Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

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Password
by Dom Martin 05 Jun '22

05 Jun '22

External Email - Use Caution Good Evening, Could you please send me the password for the Ubuntu VB file? Cheers

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Recon-all Runtime
by Joanna L Eckhardt 03 Jun '22

03 Jun '22

External Email - Use Caution Dear FreeSurfer Support, I have a question about the run time on FreeSurfer version 7.1.1. I have been processing scans with recon-all that have been completing in as short of a time as 4.782 hours. My PI was a little worried about how short of a runtime this is as previous processing of scans (maybe of more atrophied brains) have historically taken much longer, up to a day, for all the processing steps of recon-all. Is 4.782 hours a normal runtime for recon-all on FS 7.1.1? I have also attached the log for this job that took 4.782 hours in case this helps, as I do not know enough about all the steps of recon-all to ensure that everything ran correctly. I use open science grid to run multiple jobs so if this format does not work to view the log, please let me know. Thank you for your time and assistance. All my best, Joanna

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How to extract t-values from F.mgh?
by Thalhammer, Melissa 03 Jun '22

03 Jun '22

External Email - Use Caution Hey guys, I am working with Freesurfer 7.1.1. to compare two groups' cortical thickness values within Desikan-Killiany ROIs while correcting for (mean-centered) sex. I have extracted thickness values within ROIs into a txt using aparcstats2table and have then used mri_glmfit --table Study.txt to perform group analysis on thickness values within ROIs. For a future analysis, I want to extract the t-statistic (corrected for sex) per ROI into a txt/csv. This post (https://secure-web.cisco.com/1AckjDBImCzyv658H_aa2jCFZOZfDab0c5vz4aXbS0uIdr…) states that F.mgh stores the F-ratio, which is F=t^2, so t=sqrt(F). So, in principle, I should be able to calculate t from my F.mgh file. However, using the squareroot will only yield positive values. I have run a t-test on my data (using simply Python scipy.stats.ttest_ind): the values are actually the same as using sqrt(F), but signs differ (since t calculated from F can only be positive). Is there a better way to calculate a t-statistic while regressing out a covariate within ROIs? Many thanks in advance, Melissa

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Password request for Freesurfer 7
by Catarina Duarte 03 Jun '22

03 Jun '22

External Email - Use Caution Hello, I am writing to request the password to unzip the Freesurfer 7 image (for VirtualBox running on windows). I appreciate your help. Best, Catarina Duarte

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Wrong annotation after mris_sample_parc
by Samuel Hollý 03 Jun '22

03 Jun '22

External Email - Use Caution Dear Freesurfer experts, I'm trying to convert a volumetric atlas (MICCAI_2012) in NIFTI format to a surface annotation using mris_sample_parc and I would like to kindly ask for your support. I ran recon-all on the corresponding template brain (which I will refer to as ICBM2009 with subject ID "fs_DBS_ICBM2009_T1_1mm"). I also created a custom color LUT called "MICCAI_2012_freesurfer.txt". However when I run the command mris_sample_parc -ct MICCAI_2012_freesurfer.txt fs_DBS_T1_1mm lh MICCAI_2012.nii MICCAI_2012.annot and check the results in Freeview, the result is very bad: most of the hemisphere is labelled as the 3rd ventricle, and other labels are completely off as well. To me it looks like it's got something to do with the orientation of either the NIFTI atlas or the white matter surface. Not sure if this relevant but the NIFTI atlas has RAS orientation and has no Qform matrix (the Sform is present and Sform code is "Scanner Anatomical"). Could you please help me with this? Thank you very much in advance. Best regards -- Mgr. Samuel Hollý JESSENIUS - diagnostické centrum a.s. Špitálska 6 - areál Fakultnej nemocnice 949 01 Nitra

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Re: [Freesurfer] Seeking pass code
by fsbuild 02 Jun '22

02 Jun '22

External Email - Use Caution Sending the info to your email shortly. - R. On Jun 1, 2022, at 23:20, FELICITY SIMPSON <felicity.simpson(a)students.mq.edu.au> wrote:        External Email - Use Caution        Hi there,I am hoping to access the pass code required to open my .ova.7z file as a 7zip file.Thank you in advance for your assistance,Felicity Simpson,University of Newcastle,_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer

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Seeking pass code
by FELICITY SIMPSON 01 Jun '22

01 Jun '22

External Email - Use Caution Hi there, I am hoping to access the pass code required to open my .ova.7z file as a 7zip file. Thank you in advance for your assistance, Felicity Simpson, University of Newcastle,

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samseg2recon error / missing files
by Jacob Levenstein 01 Jun '22

01 Jun '22

External Email - Use Caution Hello Freesurfer team + users, I am looking to run segmentHA_T1.sh following samseg + samseg2recon, and came across this previous thread where it seemed to workout: https://secure-web.cisco.com/1u2xTmmnCUaxQQuSTDRURAlZzdIaStC1AkxmbcmeQ18lFv… Given that I am writing in, I have not yet gotten this to run properly... Below is my samseg command: samseg --t1w ${subject}_${ses}_T1w.nii.gz --sd . --s ${subject}_${ses}_samseg --refmode t1w --threads 16 --parallel >From the log file, samseg seems to run correctly, but once it reaches the samseg2recon steps, I receive the following error: ln -sf orig.mgz rawavg.mgz ERROR: ln -sf orig.mgz rawavg.mgz ERROR: samseg2recon --s ${subject}_${ses}_samseg --tmpdir ${SUBJECTS_DIR}/${subject}_${ses}_samseg/mri/samseg/tmp.pyBLVF/tmp.mergeseg --cleanup If I then (re)run samseg2recon on the samseg directory (see cmd below) , I can execute the failed lines, and this script completes without error. samseg2recon --s ${subject}_${ses}_samseg However, when I then try to run: segmentHA_T1.sh ${subject}_${ses}_samseg, I receive the following error: Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all? As the error message correctly states, within that subject's dir, I do not have an mri/norm.mgz or mri/wmparc.mgz. I do have an mri/samseg/transforms/samseg.talairach.xfm, but it is not in the scripts expected location/naming convention. If it is helpful to know: i. Running recon-all then segmentHA_T1.sh completes without error... ii. Copy over the mri dir from the recon-all to the samseg subject dir, then running segmentHA_T1.sh also completes without error... iii. I am running Ubuntu 20.04.4, freesurfer-linux-ubunu18x86_64_-7.2.0-20210721 Any idea what may be going wrong with samseg/samseg2recon? I am happy to use the workaround listed above, but I suspect there may be a more efficient way, and or unintended implications when mixing and matching recon-all and samseg...? Thank you for your help and insight! All the best, Jacob

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fmcpr.up.sm5.mni305.2mm.nii.gz label
by Mingyang Xia 01 Jun '22

01 Jun '22

External Email - Use Caution Dear Freesurfer expert: I am Mingyang Xia. I use freesurfer to preprocess the fmri data and map to the fsaverage and generate a file named fmcpr.up.sm5.mni305.2mm.nii.gz. I want to get the label of this file however I could not find the label in the fsaverage folder. Could you give me some advice? Thank you Mingyang Xia

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extracting BAs in freesurfer
by Sam W 01 Jun '22

01 Jun '22

External Email - Use Caution Hello! Is it possible to extract brodmann areas not included in the aparc? For example, BA9, BA10 and BA32? Thanks! Best regards, Sam

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Freesurfer June 2022