[Freesurfer] `recon-all -base` fails with glibc/license error, but cross-sectional `recon-all` works

External Email - Use Caution Hi FreeSurfer community, I'm running into an issue with the longitudinal FreeSurfer pipeline. Background: I'm working with T1-weighted MRI scans from an aerobic exercise intervention study in older adults (age 60+). I have two timepoints per subject

[Freesurfer] Recon-all clinical vs. FS version 8.0.0

External Email - Use Caution Hi there, I am analyzing some pediatric brains with clinical pathology, and I was wondering if I would expect a difference in the reconstructions from regular recon-all (Freesurfer version 8.0.0) vs. recon-all clinical, since they both use SynthSeg

Re: [Freesurfer] Recon-all using mni152 as template

External Email - Use Caution i am working with pet images and after running recon-all i used the transformation .lta to move the pet image in the standard space (pet and mri are already in the same space). By looking at the segmentation template aparc+aseg i noticed there is a loot

Re: [Freesurfer] Recon-all using mni152 as template

I'm not sure what you mean. by itself mni152 is not a segmentation template. Or do you want to do the analysis in mni152 space? If so, why? On 3/27/2025 10:17 AM, Davide Sabbadin wrote: External Email - Use Caution Hi all, Is there the possibility to perform the segmentation through r

[Freesurfer] Recon-all using mni152 as template

External Email - Use Caution Hi all, Is there the possibility to perform the segmentation through recon-all using a different template, e.g. mni152? Thanks, Sabbadin Davide ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Recon-all-clinical pipeline

@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all-clinical pipeline External Email - Use Caution Dear sir/madam, I am implementing the recon-all-clinical pipeline on clinical MRI scans. I have done a test-run of around 70 T1-w clinical MRI scans. Processing of 9 out of 70 scans have failed

[Freesurfer] Recon-all-clinical pipeline

External Email - Use Caution Dear sir/madam, I am implementing the recon-all-clinical pipeline on clinical MRI scans. I have done a test-run of around 70 T1-w clinical MRI scans. Processing of 9 out of 70 scans have failed. In almost all the failed processing scans, the pipeline

[Freesurfer] Recon-all: skip initial inhomogeneity correction

External Email - Use Caution Dear FreeSurfer developers, I am currently working with a T1-weighted MRI dataset that has already undergone intensity inhomogeneity correction. Since I would like to run recon-all on this data, is it possible to include a flag in recon-all to skip thi

Re: [Freesurfer] recon-all failed

External Email - Use Caution I was able to fix the problem with this single line of command: sudo chmod -R a+w $SUBJECTS_DIR but thank you as always! Il giorno sab 15 feb 2025 alle ore 23:13 fsbuild ha scritto: > External Email - Use Caution > > > You can read from but

Re: [Freesurfer] recon-all failed

External Email - Use Caution  You can read from but not write to where freesurfer is installed under /usr/local/freesurfer as your normal userid.   Just change the setting of SUBJECTS_DIR to be, e.g., in your home directory or some location you can always write to as your normal

[Freesurfer] recon-all failed

External Email - Use Caution hi everyone, i have succesfully managed to download freesurfer with ubuntu 22 on a virtual machine. i've tried some tutorials and everything is working fine. now i am trying to run my first recon-all, but this is the error I get: freesurfer-li

Re: [Freesurfer] recon-all: aparc+aseg.mgz missing labels

The 5th vent, non-wm-hypos, left and right vessel are not worrisome. The left and right cerebral cortex are probably just a few voxels that did not get recoded to the surface parcellation. The ento and parahippo  are probably a segmentation error (good that there are only a few of them:) On 2/

Re: [Freesurfer] Recon-all error - release 8.0.0-beta

u> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThe new version will be announced  in the next couple of days. From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Yanez-Ramos, Lupita Sent: Tuesday, February 1

Re: [Freesurfer] Recon-all error - release 8.0.0-beta

PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all error - release 8.0.0-beta External Email - Use Caution From: Yanez-Ramos, Lupita mailto:yanez-ramos.mariaguadal...@mayo.edu>> Date: Tuesday, February 11, 2025 at 11:53 To: freesurfer@nmr.mgh.harva

