Freesurfer

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30088 discussions

Re: [Freesurfer] map parcellations into DWI space?
by Greve, Douglas N.,Ph.D. 03 Jan '19

03 Jan '19

you might try this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 On 12/30/18 1:45 AM, Yerong Li wrote: > 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: >> >> 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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Diagnosing a recon error
by Maksimovskiy, Arkadiy 03 Jan '19

03 Jan '19

Dear Experts, I was wondering if someone might be able to help diagnose a recon error. I used the following command to initiate recon: recon-all -subject RMD002 -i /ncf/anl/anl01/MultiMode/Data/structural/T1_MEMPRAGE_5_RMD002_e1.nii -T2 /ncf/anl/anl01/MultiMode/Data/structural/T2_SPACE_6_RMD002.nii -T2pial -3T -all The recon log indicates an error: recon-all -s RMD002 exited with ERRORS Attached is the log file. I used grep to search through it for “failed” or “error”, but am unable to see any indices of errors, other than this message at the bottom of the log. I would love to hear any info for what might have gone wrong. Thank you for all your help, Arkadiy

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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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