Freesurfer

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30076 discussions

Creating a seed sphere using MNI coordinate
by Addison, Reuben 16 Oct '22

16 Oct '22

1. I am planning to add a seed sphere 6mm cortical and 4 millimeters subcortical and I want to do this with Fsfast using given MNI coordinates from a previous study. I am wondering if there is a command on fsfast to achieve that, I have gone through the connectivity analysis but couldn't quite figure a way to do that. 1. Also I want to add a covariate (behavioural score) to my second level connectivity map. I want to use fsfast for consistency sake. If I can be pointed to the command it will be very helpful. Thanks, Reuben N. Addison Postdoctoral Fellow Brain Recovery Lab MGH Institute of Health Professions<https://www.mghihp.edu/> Charlestown Navy Yard | 36 1st Avenue, Boston MA 02129 Get Outlook for iOS<https://aka.ms/o0ukef>

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fft
by Proulx, Jean Sebastien 16 Oct '22

16 Oct '22

Hello, Is there an easy way to perform fast fourier transform (fft) or other fancier spectral analysis with freesurfer tools (e.g. with mris_calc)? Thanks and Have a good day! Sebastien

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Specify random seed with recon-all
by Elizabeth Kenneally 16 Oct '22

16 Oct '22

External Email - Use Caution Hi FreeSurfer Developers, I’m trying to run FreeSurfer with a specified random seed with recon-all. I found the -rng-seed flag, but it seem to have been deprecated. I also found the -randomness flag, but I was hoping to specify the random seed myself for testing purposes. Is there a way to do this in the newer versions? I searched the mail archives and didn’t find anything recent. Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: OSX Monterey Thanks for your help! Elizabeth Kenneally Assistant Research Engineer Computational Neuroimaging Laboratory Child Mind Institute 917.472.1812 childmind.org<http://secure-web.cisco.com/1NFHUQ9u0R9_V3v6SHV7fVhQQ59J34BHwuVu635hIarQk28…> | Location<https://secure-web.cisco.com/1gABeb_5rSD3SPHRFC1-gDfs_uSvEujbgodCtMz86CHALX…> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error, please notify the sender by return email and delete the original message.

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Creating a lobar atlas
by James Brown 16 Oct '22

16 Oct '22

External Email - Use Caution Dear colleagues Freesurfer experts, I would like to create an atlas (my atlas) for the white matter like "wmparc.mgz" so I can generate statistics. I would like this atlas to be limited to the following structures (frontal lobe, parietal lobe, occipital lobe and temporal lobe). I reviewed Freesurfer tutorials and Q&A in Freesurfer forum then ran the following commands: mri_annotation2label --subject subject --hemi lh --lobesStrict lobes mri_annotation2label --subject subject --hemi rh --lobesStrict lobes mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz --annot lobes --base-offset 200 Then, mris_ca-train -t ./color.tab lh ../surf/lh.sphere.reg ../label/lh.lobes.annot SUBJECT_TEST lh.my_atlas.gcs mris_ca-train -t ./color.tab rh ../surf/rh.sphere.reg ../label/rh.lobes.annot SUBJECT_TEST rh.my_atlas.gcs I would like to use mri_segstats with “my atlas” to generate statistics in lobes not in parcellates. How can I convert lh.my_atlas.gcs and rh.my_atlas.gcs to myatlas.mgz ? Thanks for your help James

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mri_glmfit error
by fernanda rohrsetzer 16 Oct '22

16 Oct '22

External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C Contrasts/LR-HR_testcov.mtx --C Contrasts/LR-MDD_testcov.mtx --C Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir lh.groupteste.thickness.glmdir --eres-save But it gives me an error (attached below) indicating a formatting problem in my FSGD file (attached). I have been trying to figure that out for a while. But I am unable to debug it. The design matrix (examining difference in thickness after controlling for effects of age, sex and Average thickness) 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx Could someone please help me resolve it? Thanks for your time.

