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

2025-03-27 Thread Davide Sabbadin
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

2025-03-27 Thread Douglas N. Greve
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

Re: [Freesurfer] Recon-all-clinical pipeline

2025-03-20 Thread Iglesias Gonzalez, Juan E.
Dear Pauline, Did the skull stripping fail? What does norm.mgz look like? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lieshout, P.B. van (Pauline) Date: Thursday, March 20, 2025 at 10:40 AM To: freesurfer@nmr.mg

Re: [Freesurfer] recon-all failed

2025-02-16 Thread Paola Di Filippo
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

2025-02-15 Thread fsbuild
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

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

2025-02-12 Thread Douglas N. Greve
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

2025-02-11 Thread fsbuild
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

2025-02-11 Thread Huang, Yujing
There are no details of the error message in the log. Does your error look something like this? (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_merge_4/concat/_64]] (1) INVALID_ARGUM

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

2025-02-05 Thread fsbuild
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

2025-01-23 Thread Douglas N. Greve
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] Recon-all error...

2025-01-23 Thread Douglas N. Greve
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"

2025-01-02 Thread fsbuild
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 poin

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

2024-12-11 Thread Huang, Yujing
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

2024-12-11 Thread Huang, Yujing
/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

2024-12-11 Thread Melissa Marie Rundle
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

2024-12-10 Thread Douglas N. Greve
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!

2024-12-10 Thread Douglas N. Greve
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

Re: [Freesurfer] Recon-all failing

2024-12-01 Thread Douglas N. Greve
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

2024-12-01 Thread fsbuild
External Email - Use Caution  Hello Chemda, Maybe you could let us know what version of freesurfer you are running, what version of Linux or Mac OS your machine is running, and how much memory the machine has.  The recon-all.log could also be useful to send along.    A machine l

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

2024-10-30 Thread Melissa Marie Rundle
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

2024-10-30 Thread Iglesias Gonzalez, Juan E.
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

2024-10-30 Thread Melissa Marie Rundle
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 -all for many MRI sequences?

2024-08-23 Thread Douglas N. Greve
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

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

2024-08-16 Thread fsbuild
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

2024-06-25 Thread Douglas N. Greve
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

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

2024-06-24 Thread Douglas N. Greve
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

2024-06-24 Thread Douglas N. Greve
> 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?

2024-06-14 Thread Iglesias Gonzalez, Juan E.
Dear Barbara, you could in principle use recon-all-clinical for the enhanced T1 but the surface reconstruction would probably fail. Instead, I’d probably run SynthSR to synthesize 1mm T1 intensities while inpainting abnormalities and then run the standard recon-all. Cheers, /Eugenio -- Juan Euge

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

2024-06-13 Thread Gopinath, Karthik
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

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

2024-06-03 Thread Douglas N. Greve
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

2024-05-29 Thread Douglas N. Greve
sounds like something is wrong with the image. Did you look at ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a head? On 5/28/2024 6:07 AM, Chen Yang wrote: > External Email - Use Caution > > Hi everyone, > > I tried to run the reconstruction with the command line:

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

2024-05-28 Thread Chen Yang
External Email - Use Caution Hi everyone, I tried to run the reconstruction with the command line: recon-all -i ANTS_QS_template_MNI.nii.gz -subject CGBT -all then I got the error message: talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log fil

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

2024-05-08 Thread Douglas N. Greve
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

2024-05-03 Thread Dong, Yilei
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] recon-all process still not finishing properly

2024-04-23 Thread Dong, Yilei
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

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

2024-04-18 Thread Douglas N. Greve
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

2024-04-11 Thread Fischl, Bruce R.,PHD
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

2024-04-10 Thread Fischl, Bruce R.,PHD
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

2024-04-10 Thread Bhole, Salil
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

2024-04-08 Thread William Graves
External Email - Use Caution That worked beautifully. Thank you Yujing! Best, Will On Apr 8, 2024, at 8:58 AM, Huang, Yujing wrote: It looks like mris_fix_topology for lh hemisphere core dumped. This is from your recon-all.log: “ An extra large defect has been detected... Thi

