Freesurfer October 2022

freesurfer@nmr.mgh.harvard.edu

89 participants
132 discussions

Recon-all output in MNI305, patient space, or other?
by Andrew M 17 Nov '22

17 Nov '22

External Email - Use Caution Greetings, I am running recon-all as per the iElvis pipeline with: recon-all -s <id> -i $SUBJECTS_DIR/.../T1.nii -all -localGI And followed by ct2mri My questions are: 1. What is the actual output "space" of the resulting T1.nii and postInPre.nii ? Does recon-all do keep everything in patient space, or does it register them to fsaverage space automatically? If so, how would I convert these MRIs and CTs to MNI305 space? Thank you very much. Andrew

2 1

Forum Question
by Rubenstein, Samantha Leigh 17 Nov '22

17 Nov '22

External Email - Use Caution Hi, Our lab has previously used Freesurfer version 6, but we are interested in upgrading to 7.3.2. What are pros and cons for the different versions? I did not set the computer up or download the original version 6. We were previously using the CentOS version on Ubuntu 16 (unsure why CentOS vs Ubuntu), but upgraded to Ubuntu 20 for the 7.3.2 installation, using the Ubuntu version instead (not CentOS). From what I understand it’s not recommended to mix data between the versions so I’m just interested in anyone’s opinion on differences/advantages between 6.0 and 7.3.2 since I would have to redo ~60 subjects. Unsure if this is useful, but right now we do pial edits, CP edits, and our output is volumetric/segmentation/hippocampal subfields data (output in the aseg/aparc excel spreadsheet). Thanks, Samantha

2 1

Glasser parcellation labelling
by Paulk, Angelique C.,PhD 17 Nov '22

17 Nov '22

Hello, I have yet another, likely obvious, question and I apologize if this is answered elsewhere. I ran the below series of functions to apply the HCP-MM1 (Glasser) atlas to the FreeSurfer output. I was able to produce an annotation file that had the labels in the right locations and mapping. Yet, when I look at the output HCP-MMP1.mgz and HCP-MMP1+aseg.mgz files in FreeView or 3DSlicer, the old DKT FreeSurfer labels are applied to the brain labels (which are inaccurate). Is there an additional step I need to convert the labels such as using a modified HCP-MMP1 LUT look up table (such as linked here<https://github.com/MRtrix3/mrtrix3/issues/1279>)? using the HCP-MMP1 annotation files: https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_fsaverage/349… And the use of mri_surf2volseg in the following sequence: https://github.com/ftadel/IntrAnat/issues/7#issuecomment-768996270 Thank you for any and all help, Angelique

2 1

Segmentation of hippocampus(left), grey and white matter regions.
by PRASAD D 10 Nov '22

10 Nov '22

External Email - Use Caution Hello everyone. I’m new to FREESURFER I would like to segment the sMRI images. I have extracted(skull stripped) the brain region from the sMRI image using BET. but i'm interested in hippocampus(left), grey and white matter regions. Can you please guide me how to segment those specific regions automatically. Thanks in advance. -- *Yours sincerely* *D.PRASAD* *Full Time Research Scholar(QIP)* *Dept. of ECE, PTU.*

3 2

Preproc-sess crashed - 3dvolreg.afni error
by Gillian Grennan 09 Nov '22

09 Nov '22

External Email - Use Caution Hello FreeSurfer Developers, I downloaded Freesurfer v7.3.2 <https://secure-web.cisco.com/1VuI2ndzXo5YBm-YeBraBeuWIVo2R7T-txZ30nSNYbmoPI…> onto my local drive and am attempting to run preprocessing through FSFAST. I wasn't able to get access to the .tar.gz Darwin file but downloaded Xquartz, Freesurfer, FSL, and Matlab individually and was able to source Freesurfer using the following commands: export FREESURFER_HOME=/Applications/freesurfer/7.3.2 export PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt export SUBJECTS_DIR=$PROJECT_DIR/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh However, when I run preproc-sess in my analysis folder I get the following error: command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run error message: ++ Initializing alignment base Choleski factorization failure in startup_lsqfit mri_startup_lsqfit: bad call to startup_lsqfit! ++ Starting final pass on 44 sub-bricks: 0 Fatal Signal 11 (SIGSEGV) received mri_3dalign_one 3dvolreg main Bottom of Debug Stack ** AFNI version = AFNI_2011_12_21_1014 Compile date = May 22 2013 ** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]] ** Program Abort ** ** If you report this crash to the AFNI message board, ** please copy the error messages EXACTLY, and give ** the command line you used to run the program, and ** any other information needed to repeat the problem. ** You may later be asked to upload data to help debug. ERROR: 3dvolreg.afni Invalid null command. I'm confused on what more I need to install? Is there a way I can get an updated link to the tar file with the relevant software packages needed to run FSFAST? Best, Gillian Grennan

