Re: [Freesurfer] Scalable recon workflow

External Email - Use Caution Hi Mitch, In our experience, -openmp 8 gives faster recons than -openmp 4, but the gains after -openmp 8 diminish quickly and aren't worth it. -Paul On Tue, May 3, 2022 at 12:51 PM Horn, Mitchell Jacob wrote: > Hi Experts, > > > > If I have 100s of

Re: [Freesurfer] License for 5.X versions of FreeSurfer

External Email - Use Caution Hi Jacob, Can you provide more details on how FreeSurfer was installed, how you are using the license key and the errors you are receiving? I just created a docker container with FreeSurfer v5.3.0-HCP ( https://secure-web.cisco.com/17NmBKDBeKQ2s5KCPv_

Re: [Freesurfer] differences between Freesurfer 6.0 and 6.0-beta

External Email - Use Caution Hi Matt, freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c was compiled from this commit of the source code on Jan 18, 2017 https://secure-web.cisco.com/1R8sitpPrVS-YQ5moGJknSMxciGckoDhuS0Y3u2-hSRaaPooepbj4aav__WDyLe57fmXppmrQZY7HsTnQ5NF0_qgy7p

Re: [Freesurfer] license text

External Email - Use Caution Hi Krystal You can have a license key automatically emailed to you by filling out this webform https://secure-web.cisco.com/1dJn5w1252g7xwEmnTP0-OuKPrvRxy3bfVpdmTz5t7ST4BBv5lsV-dt9MjlOKKWnJ22uiAmLOvk90MgBZPxPxJSEvZv_mAmWocmdVaO0-mppHCdP-XMT1f7va0sJ4WIH

Re: [Freesurfer] Tracula fsl commands fail in Freesurfer docker

External Email - Use Caution Hi Clément The container `freesurfer/freesurfer:7.2.0` simply installs freesurfer into a docker container, and does not support use cases that require additional software. There are a couple options. You could create your own container, which derives

Re: [Freesurfer] Using -bigventricles for infant segmentation

External Email - Use Caution A quick correction: The -bigventricles flag is supported in `recon-all` and in `samseg` but not in `infant_recon_all`, unfortunately. -Paul On Mon, Feb 7, 2022 at 2:17 PM Paul Wighton wrote: > Hi Fateme, > > Unfortunately, `-bigventricl

Re: [Freesurfer] Using -bigventricles for infant segmentation

External Email - Use Caution Hi Fateme, Unfortunately, `-bigventricles` isn't supported on the infant recon stream, that's a feature of the samseg stream. -Paul On Fri, Feb 4, 2022 at 1:58 PM Fateme Sadat Haghpanah wrote: > External Email - Use Caution > > Dear FreeSur

Re: [Freesurfer] recon-all stuck at -fill on AWS batch processing

External Email - Use Caution Hi Xin, If I understand correctly, recon-all runs successfully in your docker container when testing it on an EC2 instance, but when trying to run the same container on AWS batch or fargate, it doesn't make it past the `-fill` step. Is that correct?

Re: [Freesurfer] Running local lGI for longitudinal subject gives error: Unmatchted "'"

time point id (SAME as cross sectional > >ID) and is the ID created in the -base run. > >The directory .long. will be created > >automatically or used for output, if it already exists. > > > > I will try your second suggestion and run `mris_compute_lgi` directly. &

Re: [Freesurfer] Running local lGI for longitudinal subject gives error: Unmatchted "'"

External Email - Use Caution Hi Tim, I don't think you need to use the `-long` flag when using the `-localGI` flag since that just invokes `mris_compute_lgi` on the lh/rh.pial files. So after running the longitudinal pipeline to generate lh/rh.pial files, I think you can simply r

Re: [Freesurfer] How to quickly check whether the segmentation of thalamic nuclei or the amygdala is correct

External Email - Use Caution HI Xiaofang, I'm not sure there is an out-of-the box method to do this, but you should be able to modify FreeSurfer's qatools to generate relevant metrics and screenshots for your application. See https://secure-web.cisco.com/1qSsYKc06MzXRP-vLirz5AAd