[Freesurfer] Recon-all error - release 8.0.0-beta

External Email - Use Caution From: Yanez-Ramos, Lupita Date: Tuesday, February 11, 2025 at 11:53 To: freesurfer@nmr.mgh.harvard.edu Subject: Recon-all error - release 8.0.0-beta Hello FreeSurfer Developers, I'm attempting to run recon-all and recon-all-clinical, but it is the fi

[Freesurfer] recon-all: aparc+aseg.mgz missing labels

External Email - Use Caution Hello, I have run recon-all on ~1600 participants and will use the aparc+aseg.mgz parcellation to extract structural connectomes.Across the dataset, the number of labels in each parcellations ranges from 109 to 115. Where can I find a complete list o

Re: [Freesurfer] recon-all failed with FreeSurfer v8.0.0 (beta) on Mac

External Email - Use Caution  The fix for the error you posted when running the 8.0.0 beta release - which has to do with how some python code is run - will be fixed in the forthcoming 8.0.0 release; it’s unrelated to your environment setup. The commands that run the recon-all pi

Re: [Freesurfer] recon-all error

It says that it cannot find /run/media/user/2TB/freesurfer/ASegStatsLUT.txt does that file exist on your system? On 1/16/2025 6:20 PM, 박경일 wrote: External Email - Use Caution Dear FS Development Team, I recently encountered an error while running the recon-all process. This is the

Re: [Freesurfer] [freesurfer] recon-all error

it says finished without error On 1/15/2025 5:13 PM, 박경일 wrote:     External Email - Use Caution Dear FS Development Team, I recently encountered an error while running the recon-all process. This is the first time I’ve experienced an issue with this routine process. Please refer to the

Re: [Freesurfer] Recon-all error...

That recon-all.log file says it returned without error: "recon-all -s E0001 finished without error at Mon Dec 23 12:20:40 KST 2024" what's the problem? On 1/13/2025 10:26 PM, 박경일 wrote: External Email - Use Caution Dear FS Development Team, I recently encountered an error while runn

Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"

External Email - Use Caution  Hello Pei-Ying,  It does not work to run freesurfer/recon-all command(s) on subject data that lives on a Windows formatted drive (in your case visible from inside the Linux VM via the mount point to drive d, /mnt/d).   The SUBJECTS_DIR needs to

Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

support list mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Benjamin Billot mailto:bbil...@mit.edu>>; Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> Subject: Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error External Email - Use Caution Hell

Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

/distribution/average/colortable_BA_thresh.txt Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Melissa Marie Rundle Sent: Wednesday, December 11, 2024 11:24 AM To: Freesurfer support list Cc: Benjamin Billot ; Iglesias Gonzalez, Juan E. Subject: Re: [Freesurfer] recon-all-clinical

Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

External Email - Use Caution Hello, We are getting the error below for every subject when we run recon-all-clinical. It's only for the rh, not the lh. We are using Freesufer 7.4.1 with the synthseg python script. Let me know if there is a fix/update/patch for this. Thanks, M

[Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

External Email - Use Caution Hello, We are getting the error below for every subject when we run recon-all-clinical. It's only for the rh, not the lh. We are using Freesufer 7.4.1 with the synthseg python script. Let me know if there is a fix/update/patch for this. Thanks, M

Re: [Freesurfer] recon-all on poor MRI quality

It is probably indirectly related to the large slice thickness. You might try running recon-all_clinical.sh On 12/10/2024 11:28 AM, Francesco Lomi wrote: > External Email - Use Caution > > Dear all, > I am writing you because I would like to know why recon-all on this > subject exited w

Re: [Freesurfer] Recon all across different image dimensions of different clinical subjects!

On 12/5/2024 10:14 PM, JM wrote: External Email - Use Caution Hi FreeSurfer experts, In our hospital research settings, we collected structural MRI data from patients while they were admitted for treatment. Some of the patients were scanned before contrast agent was injected and s

[Freesurfer] Recon all across different image dimensions of different clinical subjects!

