Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30078 discussions

Request for the password to expand the ova.7z for FS on VirtualBox
by 김한기 29 Aug '22

29 Aug '22

External Email - Use Caution Hello, I am a post-graduate student at Ajou University, School of Medicine, Department of Brain Science in South Korea. I am planning to use Freesurfer on VirtualBox! I would be grateful if you could tell me the password to expand the .7z file. Thank you so much

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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
by Trolle, Carl 28 Aug '22

28 Aug '22

Hi! Thank you, yes, using the Freesurfer dev-version available through the Martinos cluster produced the desired result with the Destrieux-atlas. I’ve been using the 711-version throughout, I hope that I specified the version in my first email. Is it possible to use these commands (mris_register and mris_ca_label) as expert option files during recon-all to correct the incorrect parcellation of the annot.aparc-file? If so, would that also require a later Freesurfer vesion than what we’ve been using? Kind regards, Carl

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Re: [Freesurfer] Freeview quitted unexpectedly
by fsbuild 28 Aug '22

28 Aug '22

External Email - Use Caution Hello Danesh, Try putting your license.txt file into your home directory and setting the environment variable FS_LICENSE to point to it. $ export FS_LICENSE=$HOME/license.txt$ cd $HOME$ cat $FS_LICENSE… you should see your email address used to register for the license plus other license code … Then try source’ing the Freesurfer script to setup the environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.3.2-20220804-6354275 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.3.2 FSFAST_HOME       /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjects MNI_DIR           /Applications/freesurfer/7.3.2/mni Then try running freeview with no arguments and it should bring up an empty window,$ which freeview/Applications/freesurfer/7.3.2/bin/freeview$ freeview - R. On Aug 23, 2022, at 10:36, Danesh kajbaf <daneshkajbaf(a)gmail.com> wrote:        External Email - Use Caution        Dear support team,After installing Freeview, I tried to load a volume, while checking how it works with samples, from the subject folder in the Freesurfer folder. Unfortunately after choosing the file, Freeview crashed out and popped up an error message “Freeview quitted unexpectedly!”. I tried with other files and the same happened again, while all these files could be loaded by FSLeyes, so the problem was not with data. I run Apple Diagnostics to find if the problem was with the hardware or OS and there was no issue.Attached is the text file of the error as I copied and pasted it so it might help to tackle the problem.Freeview 2.0 is installed ,via the Freesurfer 7.3.2 package installer, on macOS Catalina 10.15.7, and my MacBook Pro’s part number is A1706.Regards,Danesh<Error txt.rtf>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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Problem with longitudinal processing
by Wittayer, Matthias 28 Aug '22

28 Aug '22

External Email - Use Caution Dear community, I tried to process MS- patient's MRIs (mostly same scanner, same settings) Longitudinally over a long period of time. I first processed all timeponits crosssectionally and then initialised the base image by recon- all - base TP1 TP2 TP3 etc. Now I am trying to run label based morphometry and it seems some areas are growing rather than shrinking. Which is highly unlikely. I tried to exclude timepoint of a relapse to rule out perifocal edema interfering with measures but the problem remains. Did anybody have the same problem? Is it a potential bug or just a garbage in garbage out problem (though I don't know what would be wrong with our scans)? Does it make sense to make an intermediate template for two timeponits only? I.e. recon- all -base TP1 TP2; recon -all -base TP2 TP3 ... and use them for longitudinal runs? Thanks for your opinions. Best Matthias

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T1 gadolinium
by Gonzalo Rojas Costa 28 Aug '22

28 Aug '22

External Email - Use Caution Hi: SynthSeg is useful for T1-GD volumetric images? Another algorithm, software? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1I2XJrWdFnZxY-dYDbiZg0PV2H4bghSVXCQk63X1VSya6a… https://secure-web.cisco.com/13zfZJFRpU2hG9Abh2YAV0LPmd1V6ff2BdGkKw7NLlRJY9… https://secure-web.cisco.com/1p2HQdyHZcPFsEa80XIMcd_JLnEOosZMvxjlvKnim0-NVW… http://secure-web.cisco.com/1t-sL6HvQklTyxVFyP8KzIDoaaMPtJscszD92RHMNQuJE8k… https://secure-web.cisco.com/1DKuT3Zodsn-rxAY5cLCK0zkUQtPg9820KtzYLjm_ymXLa…

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Inflating norm.mgz
by Elizabeth Haris 28 Aug '22

28 Aug '22

External Email - Use Caution Hi developers! I am running connectivity analyses for amygdala subregions using images from a 7T scanner. I am wanting to transform the amygdala segmentations into fMRI space (1.6 iso voxel) for individual analyses and am looking for the best way to do this. Would it make sense to: 1. Inflate the norm.mgz brain, then run the segmentHA_T1.sh script, and then extract the individual segments. 2. Run the segmentHA_T1.sh script as usual, but inflate the rawavg brain. Then, warp the full segmentation to fit the rawavg space (using mri_convert -input <original_amygdala_segment> -at -rt nearest -reference <inflated_rawavg_brain> -output <inflated_amygdala_segment>), and then extract the individual segments. Does it matter which way I do it? Is there another way to do it that would be better? Many thanks, Elizabeth

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Shift in cortical parcellation, issues with previously suggested solution
by Trolle, Carl 28 Aug '22

28 Aug '22

Ok. I'm trying to attach a copy of the output I get in the terminal-window. The commands I've been running for the mris_register and mris_ca_label are "mris_register -L subject/label/?h.central_sulcus.label FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sphere FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif subject/surf/?h.sphere.reg" and "mris_ca_label subject ?h subject/surf/?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs subject/label/?h.aparc.a2009s.annot". I hope I'm sending what you asked for, otherwise I'll be happy to correct this. Kind regards, Carl

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primary diffusion direction & surface normal vector
by Zeng, Qi 28 Aug '22

28 Aug '22

External Email - Use Caution Hi Freesurfer experts, After DTI tensor fitting, usually we obtain primary, secondary, and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2, L3). So what do we use to describe the primary diffusion direction, FA or AD(=L1)? I read the term "surface normal vector" from a paper and the formula r=[Vn * e1|. V presents the surface normal vector, which can be computed using the cross-product between edges. Where can I find this information? The paper named: "Surface-based analysis of diffusion orientation for identifying architectonic domains in the in vivo human cortex" Thank you so much! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Gyrification Index
by Steger Celine 28 Aug '22

28 Aug '22

External Email - Use Caution Dear FreeSurfer experts, I try to explore the Gyrification Index of both hemispheres in a population. For this I computed the LGI using the Freesurfer pipeline and used the command suggested in previous mails: mri_segstats --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi -excluded 0 --sum lh.aparc.pial_lgi.stats Based on:(https://secure-web.cisco.com/1_9wsKWw32_G-UJUtVnh9GwxfZh3NF5eNv2TMJEx0j… With this I get one line of results for this hemisphere in this subject in the file lh.aparc.pial_lgi.stats .... # NRows 1 # NTableCols 10 # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 115191 82607.4 Seg0001 3.5515 0.8629 2.1340 5.9443 3.8103 I would like to clarify, which variable is reporting the gyrification index? Thank you for your help and time. Kind regards, Céline Steger

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