2 5

acompcor in fsfast
by Addison, Reuben 09 Nov '22

09 Nov '22

Hi, I am running resting State functional connectivity and I want to run everything in freesurfer and fsfast. I wanted to know is it is possible to run acompcor in fsfast. If so, how do I go about it. Thanks. Get Outlook for iOS<https://aka.ms/o0ukef>

2 3

design is ill-conditioned
by Loeffler, Martin 08 Nov '22

08 Nov '22

External Email - Use Caution Dear experts, I’m running into an error when running selxavg3. It says the design is ill-conditioned. I’m a bit stuck, because the same pipeline works in most subjects, but not all. Also, if I exchange the functional scan (f.nii.gz) with a scan from a working session of the same subject (same number of volumes etc.) I don’t get any errors. I’m grateful for any advice that helps to track down the mistake I’m doing. Here the content of the selxavg3.log file: cd /home/hector/SENS_MAPPING_BLOCK/sessions /opt/software/freesurfer/fsfast/bin/selxavg3-sessbc -s HEC_035_1 -analysis MPBDandefs_orig_lhrh_revd11.5_sm2.lh -no-preproc -fwhm -force Found 42449/139130 (30.5) voxels in mask Creating Design Matrix ... creation time = 0.004 sec DoMCFit = 1 ntptot = 500, nX = 33, DOF = 467 XCond = 2.63784e+16 (normalized) ERROR: design is ill-conditioned Before the error it gives a warning that the design matrix is singular or badly scaled: [Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.271035e-17.] [> In fast_selxavg3bc (line 318)] norm(inv(XtX),2) = [14601308845709730.0] Saving X matrix to /home/hector/SENS_MAPPING_BLOCK/sessions/HEC_035_1/bold/MPBDandefs_orig_lhrh_revd11.5_sm2.lh/Xtmp.mat XCond = 2.63784e+16 (normalized) ERROR: design is ill-conditioned >> ------------------------------------------ ERROR: fast_selxavg3bc() failed\n Many thanks in advance, Martin

2 1

Cutting an occipital patch
by Noam Khayat 08 Nov '22

08 Nov '22

External Email - Use Caution Hello, I need to cut the occipital pole in order to make a retinotopy analysis. I read that tksurfer no more exists, and with freeview I only succeed in cutting the plane but I'm having trouble with separating it into a patch with the occipital part only. Do you know if there is a way to do this? Thanks! Noam

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Question about color look up table
by Yoshito Saito 08 Nov '22

08 Nov '22

External Email - Use Caution Hello. I would like to ask a question about the color look-up table. I want to change the opacity of color on a brain atlas in Freeview. I changed the number in a column of opacity in the Color Lookup Table file by following the instructions on this website ( https://secure-web.cisco.com/1DQQao3VQ454IQKL-p8fj3rK0Jciinx1EwjIuNuRgfloa5…) but I could not change the opacity at all. I am using a bit old version of FreeSurfer (ver 6.0) on the HPC of my university, but is this the reason I couldn't change it? I am looking forward to hearing from you. Sincerely, Yoshito -- Yoshito Saito MBBS Master's candidate (Master of Philosophy - Medicine) Melbourne Neuropsychiatry Centre The University of Melbourne

2 1

intensity statistics in aseg.stats
by Zeng, Qi 08 Nov '22

08 Nov '22

External Email - Use Caution Hi Freesurfer scholars, The output of recon-all "aseg.stats" file contains information on volume and intensity statistics of each segmentation of subcortical brain regions. May I ask what is this intensity measurement (e.g. intensity mean)? How is it different from volume? What characteristics of the brain did it try to explain? Thank you! Best, QZ

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Freesurfer October 2022