External Email - Use Caution Hi FreeSurfer experts, In our hospital research settings, we collected structural MRI data from patients while they were admitted for treatment. Some of the patients were scanned before contrast agent was injected and some were scanned after contrast a

Re: [Freesurfer] Recon-all failing

Not sure what is going on. The log file uses 7.3.2, not 7.2.0, at least on the last invocation. Also, it does not indicate an error on the last call. If you are running it on a previously existing folder, maybe a file is there but corrupted. On 11/26/2024 5:33 PM, Mark Wagshul wrote:   

Re: [Freesurfer] recon-all command stuck before creating pial files

tients with epilepsy and I am attempting to use freesurfer to create the mesh .pial files. When I run the freesurfer recon-all command, the command gets stuck at "correcting defects" with the last file it creates being the "lh.defect_chull". It has been stuck for a few

[Freesurfer] Recon-all failing

External Email - Use Caution Hi, I'm hoping someone can help with this strange error. Have been using recon-all on this dataset forever, and now all of a sudden it is completely failing just a few minutes into the processing. Attaching the recon-all.log file (had run a bunch of

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)

[Freesurfer] recon all data for classification between groups !

External Email - Use Caution Dear FS experts, I have longitudinal data: Three time-points [T1-T3] with an interval of about 6 months between T1 and T2 and 6 months between T2 and T3 from a control group as well as from a clinical group (again three time-points [T1-T3] with an int

Re: [Freesurfer] Recon-all -all for many MRI sequences?

you have to pass it the file(s) you want to analyze. If you have a bunch of dicoms, and your T1 is just one of many, you have to figure out one of the files that corresponds to the T1. Or you can use dcmunpack, eg, dcmunpack -src /path/to/your/dicoms -targ outputfolder -auto-runseq mgz That comm

[Freesurfer] Recon-all -all for many MRI sequences?

External Email - Use Caution Hello,I have many dicom files with many MRI sequences from one person.(T1, T2, FLAIR, DWI, ...)I didn't divided the folders according to the sequences-they are all in one folder.Then does the program sort T1 image automatically and make results whe

Re: [Freesurfer] recon-all terminates at fix topology rh step

External Email - Use Caution  You’re using the 7.2.0 release from 2021 whereas the latest release is 7.4.1 from 2023.   Unless you have to stick with the older release because floating point math results could differ with a newer one, then you could try downloading and installin

Re: [Freesurfer] Recon-all manual edits - multiple re-runs

It will take all edits you have made into account when you rerun it. On 6/25/2024 1:00 PM, Blujus, Jenna wrote: External Email - Use Caution Hi all, I have processed a set of T1w data through recon-all (v7.3.2) and am now making manual edits, if necessary. I have had a few cases wher

[Freesurfer] Recon-all manual edits - multiple re-runs

External Email - Use Caution Hi all, I have processed a set of T1w data through recon-all (v7.3.2) and am now making manual edits, if necessary. I have had a few cases where control points, wm.mgz, and brainmask edits are needed and incorporated via 'recon-all -autorecon2-cp -auto

Re: [Freesurfer] Recon-all for a common template

gt; Chen > > > - Original Message ----- >> From: "Douglas N. Greve" >> To: "freesurfer" >> Sent: Monday, 3 June, 2024 18:42:14 >> Subject: Re: [Freesurfer] Recon-all for a common template >> Why did you do an lr reversal if it looked goo

Re: [Freesurfer] Recon-all for a common template

> Best regards, > Chen > > > - Original Message ----- >> From: "Douglas N. Greve" >> To: "freesurfer" >> Sent: Monday, 3 June, 2024 18:42:14 >> Subject: Re: [Freesurfer] Recon-all for a common template >> Why did you do an lr rev

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 for a common template

n case of any clue? Thank you so much! > > Best, > Chen > > > > - Original Message - >> From: "Douglas N. Greve" >> To: "freesurfer" >> Sent: Wednesday, 29 May, 2024 15:26:25 >> Subject: Re: [Freesurfer] Recon-all for a common temp

