Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

Extracting cortical thickness from a significant cluster in an independent sample
by Tamara Sussman 03 Jan '19

03 Jan '19

External Email - Use Caution Hello Freesurfer Experts! Thank you in advance for considering this question. I did a cortical thickness analysis (surface-based), and found a significant cluster. I found the average cortical thickness in* this group*, in the .*y.ocn.dat* file, which is great. Now I want to find the average cortical thickness in the same cluster, in a separate group of subjects. I tried using mri_segstats, but it doesn't seem to work: mri_segstats --slabel $label --i $input --nonempty --excludeid 0 --avgwf test.dat --sum Test_SupParietal.sum The error I am getting is: ERROR: cannot do frame average without input volume Any thoughts about a better way to approach this analysis? Thanks again in advance! -T

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Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047
by 허정선 03 Jan '19

03 Jan '19

External Email - Use Caution Thank you for your reply. Is it impossible with 2mm? Unfortunately, the data we collect for the study all have same thickness of voxel. And, there was a problem like the photo below, and only the recon-all.log could be attached to you. Thanks, Jeongson ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Dec 2018 10:13:16 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047 (60827, 60826, 59444) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1812201012130.17732(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Jeongson it certainly looks like something went badly wrong. 2mm may be too thick - we typically recommend <=1.5mm for any voxel direction. Can you send us the recon-all.log? And maybe a snapshot of the volume with the lh.orig.nofix and rh.orig.nofix overlaid? cheers Bruce On Thu, 20 Dec 2018, ??? wrote: > External Email - Use Caution > > Hello Freesurfer developers > I'm starting using FS and I have a problem running recon-all. > #recon-all -s /usr/local/freesurfer/subjects/20180108 -all > I've attached the output to a ERROR image file. > > We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice thickness of 2.0mm. > freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 > > Any help is greatly appreciated. > > Thanks. > > Jeongson ------------------------------

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Which T1 volume to use for coregistration with PET volume
by Matthieu Vanhoutte 03 Jan '19

03 Jan '19

External Email - Use Caution Dear Freesurfer’s experts, I used mri_coreg command to coregister PET image onto T1 volume. Basically, this command coregister PET image onto orig.mgz volume (default target). However, I wonder if T1.mgz wouldn’t be a better target since it has been corrected for inhomogeneities and intensity normalized ? Thanks for helping ! Best, Matt

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mri glm fit matrix is ill-conditioned
by Sahil Bajaj 02 Jan '19

02 Jan '19

External Email - Use Caution Hi experts, I am running following command: mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir Both FSGD and Contrast files are also attached. After I run above command, I get following error (highlighted in red): mri_glmfit --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir gdfRead(): reading PAI_SUI_ONLY_MILD_DEP2.fsgd INFO: demeaning continuous variables Continuous Variable Means (all subjects) 0 SUI 52.4444 2.11403 1 Age 32.1111 7.23332 2 DEP 55.1111 7.83786 Class Means of each Continuous Variable 1 Male 52.0000 32.0000 54.0000 2 Female 52.6667 32.1667 55.6667 INFO: gd2mtx_method is dods Reading source surface /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral cmdline mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir sysname Linux hostname hyperion machine x86_64 user scanlab FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh logyflag 0 usedti 0 FSGD PAI_SUI_ONLY_MILD_DEP2.fsgd labelmask /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/fsaverage/label/lh.cortex.label maskinv 0 glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir Loading y from /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 1e+08 Design matrix ------------------ 0.00000 1.00000 0.00000 1.68188 0.00000 -0.01536 0.00000 -1.67279; 1.00000 0.00000 -0.68326 0.00000 1.09063 0.00000 -0.77969 0.00000; 0.00000 1.00000 0.00000 -0.68326 0.00000 -1.39785 0.00000 2.02720; 0.00000 1.00000 0.00000 -0.68326 0.00000 1.22888 0.00000 -0.14176; 1.00000 0.00000 0.73582 0.00000 -0.29186 0.00000 0.62375 0.00000; 1.00000 0.00000 -0.68326 0.00000 -0.84486 0.00000 -0.26935 0.00000; 0.00000 1.00000 0.00000 1.68188 0.00000 -1.12135 0.00000 0.11341; 0.00000 1.00000 0.00000 -0.68326 0.00000 1.50538 0.00000 -0.65211; 0.00000 1.00000 0.00000 -0.68326 0.00000 -0.15361 0.00000 0.75134; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=1.034183 (col 7), Max=2.816108 (col 8) ... could not determine the cause of the problem Both fsgd and contrast files are created in LINUX, and I also normalized my data using DeMeanFlag 1 ReScaleFlag 1 as suggested here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49123.html Could you please help in resolving this issue? Thanks ! Sahil

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Re: [Freesurfer] the pial and wm are larger than the inflated (beyond the inflated image)
by xi star 02 Jan '19

02 Jan '19

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the pial and wm are larger than the inflated (beyond the inflated image)
by xi star 02 Jan '19

02 Jan '19

2 1

voxel cordinates
by Sadia Sheikh 02 Jan '19

02 Jan '19

External Email - Use Caution Dear Freesurfer experts I am using freesurfer version 6.0. I have extracted ROI's from the aseg.mgz file. Now is it possible to get the cordinates of each voxel for a particular ROI? Thanks in advance Regards Research student

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Freesurfer January 2019