Freesurfer

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30076 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

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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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map parcellations into DWI space?
by Yerong Li 31 Dec '18

31 Dec '18

External Email - Use Caution Dear FreeSurfer experts: I am trying to map ./mri/aparc.a2009s+aseg.mgz and ./mri/aparc+aseg.mgz into DTI file. Let's say, we have a DTI file with its b-vectors: ./bvals ./bvecs ./data.nii.gz I am trying to use the command from this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat So I used the command : mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz --o dk-in-rawavg.mgz --regheader aparc+aseg.mgz The output file seems not very reasonable. Could you help me with this? Yerong ================================== Can you be more specific about which files you want to map into your DWI space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You will need a registration file which you can obtain with bbregister On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: [Hide Quoted Text] External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh,

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plotting mean T1/T2 values in the different cortical layers
by Anik Dar 31 Dec '18

31 Dec '18

External Email - Use Caution Hi All, I have created cortical surfaces corresponding to 25%, 50%, 75% of the cortex. Now I want to plot the T1/T2 values corresponding to these different layers.I believe I have to use mri_vol2surf. What options in the mri_vol2surf do I need to use to create these T1/T2 maps corresponding to these different layers of the cortex ? Please let me know. Merry christmas and a happy New Year. Thank you, Ani

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Notebook specification
by mustafa amin 30 Dec '18

30 Dec '18

External Email - Use Caution Dear Freesurfer Members, First I would like to introduce myself my name is Mustafa Amin, and I’m planning to do a study to measure the volume of prefrontal cortex, hippocampus, and ventricle of patients with schizophrenia comparing them with control in Medan Indonesia. I read and saw information that freesurfer is capable in doing the measurement, however I am still not sure about what kind of notebook specification that I need to download and install it. For my knowledge, this is the first study that will be done in Indonesia so every explanation and further information about freesurfer and the notebook will make me very grateful. I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here that can share the minimum requirements of the notebook, it will help me a lot to choose which one to buy. Thank you in advance. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

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