Freesurfer

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18 participants
30131 discussions

Recon-all exiting with Errors during surface inflation
by Koch, Erin M. 01 Mar '21

01 Mar '21

External Email - Use Caution Hi all, The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug\" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log. This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 . As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now. Thank you for your help. Best, Erin

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mri_vol2surf resolution warning
by Russo, Andrew William 01 Mar '21

01 Mar '21

Hello, I am moving a 6mm volume from MNI152 to fsaverage for group analysis and I get the following warning: mri_vol2surf --src MNI_6mm.nii.gz --out surf_sm4_lh.mgh --mni152reg --hemi lh --interp nearest --surf-fwhm 4 WARNING: the voxel resolution in the source volume (6,6,6) differs from that listed in the registration file (1,1,1) Do you know if this needs to be corrected or if there is a better method? Thanks for the help, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

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Talairach to RAS conversion
by Nasiriavanaki, Zahra 01 Mar '21

01 Mar '21

Hi Freesurferers I have some talairach coordinates on the cortical surface (extracted from a paper) and I need to see their location on my fmri maps. I used "tksurfer> go to saved point “ to see the location of that coordinate on my map. However, that coordinate is in talairach. Should I convert it to RAS and then save it as a point in tmp folder? If so, could you please let me know how I should convert them from talairach to RAS? Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Hippocampal segmentation
by Alberto Del Cerro Leon 01 Mar '21

01 Mar '21

External Email - Use Caution Hello Freesurfers, I am doing an AAL atlas on freesurfer using mri_vol2surf and editing the labels manually. However when I was editing the labels in tksurfer the hippocampal field is quite bad. I tried to look the segmentation used by you in labels but I didn't find it. How could I segment the Hippocampus????

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Installing freesurfer 6 in a preexisting conda environment
by Bruno Mansur 01 Mar '21

01 Mar '21

External Email - Use Caution Dear community members, I created a conda environment for installing MNE. Now I want to install freesurfer in this same environment to use freesurfer in combination with MNE. Does anyone have already installed and configured freesurfer in an environment and could give me some support with it? The mailing list has no entries related to 'conda environment' and the freesurfer installation guide webpage has no instructions related to this. I would appreciate any help, Best regards -- *Bruno*

2 1

mincRead error
by Michele Valotti 01 Mar '21

01 Mar '21

External Email - Use Caution Hi all, I am running long FreeSurfer and after successfully testing it on my local machine I tried to run it on a server (which should however have the same FreeSurfer version and setup), but I am getting this error mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz --conform ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file miopen: MINC package entry point Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.533/nu1.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc... Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 UTC 2020 x86_64 GNU/Linux recon-all -s base_freesurfer exited with ERRORS at Fri Feb 5 17:45:34 UTC 2021 Any idea what the cause of this might be? Thank you!