Re: [Freesurfer] Obtaining single file from segmented images

External Email - Use Caution Hi Gregorio, You should be able to use mri_binarize to create masks from the hippocampal seg files https://secure-web.cisco.com/1qpMewyxfLa5R6eiYrzcf1qqqYJYO4CO0D3YKhBtxNKEZ97mm-iZPnbTazVbnV6aErI2Y4G6Iodqtpa7eRC6MzifD_tow_ROWRGLcJnlSoJoMvp7kVi4-NzdGcgO

Re: [Freesurfer] /usr/pubsw reference in 7.1.1

External Email - Use Caution I'm not familiar with FLICA, but you should be able to make a symlink for compatibility issues like this. First, backup the original tksurfer: mv $FREESURFER_HOME/bin/tksurfer $FREESURFER_HOME/bin/tksurfer.orig Then: ln -s $FREESURFER_HOME/bin/tksurfe

Re: [Freesurfer] Missing freesurfer files after running recon-all

External Email - Use Caution Hi Lisa, I think is has something to do with these lines from the log: ``` INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /dfs6/pub/ltaylor2/downs; ln -s /data/opt/apps/freesurfer/6.0.1/subje

Re: [Freesurfer] RAM per CPU for running Freesurfer 7.1

External Email - Use Caution Hi Ajay The memory footprint of each pipeline is something I wish there were better records of! You're right that 4GB is outdated. It really depends on the pipeline. For cross-sectional recon-all, 20Gb should do it. For longitudinal pipelines I sus

Re: [Freesurfer] BERT - Example of segmentation

/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=red so you could try: cd $SUBJECTS_DIR then the command above, replacing "pial_edits_before" with the subject name. That's just a guess though! -Paul On Thu, Jul 8, 2021 at 1:42 PM Paul Wighton wrote: >

Re: [Freesurfer] BERT - Example of segmentation

, > > Not sure what command I should run when I edit the brainmask because the > pial got too much. > > Kind regards, > Rosie > > > > > On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton > wrote: > >> External Email - Use Caution >> >> H

Re: [Freesurfer] BERT - Example of segmentation

External Email - Use Caution Hi Rosie, > It is my first time editing wm segmentation (white matter segmentation > errors + topological errors). > > I wonder if there is a good tutorial on which I could rely. > There are a few tutorials that may be helpful (a full list of tutoria

Re: [Freesurfer] Segmentation of hippocampal subfields

Use Caution > > Hi Paul, > > Thank you. > > The think is that I already run recon-all in all the participants and I > made some corrections (control points,...). I just want the hipocampal > subfields...What should I do in this case scenario? > > > > El mié., 7 ju

Re: [Freesurfer] Segmentation of hippocampal subfields

rfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ > > > > > On Wed, Jul 7, 2021 at 8:17 PM Paul Wighton > wrote: > >> External Email - Use Caution >> >> Ok, it looks like the file $FREESURFER_HOME/bin/segme

Re: [Freesurfer] Segmentation of hippocampal subfields

gt;>> export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI >>> source $FREESURFER_HOME/SetUpFreeSurfer.sh >>> >>> And I even re-started the computer but it does not seem to recognize the >>> command: >>> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA

Re: [Freesurfer] Segmentation of hippocampal subfields

FREESURFER > export FREESURFER_HOME=/usr/local/freesurfer > export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > I would greatly appreciate it if you could be more specific with my > example as I am new on this and I am a bit lost. &

Re: [Freesurfer] Interscanner variability

External Email - Use Caution Hi AJ, The longitudinal stream does not account for inter-scanner variability, but does reduce biases related to registering subsequent timepoints to the initial one. Perhaps longitudinal experts could confirm, but I would run the longitudinal stream,

Re: [Freesurfer] Segmentation of hippocampal subfields

External Email - Use Caution Hi Rosie, The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory. If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_H

Re: [Freesurfer] InfantFS witg segfile exiting with errors

External Email - Use Caution Hmm, it looks like the command `mri_binarize` isn't recognizing the `--noverbose` flag. I tested this in my env, and I'm not getting that ("ERROR: Option --noverbose unknown") error. Could it be that $FREESURFER_HOME is pointing to an older version of

Re: [Freesurfer] SAMSEG thresholds

External Email - Use Caution Hi Alberto, Koen and Stefano, You can get the behavior you want/expect by counting the number of voxels > assigned to lesions in the seg.mgz file - there is a ready tool for that in > FreeSurfer but I don't remember off the top of my head what the corr