Re: [Freesurfer] Recon-all for a common template

gt; > Does anyone know how to solve this problem? Thanks so much! > > Best, > Chen > - Original Message - >> From: "Chen Yang" >> To: "freesurfer" >> Sent: Monday, 20 May, 2024 13:59:13 >> Subject: [Freesurfer] Recon-all for a common template

Re: [Freesurfer] Recon-all for a common template

rted Does anyone know how to solve this problem? Thanks so much! Best, Chen - Original Message - > From: "Chen Yang" > To: "freesurfer" > Sent: Monday, 20 May, 2024 13:59:13 > Subject: [Freesurfer] Recon-all for a common template > External Email

Re: [Freesurfer] recon-all process still not finishing properly

Sincerely, Yilei *From:* Dong, Yilei *Sent:* Tuesday, April 23, 2024 3:34 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] recon-all process still not finishing properly Hi Freesurfer support, I ha

Re: [Freesurfer] recon-all process still not finishing properly

it's more of a cluster issue I have to talk with the staff that manage it? Sincerely, Yilei From: Dong, Yilei Sent: Tuesday, April 23, 2024 3:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all process still not finishing properl

Re: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error

024 16:58:18 To: Freesurfer support list Subject: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error External Email - Use Caution Dear FS experts, I am encountering an error when running recon-all. I followed the FAQ <https://se

Re: [Freesurfer] recon-all process still not finishing properly

behalf of Douglas N. Greve Sent: Thursday, April 18, 2024 2:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all process still not finishing properly not sure what is happening. You can run recon-all with -debug and capture the output (both stdout and stderr) into a

[Freesurfer] recon-all error

External Email - Use Caution I installed freesurfer 7.4.1 on Debian 12 (using the Ubuntu 22 .tar.gz). Some programs run fine, but some do not. When running recon-all, I get the following error: -bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file no

Re: [Freesurfer] recon-all process still not finishing properly

not sure what is happening. You can run recon-all with -debug and capture the output (both stdout and stderr) into a file. This will cause it to print out huge amounts of text specifying what it is doing on each line. You should also see if there is some stderr output that is not being caught.

Re: [Freesurfer] Recon-all stuck at topology fix

support list Subject: Re: [Freesurfer] Recon-all stuck at topology fix External Email - Use Caution Here are some images from the patient. I also have the recon-all log posted here is well. This is the same patient but taken from a file where I tried to manually skull strip to fix the

Re: [Freesurfer] Recon-all stuck at topology fix

Can you post some pictures? The norm.mgz, the wm.mgz, the lh.orig.nofix, the aseg.mgz, that kind of thing? Something is badly wrong…. Bruce On Apr 10, 2024, at 7:05 PM, Bhole, Salil wrote:  External Email - Use Caution Hello, I have tried to process this MRI a few times now and it a

Re: [Freesurfer] Recon-all stuck at topology fix

External Email - Use Caution Hello, I have tried to process this MRI a few times now and it always seems to get stuck on the step I have pasted below here. I have tried to fix the defect myself by editing the voxels manually, but that has also not seemed to help. I've looked th

Re: [Freesurfer] recon-all exits with errors

rd.edu> Subject: [Freesurfer] recon-all exits with errors External Email - Use Caution Dear FreeSurfer Developers, I’m trying to run recon-all as a pre-processing step in the AFNI resting-state analysis pipline, using the command: recon-all -subject $subj -i $anat_cm -all -parallel So far i

Re: [Freesurfer] recon-all exits with errors

‘-parallel’ option. Use ‘-nthreads ’ instead. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of William Graves Sent: Sunday, April 7, 2024 10:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all exits with errors External Email - Use Caution

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 mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")

name and try again. Best, Yujing *From:*freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *??? *Sent:* Sunday, March 31, 2024 11:18 PM *To:* FreeSurfer *Subject:* [Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/00

Re: [Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")

: FreeSurfer Subject: [Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz") External Email - Use Caution Hello FreeSurfer Developers, I'm writing to ask for help while using "recon-all" command.

[Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")

External Email - Use Caution Hello FreeSurfer Developers, I'm writing to ask for help while using "recon-all" command. I have converted some dcm format files to to nii format. Then I ran the command "recon-all -s maoyipeng -i first_sT1W_3D_TFE_tra_MR350895.nii -all", an err

Re: [Freesurfer] recon-all nu_correct error

er support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] recon-all nu_correct error Hi Yilei, I think "nu_correct: Command not found. FREESURFER: Undefined variable." is unrelated to your recon-all didn’t finish. That error happens in the beginning of recon-all an

Re: [Freesurfer] recon-all nu_correct error

rror in our dev version. I'm wondering if your cluster computer enforces some time, memory ... limit on your job. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Dong, Yilei Sent: Thursday, March 28, 2024 2:18 PM To: Freesurfer support list Subject: [Freesurfer] recon-

Re: [Freesurfer] recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh

du < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Dan Levitas > *Sent:* Thursday, March 21, 2024 11:56 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] recon-all mris_preproc error: Cannot find > surf/lh.w-g.pct.mgh > > > > *

Re: [Freesurfer] recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh

@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh External Email - Use Caution Hello, I have a longitudinal dataset where each participant was scanned twice over the course of 5 months. I have been following FS's Longitu

Re: [Freesurfer] Recon-all command produces only 001.mgz file in the mri/orig directory

To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all command produces only 001.mgz file in the mri/orig directory External Email - Use Caution Hi all, I am using Ubuntu 23.1 with freesurfer 7.4.1 to run the recon-all command and the command runs without error and I do get

[Freesurfer] Recon-all command produces only 001.mgz file in the mri/orig directory

External Email - Use Caution Hi all, I am using Ubuntu 23.1 with freesurfer 7.4.1 to run the recon-all command and the command runs without error and I do get a set of directories including: label, mri, scripts, stats, surf, tmp, touch, and trash. However, the only folders that ar

Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area

.area' report? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area External

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 with optiBET brain mask

: [Freesurfer] recon all with optiBET brain mask This is from Freesurfer wiki - MailScanner has detected a possible fraud attempt from "secure-web. cisco. com" claiming to be https: //surfer. nmr. mgh.  harvard. edu/fswiki/UserContributions/FAQ Q. I have already skull-stripped data. Can Th

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 Longitudinal Talairach issue

Can you send the recon-all.log file that contains the error? On 1/24/2024 4:01 AM, Kapteijns, Kirsten wrote: External Email - Use Caution Dear all, I have run recon-all successfully on multiple subjects on multiple timepoints. If I open the mri folder, it shows the correct talairach

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: 16 January 2024 13:41 To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure The command should look like this ‘recon-all -s subjid -qcache -all -i input-file

Re: [Freesurfer] recon-all ends prematurely without error

z, Daniel S.,MD Sent: Thursday, January 25, 2024 12:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all ends prematurely without error Hello FreeSurfer team, I have been using FreeSurfer for some time without difficulty, but I recently encountered a problem that I cannot overco

[Freesurfer] recon-all ends prematurely without error

Hello FreeSurfer team, I have been using FreeSurfer for some time without difficulty, but I recently encountered a problem that I cannot overcome. When I run recon-all using a command like this: recon-all -s b047test -i /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_J

[Freesurfer] Recon-all Longitudinal Talairach issue

External Email - Use Caution Dear all, I have run recon-all successfully on multiple subjects on multiple timepoints. If I open the mri folder, it shows the correct talairach files and no issues arose during processing. However, when I then run the longitudinal pipeline (first

Re: [Freesurfer] recon-all cannot execute: required file not found

edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu>Sent: Friday, January 19, 2024 3:10 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all cannot execute: required file not found I’m wondering how you ran

Re: [Freesurfer] recon-all cannot execute: required file not found

esurfer support list Subject: Re: [Freesurfer] recon-all cannot execute: required file not found I’m wondering how you ran recon-all. Do you see the error even running it w/o any arguments? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Peled, Noam,PhD Sent: Friday, January 19,

Re: [Freesurfer] recon-all cannot execute: required file not found

I'm wondering how you ran recon-all. Do you see the error even running it w/o any arguments? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Peled, Noam,PhD Sent: Friday, January 19, 2024 2:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all cannot ex

