desktop/CorticalThickness/Data/myGLM 2. GroupDescriptorFile 1 Title MDD_correlation Class MaleMaxT Class MaleKahn Class MaleNone Class FemaleMaxT Class FemaleKahn Class FemaleNone Variables Age HRSD_Reduction SessionNumber Input yct-001 FemaleMaxT 24 62.5 20 Input yct-002 MaleKahn 18 70 20 Input yct-004 MaleMaxT 21 50 20 Input yct-005 MaleMaxT 24 25 20 Input yct-006 FemaleKahn 24 65.2173913 20 Input yct-012 FemaleKahn 17 71.42857143 20 Input yct-013 MaleMaxT 22 53.84615385 20 Input yct-014 FemaleMaxT 19 63.63636364 20 Input yct-015 FemaleMaxT 16 80.95238095 20 Input yct-016 FemaleKahn 24 65.2173913 20 Input yct-017 FemaleKahn 22 55 20 Input yct-018 FemaleMaxT 18 82.60869565 20 Input yct-019 MaleKahn 16 85 20 Input yct-020 FemaleMaxT 22 85 20 Input yct-021 MaleMaxT 24 81.81818182 20 Input yct-022 FemaleKahn 21 70.83333333 20 Input yct-023 FemaleMaxT 20 52 20 Input yct-024 MaleKahn 16 73.68421053 20 Input yct-025 MaleKahn 21 23.80952381 20 Input yct-026 FemaleMaxT 20 78.26086957 20 Input yct-027 FemaleMaxT 17 20 20 Input yct-030 FemaleMaxT 19 52 20 Input yd-p002 MaleNone 20 54.54545455 10 Input yd-p006 FemaleNone 23 30 10 Input yd-p008 MaleNone 22 44 10 Input yd-p010 FemaleNone 16 50 10 Input yd-p014 FemaleNone 22 3.846153846 10 Input yd-p015 MaleNone 19 10 10 Input yd-p022 FemaleNone 24 37.03703704 10 Input yd-p026 FemaleNone 21 47.61904762 10 Input yd-p027 MaleNone 23 31.57894737 10 Input yd-p032 FemaleNone 21 75 10 Input yd-p033 MaleNone 24 22.22222222 10 Input yd-p034 FemaleNone 22 25 10 Input yd-p035 MaleNone 24 30.43478261 10 Input yd-p047 MaleNone 16 78.26086957 10 Input yd-p048 MaleNone 17 20 10 Input yd-p051 FemaleNone 18 45 10 Input yd-p052 FemaleNone 20 47.82608696 10 3. 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 Any help would be greatly appreciated. Thank you, Paul

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amygdala segmentation on anatomy
by Elena Aggius-Vella 19 Oct '20

19 Oct '20

External Email - Use Caution Dear freesurfer, This is Elena Aggius Vella. I'm writing to ask for your help. I need to do amygdala segmentation based on anatomy.... I see freesurfer has a nice tool to do it, but i'm new in freesurfer. Is it possible to have any help on this? many many thanks elena

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Qdec - talairach to vertex for display purposes
by Paul Dhami 19 Oct '20

19 Oct '20

External Email - Use Caution Dear Freesurfer community, I have an experiment in which participants received brain stimulation using anatomical coordinates which I have in talairach space. I have run a whole-brain analysis using qdec, and I have a surviving cluster. For display purposes, I would like to show that the coordinates that were stimulated fall within this cluster. Is there a way to plug in talairach coordinates within the qdec display so that the cross hair (or some sort of other marking) appears at that specific corresponding vertex? Thank you, Paul

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The usage about annotation view
by 1248742467 19 Oct '20

19 Oct '20

External Email - Use Caution hello, FreeSurfer  I have loaded rh.pial and rh.aparc.2009s.annot, why my version does not have the label view option that can see the annotation? Is it a version issue? My FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Looking forward to your reply  

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Put the updated vertex_label into .annotation
by 1248742467 19 Oct '20

19 Oct '20

External Email - Use Caution hello, After I updated the vertex_label of rh.aparc.a2009s.annot with an algorithm, now I want to replace the vertex_label in the .annot with the updated vertex_label, mainly to see the effect of the segmentation, do you know what to do ? if you know, please give me a example looking forward to your reply

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Freesurfer October 2020