3 11

FreeSurfer 7 vs FreeSurfer 6 surface differences
by Mike Schmidt 01 Mar '21

01 Mar '21

External Email - Use Caution I have written a script that reads the binary representations of the vertices and faces from FreeSurfer's surf/{l,r}h.pial files and saves them out unchanged to stl and obj file formats for 3D rendering. I have used it with FreeSurfer 6 and several MRI images, everything working fine. Processing the identical input, a single T1-weighted MPRAGE MRI, FreeSurfer 7 works great and finishes faster than FreeSurfer 6, but we see strange aliasing on the 3D objects. The aliasing is identical if I avoid all of my own code and use mris_convert (from either FreeSurfer version) to generate an stl file from the pial file. I've spent a lot of time debugging, messing with different materials and textures, generating vertex normals at different stages, but I can't find anything that makes any difference except the FreeSurfer version. I have seen several items in the release notes ( https://secure-web.cisco.com/1NYZrvHyVXqxTpZBiwiJ49J4EeeNWwqM6oBe0m-ipN8Gos…) that may be related, but I'm not sure how to go about investigating them. Left cortex images are included, with links if they don't show up in the email, of the same brain processed with FS6 and FS7. These are rendered in Firefox with the three.js library. FreeSurfer 6.0.0 works well with a smooth surface ( https://secure-web.cisco.com/1eQ5Q62ZQtG-RYtwAFFKvhYNEYp7A20Vte8M_v6fEXDVss…) This image is of surf/lh.pial with 149,968 vertices and 299,932 faces. [image: rh_pial_oblique_from_fs6.png] FreeSurfer 7.1.1 results in the same size and shape cortex, but renders strangely with mottled shading of triangles. ( https://secure-web.cisco.com/1JB4zyZhlTjmxoItAOFNb40IoMYhEZt8T-O0MINoKqg8cl…) This image is from the same T1 image as above, but processed with FS7, resulting in 147,292 vertices and 294,580 faces. [image: rh_pial_oblique_from_fs7.png] I'm out of ideas, and the only difference I can find is FreeSurfer version, so thank you to anyone who can point me in the right direction to fix this issue. Mike Schmidt

4 7

must specify a subject id
by 况况 26 Feb '21

26 Feb '21

External Email - Use Caution hello, i downloaded dev version, input FREESURFER_HOME=/home/siying/sharefolder/freesurfer-linux-ubuntu18_x86_64-dev/freesurfer export SUBJECTS_DIR=/home/siying/sharefolder/freesurfer-linux-ubuntu18_x86_64-dev/freesurfer/kuang_dev/kuang_dev_results source $FREESURFER_HOME/SetUpFreeSurfer.sh then run recon-all -s ch2 -i /home/siying/sharefolder/freesurfer-linux-ubuntu18_x86_64-dev/freesurfer/kuang_dev/kuang_dev_data/ch2/ch2.nii -all –qcache -parallel , then and appeared 'ERROR: must specify a subject id', what should i do to solve it? best wishes liangfeng kuang

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Parcellation and volume calculation - Help
by Rosalia Dacosta Aguayo 26 Feb '21

26 Feb '21

External Email - Use Caution Dear all, I would like to parcellate the brain and calculate the volumes, but I am unsure about the command lines I should use. I thought about first doing this: recon-all -subject subjectname -i /path/..../Artico1.nii.gz -all. Should I need any other argument here to get the stats? But then, I am unsure about the next command I should use, which arguments and the image from stats I should use to do the stats. Also, which smoothing should I use? Best, Rosalia

2 1

QDEC/mri_glmfit questions
by Erin Moe 26 Feb '21

26 Feb '21

External Email - Use Caution Hi Freesurfer experts, I’ve been running mri_glmfit and QDEC to investigate the effect of inflammatory markers on cortical thickness and don’t really get much. However, when I extract the cortical thickness values (with aparc/asegstats2table) and run a linear regression with those same inflammatory markers in SPSS, I get several significant results. I’m assuming it might be due to me setting up the QDEC/mri_glmfit analysis wrong. For QDEC I have a two column .dat file with the subject IDs in the FSID column and the inflammatory markers for each participant in the other column and running the QDEC thickness analysis on that and I don’t get much in terms of results. For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC with the exception of formatting. However, we wanted to constrain the analysis to an ROI (entorhinal in this case), I ran mris_preproc with the following command: mris_preproc —fsgd inflammatory_markers.fsgd —cache-in thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out lh.thickness.inflammatory.10.mgh Then fed that output into mri_glmfit as: mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx —surf fsaverage —label entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir The results from this look the same as the QDEC analysis but just masked out for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a Monte Carlo correction with mri_surfcluster. So a few questions: Would running mri_surfcluster on the sig.mgh output from the mri_glmfit analysis actually constrain the analysis to the ROI specified? How can I get my results to match that of what I’m seeing in SPSS? Is my analysis set up correctly for what I’m trying to do? Thank you in advance for your patience with this lengthy inquiry. Best, Erin

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