Re: [Freesurfer] recon-all-clinical output brainvol.stats vs synthseg.vol.csv

External Email - Use Caution 7.4.1 From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Iglesias Gonzalez, Juan E. Sent: Wednesday, October 30, 2024 4:52 PM To: Freesurfer support list Subject: [EXTERNAL] Re: [Freesurfer] recon-all-clinical output brainvol.stats vs

Re: [Freesurfer] recon-all-clinical output brainvol.stats vs synthseg.vol.csv

Subject: Re: [Freesurfer] recon-all-clinical output brainvol.stats vs synthseg.vol.csv External Email - Use Caution Hello, Recon-all-clinical outputs several files, including brainvol.stats and synthseg.vol.csv, that have volumetric data that don’t match each other. See example data

Re: [Freesurfer] recon-all-clinical output brainvol.stats vs synthseg.vol.csv

External Email - Use Caution Hello, Recon-all-clinical outputs several files, including brainvol.stats and synthseg.vol.csv, that have volumetric data that don’t match each other. See example data below. Are the stats for brainvol (as well as lh.aprac.stats/rh.aprac.stats)

Re: [Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?

Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Barbara Bellenberg Date: Thursday, June 13, 2024 at 3:30 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images

Re: [Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?

Hi Barbara, Yes, you can use recon-all-clinical for the enhanced T1. But, the surface reconstruction might fail and in that case, you might have to try running SynthSR + recon-all. Thank you, Karthik On Jun 13, 2024, at 1:30 AM, Barbara Bellenberg wrote: External Email - Use Caution

[Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?

External Email - Use Caution Dear all, I would like to use the recon-all-clinical pipeline with Gadolinium contrast-enhanced 3D-T1 weighted images. Can you tell me if recon-all-clinical is suitable for this purpose? Thanks in adcance for your support! Barbara ___

Re: [Freesurfer] Recon-All Clinical Stream: Image Output Observations in Creating ENIGMA QC Images

...@nmr.mgh.harvard.edu on behalf of Sam Sievertsen Date: Friday, April 5, 2024 at 11:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-All Clinical Stream: Image Output Observations in Creating ENIGMA QC Images External Email - Use Caution Good Afternoon, I hope this email

Re: [Freesurfer] recon-all-clinical synthseg error

External Email - Use Caution Hi! I've managed to debug the problem and it turns out that it was generated by the mri_convert function - it produced a corrupted native.mgz image that synthseg couldn't correctly read. I encounter this problem when pulling the freesurfer:7.4.1 from d

Re: [Freesurfer] recon-all-clinical synthseg error

External Email - Use Caution Hi! Thanks for getting back to me. I'm running it on CentOS Linux 7 in a singularity container. What I did is to pull the freesurfer container from the DockerHub (https://secure-web.cisco.com/1mn_DXGJRkbRZaR60gIIXGTJuR-LMjZIaTJCeez5OyFU1R7CR20ybjGOUz4

Re: [Freesurfer] recon-all-clinical synthseg error

External Email - Use Caution  It could help to know what OS version and what Freesurfer version you are running.  From your path /usr/local/freesurfer it looks like you are running a Freesurfer release, e.g., 7.4.1. - R. On Feb 25, 2024, at 21:45, Agata Wolna w

[Freesurfer] recon-all-clinical synthseg error

External Email - Use Caution Hi! I'm trying to run recon-all-clinical but I'm running into an error with the SynthSeg at the very beginning. Do you have any hints what the problem might be here? Here's the full error message: the following problem occured with image [mypath]/mri/

Re: [Freesurfer] Recon all clinical with multiple input scans

(Pauline) Date: Monday, November 13, 2023 at 03:51 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon all clinical with multiple input scans External Email - Use Caution Dear sir/madam, I have been trying out the new recon-all-clinical algorithm. In the FreeSurferWiki on recon

[Freesurfer] Recon all clinical with multiple input scans

External Email - Use Caution Dear sir/madam, I have been trying out the new recon-all-clinical algorithm. In the FreeSurferWiki on recon-all-clinical, it is not specified if I can add multiple scans (T1, FLAIR and T2, for instance) of the same individual in the recon-all-clinic

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

  Von: fsbuild <fsbu...@contbay.com> Datum: Mittwoch, 27. September 2023 um 00:55 An: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Cc: "Conrad, Julian" <julian.con...@medma.uni-heidelberg.de> Betreff: Re: [Freesurfer] Recon-all-clinical

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

35To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSegExternal Email - Use CautionDear Julian,I believe this is a problem with SynthSeg not being compatible with the new microp

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

2. Hope this works! Annabel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Date: Tuesday, 26 September 2023 at 17:35 To: Freesurfer support list Subject: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg External Emai

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

-Ki8YwhX_EsUP2Y_33P6Un8LPT3Lf_oRxCvl2rAYzvsHICA/http%3A%2F%2Fwww.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Conrad, Julian Date: Tuesday, September 26, 2023 at 4:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg External

[Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

admin@medma0236 ~ % recon-all-clinical.sh /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii RC026_sub-010_ses-mri01 8 /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer # #@# reco

