Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Building a model
by Marina Fernández 13 Feb '22

13 Feb '22

External Email - Use Caution Dear experts, We run the following analysis in Freesurfer: *Group* (2 levels) x *X1* (continuous IV) x *X2 *(continuous IV) + *Sex *(categorical covariate) + *Age* (continuous covariate) We exported the vertex with the maximum statistic after applying FWE correction to replicate the analysis in R. We want to make sure about the structure of the model to later do a Bayesian analysis using the same structure. We got significant results for most of our analyses but not for all of them, likely because we are not doing exactly the same thing. We have fitted several models in R, but the one that gave the closest results was the following: model <- lm (vertex ~ NewFactor (4 levels: Group*Sex) + X1X2 (resulting from X1*X2) * Group + Age*NewFactor, data=mydata) How should we introduce the interaction term in order to make the models fitted by Freesurfer and R comparable? Thanks a lot in advance, Marina

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Creating masks on a MNI averaged brain
by Lin Qiu 13 Feb '22

13 Feb '22

External Email - Use Caution Dear Freesurfer experts, My analysis is in FSL. But I wish to use the more detailed segmentaHA_T1.sh available in Freesurfer. I wish to avoid the time & resource to ‘recon-all’ all my participants’ T1 images, and only to transfer a set of masks superimposed on an averaged (MNI 1x 1x1 mm) brain – from Freesurfer to fsl. All my T1 images are pre-processed and registered using the FSL pipeline. So my first question is – Would it be sensible to create anatomical masks in Freesurfer directly onto the MNI standard brain image, rather that each participants’ T1, one by one? My second question is about running recon-all commands in parallel on a cluster – I read online that there is a -parallel flag in recent version of FS, so no need of installing a parallel package. However I was not able to use this flag in my FS 7.2.0. Please could you let me know how parallelization work on a cluster? Thank you very much! I look forward to hearing your advices! Best wishes, Lin -- Lin Qiu DPhil Student University of Oxford, Nuffield Department of Clinical Neurosciences John Radcliffe Hospital, Oxford OX3 9DU Email: lin.qiu(a)ndcn.ox.ac.uk<mailto:lin.qiu@ndcn.ox.ac.uk>

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rm: no match
by REEM ABU BAKR BAHATHIQ 13 Feb '22

13 Feb '22

External Email - Use Caution Hi all, I use a supercomputer to process my data When I run "recon-all –qcache", and after two days of processing there are a lot of Error messages saying "rm: No match." (although just this error message, no others). I'm wondering if this is something of concern, or something I can simply ignore. Thanks!

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-cw256 flag
by Harriet Dempsey-Jones 13 Feb '22

13 Feb '22

External Email - Use Caution Hi there, I am using AFNI to process some epi data. As part of this analysis, I am creating anatomical surfaces on which to project my data using recon-all in Freesurfer. My pre-processing in AFNI indicated that best alignment of my epi to anatomical image is achieved using a combination of affine and non-linear warping (3dQwarp in AFNI). So I was hoping to use this warped anatomical image from my experimental data to create a surface from with recon-all. I just tried to set this to run, and it errored and failed (see bottom of email) The gist appears to be that when it was completing the mri_convert stage it errored because the anatomical nifti image I had fed it, was not 256 FOV. It appears to be larger because I had to add some space to the image to rotate it during alignment. The error suggests using the flag -cw256 with recon-all, but I cannot find any documentation about how this works or what it does. I searched the forum archives as well, which came up with 60k hits, but none of them seemed to contain -cw256 when I control+f looking for it. Could someone let me know a bit more about this flag and whether it is ok to use for my purposes? I have included my recon-all code too for reference purposes. Please also let me know if there is anything glaringly wrong there, I am very new to fMRI analysis. Thank you for any help you might be able to give me! ERROR -------------------- mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz... **************************************** ERROR! FOV=273.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s P00_FG exited with ERRORS at Tue Feb 8 22:13:53 AEST 2022 MY CODE -------------------------- #!bin/tcsh # Freesurfer start-up module load freesurfer # Set up vars set subj_init = FG set subj_num = P00 set subj = {$subj_num}_{$subj_init} set recon_use = (-all) # set recon_use = (-autorecon1) set anat = /scratch/inode/uqhdemp1/Fingertip_maps/{$subj}/{$subj}.results/{$subj_init}_uniden_avg_wholebrain_unpad_warped_3dQ.nii set base_dir = /scratch/inode/ set subj = {$subj_num}_{$subj_init} set expert_file = 1b_FS_expertfile ## 1. Freesurfer recon all recon-all $recon_use -s $subj -hires -i $anat -sd $base_dir/Surfaces -openmp 12 -expert $base_dir/Parent_scripts/Surfaces/$expert_file [cid:aa7c0bba-3c94-4eb9-a0b1-34aa283c77e9]