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Quality control of longitudinal recon-all output for >500 participants
by Blujus, Jenna 16 Oct '22

16 Oct '22

External Email - Use Caution Hi all, I am processing a large longitudinal dataset of T1-weighted anatomical images through the recon-all pipeline (N=680). I know that the gold standard for quality control following recon-all is visual inspection of the output surfaces and parcellations. However, given the large sample size, I was writing to see if the community has any recommendations for automatic QC pipelines. I read a few papers discussing the use of Euler numbers to detect outlier datasets for exclusion (see citations below). Does anyone have any other recommendations? Thank you in advance! Best, Jenna References: 1. Rosen, A. F., Roalf, D. R., Ruparel, K., Blake, J., Seelaus, K., Villa, L. P., ... & Satterthwaite, T. D. (2018). Quantitative assessment of structural image quality. *Neuroimage*, *169*, 407-418. 2. de Lange, A. M. G., Kaufmann, T., Quintana, D. S., Winterton, A., Andreassen, O. A., Westlye, L. T., & Ebmeier, K. P. (2021). Prominent health problems, socioeconomic deprivation, and higher brain age in lonely and isolated individuals: A population-based study. *Behavioural Brain Research*, *414*, 113510.

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mris_make_average_surface, flirt transformations question
by Chris Adamson 14 Oct '22

14 Oct '22

External Email - Use Caution Freesurfer experts, I'm trying to make average surfaces for a collection of subjects into a template space. I have performed the following flirt registration per subject: flirt -in $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz -ref template0.nii.gz -omat $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat -out $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.nii.gz -dof 12 -searchrx -$D $D -searchry -$D $D -searchrz -$D $D Then make the talairach.xfm files for each subject lta_convert --infsl $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat --outmni $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.xfm --src $SUBJECTS_DIR/$CURSUBJECT/mri/T2.mgz -trg template0.nii.gz Then run mris_make_average_surface mris_make_average_surface -i 7 -s $CURSURFTYPE $CURHEMI $CURSURFTYPE.flirt sphere.reg2 fsaverage The resulting average surface does not overlay onto template0.nii.gz correctly, it is in the wrong orientation. It isn't in TKR space, so I convert it to TKR space. mris_convert --vol-geom template0.nii.gz $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt.volgeom mris_convert --vol-geom template0.nii.gz --to-tkr $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt.volgeom $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE The resulting surface $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE overlays onto the template template0.nii.gz but it is offset slightly and not overlaid correctly. Am I doing something wrong? Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> http://secure-web.cisco.com/1xDAoEUxMPPuCsJFESgxVj8G_Fqd-g7vRsh53KrQ6HSMvkl…<http://secure-web.cisco.com/17tnfb4NVhmhEj8eHc-vz41g2VE4LFjxQeJHBYmM2X28Zoj…> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Password for unzipping of VM
by Malina Jop 14 Oct '22

14 Oct '22

External Email - Use Caution Dear FreeSurfer experts, I would like to unzipp the VM in order to run FreeSurfer on windows. Could you provide me the password for unzipping? Thank you very much in advance, best regards, Malina

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FreeSurfer Password
by José Carlos López Mata 14 Oct '22

14 Oct '22

External Email - Use Caution Hi, my name us José Carlos López Mata. I'm a biomedical engineering at Universidad Autonoma Metropolitana in Mexico City. I'm working with fMRi images and i need to use Freesurfer for my project so, i request de activation password, please.

1 0

Password to unzip freesurfer 7.2.0
by Chien Nguyenle 13 Oct '22

13 Oct '22

External Email - Use Caution Dear freesurfer, I am a researcher at vietnam medical university.I have just downloaded FS_7_2_0_ubuntu_18_04_06.ova.7z from your website and intend to run on linux/ubuntu.May I know the password for unzip and whether this version of freesurfer requires license file?Best regardsChien Nguyen

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