Re: [Freesurfer] Masking A Surface Overlay

External Email - Use Caution Hi John, I think you can use `mris_calc` for this, e.g: mris_calc -o ~/test-output $FREESURFER_HOME/subjects/bert/surf/lh.thickness lt $FREESURFER_HOME/subjects/bert/surf/lh.curv Run `mris_calc -u` for more instructions. -Paul On Tue, Jun 29, 2021

Re: [Freesurfer] FreeSurfer cortical thickness

External Email - Use Caution Hi Rosie, For cortical thickness, check out *.aparc.*.stats files (e.g, lh.aparc.stats, lh.aparc.a2009s.stats, lh.aparc.DKTatlas.stats). There is more info in the ROI analysis tutorial: - https://secure-web.cisco.com/15BXH9iwkvAUJ2mnf7udx7SdsKrQQYNr

Re: [Freesurfer] Finding equivalent vertices on fsaverage_sym lh and rh surfaces

External Email - Use Caution Hi Tim, I think this is possible with mris_left_right_register, e.g. mris_left_right_register -dist 1 lh.sphere rh.sphere lh.sphere.d1.left_right rh.sphere.d1.left_right -Paul On Fri, Jun 11, 2021 at 10:02 AM Tim Schäfer wrote: > External

Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

External Email - Use Caution Just a quick update, running `recon-all -all -s bert` inside `freesurfer/freesurfer:7.1.1` has already made it past the stage that is failing above on my machine. -Paul On Wed, May 26, 2021 at 4:24 PM Paul Wighton wrote: > That's very stra

Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

The docker command I'm using is: > docker run -it --platform linux/amd64 freesurfer_gui > > Thanks, > Lara > > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Pau

Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

External Email - Use Caution Hi Lara, What container are you using? Is it `freesurfer/freesurfer:7.1.1`? Can you share the docker run command you're using? -Paul On Mon, May 10, 2021 at 10:00 PM Lara Foland-Ross wrote: > External Email - Use Caution > > Sure. Here's t

Re: [Freesurfer] Estimating the memory footprint of Longitudinal Stream?

sure of the peak memory used, though it is not super accurate. > Alternatively, I could add something to mri_fuse_segmentations to > periodically print out the peak memory usage > > On 10/13/2020 3:01 PM, Paul Wighton wrote: > > External Email - Use Caution > Hi FreeSurfers

[Freesurfer] Estimating the memory footprint of Longitudinal Stream?

External Email - Use Caution Hi FreeSurfers, Is there any guidance on how to estimate the memory footprint of the Longitudinal steam? We are trying to process the MacLaren test-retest dataset [1] (40 timepoints per subject) with the longitudinal stream in v7.1.1 and are running i

Re: [Freesurfer] (no subject)

External Email - Use Caution Hi Aleksandr, You could try making a minimal container with reprozip https://www.reprozip.org/ Only recon-all should be less than a Gb. -Paul On Wed, Apr 22, 2020 at 5:31 PM Hoopes, Andrew wrote: > I don’t have an exact number, but I believe the

Re: [Freesurfer] Tracula Inquiry

External Email - Use Caution Hi Jason, Tracula depends on FSL. If you have FSL installed, all that should be needed is to define FSL_DIR before sourcing `$FREESURFER_HOME/SetUpFreeSurfer.sh` So using your example above, you could go ``` export FREESURFER_HOME=/Applications/free

Re: [Freesurfer] Exporting ROI segmentation in T1 DICOM header

External Email - Use Caution Hi Vânia, You can use this repository to convert some FreeSurfer outputs to dicom. https://github.com/corticometrics/fs2dicom Unfortunately, the aparc+aseg is not supported at this time, only the aseg.mgz. -Paul On Thu, Oct 3, 2019 at 9:57 AM Bruce

Re: [Freesurfer] 2 beginner questions

Hi Brad, I don't have any experience with your first issue, but with regards to your second issue: are you running Windows10 as the host OS and Ubuntu as the guest OS? Ubuntu requires root (or admin) access to install packages. If you installed Ubuntu yourself, it should have prompted you to cre