Re: [Freesurfer] recon-all cannot execute: required file not found

ry 19, 2024 2:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all cannot execute: required file not found After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH. 1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the execute permis

Re: [Freesurfer] recon-all cannot execute: required file not found

rom: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Peled, Noam,PhD Sent: Friday, January 19, 2024 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all cannot execute: required file not found Dear group, I'm trying to run Freesurfer on digitalOcean server running Ubuntu

[Freesurfer] recon-all cannot execute: required file not found

Dear group, I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 (GNU/Linux 5.19.0-46-generic x86_64) I Downloaded freesurfer 7.4.0 (freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e) After sourcing Freesurfer, recon-all gives following error: .../freesurfer/bin/

Re: [Freesurfer] recon-all errors (cannot execute binary file +

24-01-17 (수) 13:01:17 (UTC+09:00)Subject: Re: [Freesurfer] recon-all errors (cannot execute binary file +External Email - Use Caution  do not wish to continue communication over unencrypted e-mail -Original Message-From: "윤혜정" <hyejung7...@amc.seoul.kr&g

Re: [Freesurfer] recon-all errors (cannot execute binary file +

24-01-17 (수) 10:49:56 (UTC+09:00)Subject: [Freesurfer] recon-all errors (cannot execute binary file +External Email - Use Caution Good day. When I run recon-all for my nii files I get either one of the following error messages: 1. ERROR: could not configure recon-all paramet

Re: [Freesurfer] recon-all errors (cannot execute binary file +

External Email - Use Caution It looks like you did not use the .pkg file installer to install Freesurfer on the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to use as FREESURFER_HOME.  The installer should ensure the privileges should be correct to ru

[Freesurfer] recon-all errors (cannot execute binary file +

External Email - Use Caution Good day. When I run recon-all for my nii files I get either one of the following error messages: 1. ERROR: could not configure recon-all parameters Killed 2. ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: l

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

The command should look like this 'recon-all -s subjid -qcache -all -i input-file' From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Monday, January 15, 2024 9:45 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer recon-all qcache parti

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Friday, January 12, 2024 4:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer recon-all qcache partial failure External Email - Use Caution Dear Freesurfer researchers, I have an issue with recon-all-qcashe

[Freesurfer] Freesurfer recon-all qcache partial failure

External Email - Use Caution Dear Freesurfer researchers, I have an issue with recon-all-qcashe results. (please find the recon-all.log attached.) The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but it did not create fsaverage files with different s

Re: [Freesurfer] recon-all vs. recon-all-clinical: missing ROIs

: [Freesurfer] recon-all vs. recon-all-clinical: missing ROIs External Email - Use Caution Hi, recon-all generates these volumes, amongst others: “Left-vessel”, “Left-choroid-plexus”, “Right-vessel”, “Right-choroid-plexus” recon-all-clinical does not generate these volumes. Or at least that I am

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

Flemister, Abeoseh B. <flemist...@missouri.edu> Sent: Saturday, January 6, 2024 12:24:40 PM To: fsbuild <fsbu...@contbay.com>; freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS  

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

External Email - Use Caution I’m using Ubuntu. Abeoseh Flemister From: Flemister, Abeoseh B. Sent: Saturday, January 6, 2024 12:24:40 PM To: fsbuild ; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

nux-ubuntu22_amd64-7.4.1.tar.gz> Abeoseh Flemister From: fsbuild Sent: Friday, January 5, 2024 9:35 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Flemister, Abeoseh B. Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS Did you install Freesurfer 7.4.1

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

h FlemisterFrom: fsbuild <fsbu...@contbay.com>Sent: Friday, January 5, 2024 8:27 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Flemister, Abeoseh B. <flemist...@missouri.edu>Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS  F

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

24 8:27 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Flemister, Abeoseh B. Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS For issues with Freeview displaying graphics when running via Linux on a Windows host thru WSL, you could look at the recent thread with the subject "

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

eesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu>Sent: Friday, January 5, 2024 3:05 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all -s SiroS

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