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30088 discussions

Freeview error
by Md. Mamun Al-Amin 27 Sep '18

27 Sep '18

External Email - Use Caution Dear Experts I have been encountered a problem opening Freeview window in Mac Terminal. Could you please help me troubleshooting this problem? Here is the screenshot. Thanks in advance. -- Kind regards Md. Mamun Al-Amin ------------------------------ *PhD Candidate, Queensland Brain Institute* *The University of Queensland* *Building 79, St Lucia QLD 4072* *https://qbi.uq.edu.au/profile/877/md-mamun-al-amin <https://qbi.uq.edu.au/profile/877/md-mamun-al-amin>*

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Re: [Freesurfer] Best way to update Freeview
by Maksimovskiy, Arkadiy 27 Sep '18

27 Sep '18

Hi everyone, I was able to download Freeview- the link now works. However I am having an issue with starting this version. bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer_6.0/ bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer_6.0/ FSFAST_HOME /Applications/freesurfer_6.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Volumes/DrEmetBrown/ MNI_DIR /Applications/freesurfer_6.0/mni bash-3.2$ freeview dyld: Library not loaded: @rpath/QtWidgets.framework/Versions/5/QtWidgets Referenced from: /Applications/freesurfer_6.0//Freeview.app/Contents/MacOS/Freeview Reason: image not found Abort I am running a Mac OS HighSierra (10.13.6). It seems that people had similar issues in the past, but not quiet like this one. I would love to hear any tips on how to fix it. Thanks, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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ERROR: dimension mismatch between X and contrast
by Backhausen, Lea 27 Sep '18

27 Sep '18

External Email - Use Caution Dear FreeSurfer experts, I get this error message when running group analysis on cortical thickness using glmfit: ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols Please find attached the FSGD file, the contrast file and the terminal output below. I want to do ANCOVA with three groups (ADHD, COM and TD) controlling for the effects of age and IQ. So I assume the regressors would be ADHD COM TD age IQ and my contras matrix 1 -1 0 0 0 1 0 -1 0 0 according to information from these two tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V and https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V. Can anybody help me out? Where am I wrong? Why does glmfit assume X has 9 cols? Any help would be much appreciated, thank you in advance! Best Lea Terminal Output: mri_glmfit --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir gdfRead(): reading FSGD/ADHD_COM_TD_orig_age_IQ.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 13.6015 1.73148 1 IQ 107.288 11.1649 Class Means of each Continuous Variable 1 ADHD 13.7193 104.3478 2 COM 12.8657 105.3929 3 TD 14.0119 112.3784 INFO: gd2mtx_method is dods Reading source surface /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.839844 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS cmdline mri_glmfit.bin --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir sysname Darwin hostname edr06188.dip.tu-dresden.de machine x86_64 user Lea FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh logyflag 0 usedti 0 FSGD FSGD/ADHD_COM_TD_orig_age_IQ.fsgd labelmask /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir Loading y from /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 1027 Matrix condition is 4.07619e+06 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 149926 voxels in mask Saving mask to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74490.844410 ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols

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amygdala segmentation using additional scan error
by 오진영 27 Sep '18