2 1

Freesurfer with machine learning
by REEM ABU BAKR BAHATHIQ 13 Feb '22

13 Feb '22

External Email - Use Caution Hi everyone, Now that I have done the recon all preprocessing on my structural MRI data, I want to extract the volume and thickness of the gray matter and the surface area to use in a machine learning model. I find it difficult to determine which files I should take and is there any educational course that might help me for this plz share it with me . Thanks in advance

2 1

Longitudinal Stream Error
by Willett, Andrew Sunday 13 Feb '22

13 Feb '22

This is my first time seeking support here so I apologize if I am not familiar with the community's conventions. I am encountering errors when processing Freesurfer longitudinal stream (Freesurfer v6.0). Cross-sectional streams proceeded and completed without error, but base template creation and all following longitudinal steps failed. I created a txt script for the base template creation: Here is a sample: module load freesurfer export FREESURFER_HOME=/.../.../freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh recon-all -base SA14c -tp P10 -tp P11 -tp P12 -all This script was separate from the following step (this was a separate .txt file): recon-all -long P12 SA14c -all -no-isrunning recon-all -long P12 SA14c -brainstem-structures The common error I received from the base template creation: (from the recon-all.error log==uncertain if the recon-all.log would be more illuminating for debugging) $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 user Exp $ /.../.../freesurfer/bin/recon-all PWD /.../.../subjects/SA14c/label CMD mri_label2label --srcsubject fsaverage --srclabel /.../.../subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject SA14c --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface Moreover, with the base template error, it was not possible to go from there to create the individual longitudinal mri output based on the base template I'd be really grateful for help with this debugging! Thank you. Andrew Sunday Willett, M.S. Department of Neurology, Division of Movement Disorders Brigham and Women’s Hospital awillett(a)bwh.harvard.edu<mailto:jkim@bwh.harvard.edu> brighamandwomens.org<http://www.brighamandwomens.org/> [cid:0e0fcfea-f9ea-4981-adad-c366bf0c8f00]

2 1

Recon-all reconstructed image coordinates
by Salar Dini, Elaheh 13 Feb '22

13 Feb '22

External Email - Use Caution Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject: https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft… [https://secure-web.cisco.com/1B08cXHTWamf2XLl-Do2M2Y2jFkmx7hn93F8dK1GfF1Mv6…<https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft…> Screen Shot 2022-01-26 at 1.40.23 PM.png<https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft…> Shared with Dropbox http://secure-web.cisco.com/1qgxtofGxpoR7Sqc5YpeFwa6ndZVhgCVEL8DwdalIfXi80q… while one of them is reconstructed with FS7.2, the other one is reconstructed with a pipeline that uses another code for extracting brain tissue (BET Mask) and then use FS6 for the remaining stages of the reconstruction. While the final result of both constructions matches in most aspects, they don't occupy the same coordinates in space. Is there a way that we can match the coordinates of each voxel for two images? Or in other words make them compatible. The Platform we use is CentOS7 . Thanks and all the best, Ela

2 4

Virtualbox: developer's password
by Francois Leroy 13 Feb '22

13 Feb '22

External Email - Use Caution Hi, I am trying to set-up Freesurfer (fs_ubuntu_18_04_06) from Oracle VM Virtualbox. Could you send me the developer's password useful for login? Thanks for your help Regards Francois

1 0

Re: [Freesurfer] password for FS 7.2.0 Ububntu Virtual Box seetup
by fsbuild 11 Feb '22

11 Feb '22

External Email - Use Caution Hello Malav, Sending to your email shortly. -R. On Feb 11, 2022, at 10:02, Malav Shah <malav.shah(a)bccn-berlin.de> wrote:        External Email - Use Caution        Hi,may I please have the password to FS 7.2.0 Ubuntu Virtual Box setup?Thanks and regards,malavMalav ShahPhD candidate, Michael Brecht Lab,Humboldt University zu Berlin.(+49) 163-216-9391_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

password for FS 7.2.0 Ububntu Virtual Box seetup
by Malav Shah 11 Feb '22

11 Feb '22

External Email - Use Caution Hi, may I please have the password to FS 7.2.0 Ubuntu Virtual Box setup? Thanks and regards, malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

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Freesurfer