Re: [Freesurfer] recon-all-clinical out of memory error

3eh5V-r39LuOBw6cI3QUthBZM6gUlw209v8gxO-kvtwdS91ZhwakThVxcssArdjan0pI44dQAmZRqGWdVsEjLZHtJ0DUS5BfwbrrwNtaVLv7roOHkNexs4bZOBxXPgf2eEVe9PuHqoYXleq74p438PuJCc_rgyaq2eHyYVi5Cn6dBAZj4zN7usrr6awcyPSdS5Ap1BG_tMXvI4CyNrh8GGZJF6VryQ/https%3A%2F%2Faskubuntu.com%2Fquestions%2F178712%2Fhow-to-increase-swap-space >>>>

Re: [Freesurfer] recon-all-clinical out of memory error

 On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu> wrote:External Email - Use CautionCan you try it on a computer with more ram?  From: freesurfer-boun...@nmr..mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Matthew Ly

Re: [Freesurfer] recon-all-clinical out of memory error

ed. >>> >>> >>> >>> >>> >>> On Thu, Jul 13, 2023 at 3:28 PM Matthew Lynch >>> wrote: >>> >>>> I do not have access to a computer with more RAM. I can run recon-all >>>> with 1mm T1 images without any probl

Re: [Freesurfer] recon-all-clinical out of memory error

>>> On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD < >>> bfis...@mgh.harvard.edu> wrote: >>> >>>> External Email - Use Caution >>>> >>>> Can you try it on a computer with more ram? >>>> >>>> >

Re: [Freesurfer] recon-all-clinical out of memory error

.edu> On Behalf Of Matthew LynchSent: Thursday, July 13, 2023 1:55 PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all-clinical out of memory error External Email - Use CautionI am having trouble running the new recon-all-clinical module.  I input 5mm T1 axia

Re: [Freesurfer] recon-all-clinical out of memory error

gt;>> >>> Can you try it on a computer with more ram? >>> >>> >>> >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Matthew Lynch >>> *Sent:* Thursday, July 13, 2023 1

Re: [Freesurfer] recon-all-clinical out of memory error

Sent:* Thursday, July 13, 2023 1:55 PM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* [Freesurfer] recon-all-clinical out of memory error >> >> >> >> *External Email - Use Caution* >> >> I am having trouble running the new recon-al

Re: [Freesurfer] recon-all-clinical out of memory error

*On Behalf Of *Matthew Lynch > *Sent:* Thursday, July 13, 2023 1:55 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] recon-all-clinical out of memory error > > > > *External Email - Use Caution* > > I am having trouble running the new recon-a

Re: [Freesurfer] recon-all-clinical out of memory error

External Email - Use Caution Can you try it on a computer with more ram? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Matthew Lynch Sent: Thursday, July 13, 2023 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all-clinical out of memory error

[Freesurfer] recon-all-clinical out of memory error

External Email - Use Caution I am having trouble running the new recon-all-clinical module. I input 5mm T1 axial DICOM images and it fails in SynthSeg with what appears to be an out of memory error. I am running FreeSurfer 7.4.0 in WSL with Ubuntu 22 on a computer with 16 Gb RAM.

Re: [Freesurfer] recon-all-clinical problems

External Email - Use Caution So when I fixed those two _thresh errors in https://secure-web.cisco.com/1NSg93ccyJ-d1nRYxQp22qqxh0VpV5ftKk_nXjpyVVwbCeR6Hrc55wa7clBot2_7TwVB60Mr2knHiVv8A4Mfl2qmBr5BYBGmlurvKxK7tkVb_5cRm_5FEI_GvOXQuD2koygzRKJ-i9xNxRvWZdKOxuYG-tyuRwO9v-AdgHd7Hh9JHtaZBxs

Re: [Freesurfer] recon-all-clinical problems

External Email - Use Caution Actually, that is not the problem at all. I have found two errors in your script (the one on Github) There are two lines which refer to colortable_BA_thresh.txt that should say /colortable_BA.txt The script gets further when I fix those but I still h

Re: [Freesurfer] recon-all-clinical problems

External Email - Use Caution I found the problem. Your script has the following lines : You need to delete the fsaverage from the $SUBJECTS_DIR definition because the lines following it put it in also. ln -s $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/ cd ../label # labels

Re: [Freesurfer] recon-all-clinical

: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Date: Tuesday, June 20, 2023 at 9:32 AM To: freesurfer@nmr.mgh.harvard.edu , Iglesias Gonzalez, Eugenio , Gopinath, Karthik Subject: Re: [Freesurfer] recon-all-clinical External Email - Use Caution On 5/26/2023 5:39 PM

Re: [Freesurfer] recon-all-clinical

External Email - Use Caution On 5/26/2023 5:39 PM, Andrew Dedinas Geoly wrote: External Email - Use Caution Hello Freesurfer experts! I am conducting a longitudinal GMV and CT analysis of mTBI participants who received an experimental single-dose pharmacological trea

[Freesurfer] recon-all-clinical

External Email - Use Caution Hello Freesurfer experts! I am conducting a longitudinal GMV and CT analysis of mTBI participants who received an experimental single-dose pharmacological treatment. We collected GE Bravo (0.9mm isotropic) T1w data pre, immediately after (~ 4 days af