27 Sep '18

External Email - Use Caution Hello, freesurfer experts I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala with additional scan. I already ran segmentation of hippocampal subfields and nuclei of amygdala with only T1 image, using segmentHA_T1.sh command and succeeded. After success of segmentation of amygdala with T1 image, I tried to run segmentation again with additional scan(T2 image) to get more reliable results. However, when I use command segmentHA_T2.sh, I got the following error: Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628) And the last few lines before the error are below: *Fitting mesh to image data mask took 264.2808 seconds* *Transforming points* *Transforming points* *Wrote image to file image1.mgz* *Wrote image to file image2.mgz* *INFO: dst volume info differs from the one stored in lta. gets modified now.* *volume geometry:* *extent : (232, 469, 208)* *voxel : ( 0.3333, 0.3333, 0.3333)* *x_(ras) : ( 0.0000, -1.0000, 0.0000)* *y_(ras) : ( 0.0000, 0.0000, -1.0000)* *z_(ras) : ( 1.0000, 0.0000, 0.0000)* *c_(ras) : (-21.1788, -1.8961, 3.8447)* *file : T2isotropic.mgz* *volume geometry:* *extent : (256, 256, 256)* *voxel : ( 1.0000, 1.0000, 1.0000)* *x_(ras) : ( 0.0000, -1.0000, 0.0000)* *y_(ras) : ( 0.0000, 0.0000, -1.0000)* *z_(ras) : ( 1.0000, 0.0000, 0.0000)* *c_(ras) : ( 2.3212, 8.6039, -21.1553)* *file : /Users/mnd_mac/Desktop/JY_surfer/sub_05_T2.nii* *Constructing image-to-world transform from header information (asmr1.mgz)* *Constructing image-to-world transform from header information (/Users/mnd_mac/Desktop/JY_surfer//recon_sub_05/tmp/hippoSF_T1T2_v21_T2_left/imageDump.mgz)* *Wrote image to file asmr2.mgz* *This file does not contain MRI parameters* *This file does not contain MRI parameters* *This file does not contain MRI parameters* *In an assignment A(:) = B, the number of elements in A and B must be the same.* *Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)* *MATLAB:subsassignnumelmismatch* *Darwin MnD-macui-iMac.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64* and I have no idea how to solve this problem out. I use the dev version of freesurfer. T1 scan image and T2 scan image of participant were taken on the same day. If you have any recommendations, please send me the email back. Thanks! Jinyoung

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Extra sub-cortical mass
by Alec Siegel 26 Sep '18

26 Sep '18

External Email - Use Caution Hello, I'm a computer science student interested in 3D printing a model of my brain. I've successfully used freesurfer to create STL files of both my cortical and sub-cortical regions. Everything looks good except for some non-symmetrical excess mass below my cerebellum on my sub-cortical file. I'm certainly no neurologist, but it doesn't look quite right to me. I would appreciate it if someone would point out I can correct this, I am certainly willing to provide any needed files. Thanks, Alec Siegel

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Re: [Freesurfer] Ynt: Ynt: linux data and macbook
by Maksimovskiy, Arkadiy 26 Sep '18

26 Sep '18

In case this is helpful, using a Docker (such as below), might be a helpful solution for reducing cross-platform reproducibility issues: https://mindboggle.readthedocs.io/en/latest/ -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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WM edits
by Alexopoulos, Dimitrios 26 Sep '18

26 Sep '18

External Email - Use Caution I'd like to make edits to correct the superior regions where then pial surface truncates WM (images below). Would it be more useful to use controls points in the WM or add WM to the wm.mgz. Jim [cid:image001.png@01D455A8.BDD9A0D0][cid:image002.png@01D455A9.1DD52950] ________________________________ 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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Cortical ribbon and the hippocampus
by Alon Baram 26 Sep '18

26 Sep '18

External Email - Use Caution Hello, I'm trying to understand what do the files ?h.ribbon.mgz include as part of the ribbon mask. It's obvious they include all the GM between the white and pial surfaces, but they also include some voxels which are not GM (according to aparc+aseg.mgz). For example, ?h.ribbon seems to include some of the hippocampus, but not all of it (seems to me like it's the ventral/inferior part that is included). How is it decided what is included in ?h.ribbon and what isn't? Thanks!

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Re: [Freesurfer] Reporting Cohen's D for a significant cluster
by Maksimovskiy, Arkadiy 26 Sep '18

26 Sep '18

Hi Bruce, I wanted to follow up on this as I was unsuccessful in doing what you suggested using Freeview (2.0)- entering numbers into the window does not change anything. Might there be another way to find out the Cohen’s D? Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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amygdala segmentation atlas influence
by Emily K Clarke 26 Sep '18

26 Sep '18

External Email - Use Caution Hello all, I have run the amygdala segmentation in my datasets to obtain volumes of nuclei. I am aware from the fswiki that the volumes should be interpreted with caution because of the reliance on the atlas. When running FS, is there a way to get some metric about how much the segmentation relied on the atlas relative information from the T1 being segmented. If this metric is not available to the user, is some version of it calculated by the software and therefore available internally. Thanks in advance for your help! raj

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