Freesurfer February 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
118 discussions

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!

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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

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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

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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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freesurfer to spm
by 况况 26 Feb '21

26 Feb '21

External Email - Use Caution Dear Community, I want to acquire each amygdala subnuclei volumes' mask to from freesurfer(fsaverage space) to spm(MNI space). what should i do? can you give me some tips? Thank you. student -liangfeng kuang shandong first medical university & shandong academy of medical sciences email: kuangliangfeng123(a)163.com

2 1

Creating a .gcs custom atlas from nifti file for cortical parcellation
by THIBEAU SUTRE Elina 26 Feb '21

26 Feb '21

External Email - Use Caution Hello freesurfer experts, I would like to use freesurfer recon-all to obtain the regional cortical thicknesses of subjects of ADNI dataset. I launched freesurfer recon-all and obtained the parcellations according to Destrieux and Desikan-Killiany atlases. I would like to know how to obtain the same parcellations with another atlas, AICHA (https://secure-web.cisco.com/1st38nLf-34KvmX5j8oNCBRhTI_Ki20PWEfeEACfqaaGqd…) which is only available in nifti format. I understood that I should create a .gcs file from the nifti version but I am not sure how. I saw that mris_ca_train could be used to create such a file from a a manually labelled dataset but I don’t know how to create these labelled subjects from the nifti atlas. If anyone has already this kind of conversion .nii -> .gcs I would be really interested to know how you have done that! Best regards, Elina

2 4

runClustSims.sh error
by Haewon Roh 26 Feb '21

26 Feb '21

External Email - Use Caution Hi, experts. Now, I am doing the process of group analysis between two groups on FS v.7.1.0 Previously, I had used QDEC GUI for that kind of analysis, but, because it is not available since FS 7, I am learning how to do that from video tutorial. But, I’ve got in trouble ; in the process of cluster corrosion, the script of " runClustSims.sh “ doesn’t work. (Please find error message in attached image file). Could you help me out what the problem is ? And I’d like to know whether I can use the function of automated segmentation of hypothalamus in FS v 7.1.0. Thank you! Best, Haewon Roh h.

2 1

mri_glmfit dependent variable
by miracle ozzoude 26 Feb '21

26 Feb '21

External Email - Use Caution Hello Experts, I've a question about mri_glmfit. I want to investigate the association between thickness and neuropsychiatric syndromes, controlling for age and cognition. Which model below is mri_glmfit performing? Model 1 neuropsych syndromes ~ age + cognition + cortical thickness or Model 2 cortical thickness ~ age + cognition + neuropsych syndrome Many thanks, Paul

2 3

WM volume
by Barletta, Valeria 26 Feb '21

26 Feb '21

Dear Freesurfers, In what file inside the patient_name/stats folder do I find the total white matter volume? In the file "aseg.stats" there is something called lh/rh "cortical white matter volume", is that the right value to look at? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823

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Freesurfer February 2021