Re: [Freesurfer] recon-all exits with errors

2024-04-08 Thread Huang, Yujing
It looks like mris_fix_topology for lh hemisphere core dumped. This is from your recon-all.log: “ An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://su

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

2024-04-05 Thread Iglesias Gonzalez, Juan E.
Dear Sam, The native images live in one space (typically anisotropic), whereas the recon-all-clinical files always live in their own 1x1x1mm isotropic grid (which is the whole point!). I am not familiar with the Enigma QC procedure but I wouldn’t be surprised if it’s not compatible with these va

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

2024-04-01 Thread Douglas N. Greve
You have a space in your current path (between severe and similar). That is causing the problem On 4/1/2024 8:26 AM, Huang, Yujing wrote: There is a space in your path ‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe similar/first_sT1W_3D_TFE_tra_MR350895.nii’. Rename the directory n

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

2024-04-01 Thread Huang, Yujing
There is a space in your path ‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe similar/first_sT1W_3D_TFE_tra_MR350895.nii’. Rename the directory 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: Fr

Re: [Freesurfer] recon-all nu_correct error

2024-03-28 Thread Dicamillo, Robert
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

2024-03-28 Thread Huang, Yujing
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 and recon-all uses ANTS N4BiasFieldCorrection for nu correct instead. We have addressed this error in our dev version

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

2024-03-25 Thread Dan Levitas
External Email - Use Caution Thanks Yujing, I realized that was likely the issue after sending my message. Indeed, removing the -qcache option for this longitudinal processing step resolved my issue. Thanks for the clarification. Dan On Mon, Mar 25, 2024 at 9:37 AM Huang, Yujin

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

2024-03-25 Thread Huang, Yujing
The recon-all ‘WM/GM Contrast’ step is skipped for longitudinal base processing. So, I’m not sure that ‘-qcache’ option can be used in base processing. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Dan Levitas Sent: Thursday, March 21, 2024 11:56 AM To: freesurfer@nm

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

2024-03-17 Thread Fischl, Bruce R.,PHD
What was your recon-all command line? You need to give it a directive (like -all), otherwise it will just create a subject directory tree and put the 001.mgz in the orig dir Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Naama Zur Sent: Sunday, March 17, 2024 5:13 PM T

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

2024-03-05 Thread Huang, Yujing
Hi Taylor, I don't understand how you could get that error. It seems to me that read_signa() is for reading .signa files. Can you try 'mris_calc -o rh.area.mid rh.area add rh.area.pial' directly? Pass full path to your rh.area and rh.area.pial. What does 'mri_info rh.area' report? Best, Yuj

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

2024-03-04 Thread Agata Wolna
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

2024-02-27 Thread BALBONI Irene
: [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

2024-02-26 Thread Agata Wolna
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

2024-02-25 Thread fsbuild
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

Re: [Freesurfer] Recon-all Longitudinal Talairach issue

2024-02-07 Thread Douglas N. Greve
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] recon-all ends prematurely without error

2024-01-25 Thread Huang, Yujing
Your recon-all command doesn't have the directive to tell it what to run - add option '-all' to your command. See this wiki page for detail https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Weisholtz, Daniel S.,MD Sent

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

2024-01-19 Thread fsbuild
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

2024-01-19 Thread Peled, Noam,PhD
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

2024-01-19 Thread Huang, Yujing
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

2024-01-19 Thread Peled, Noam,PhD
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

2024-01-19 Thread Huang, Yujing
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 permissions? 2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission Best, Yujing From: freesurfer-boun...@nmr

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

2024-01-16 Thread 김민지
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 +

2024-01-16 Thread 김민지
External Email - Use Caution  do not wish to continue communication over unencrypted e-mail -Original Message-From: "윤혜정" To: "Freesurfer support list" ; Cc:Sent: 2024-01-17 (수) 10:49:56 (UTC+09:00)Sub

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

2024-01-16 Thread fsbuild
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

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

2024-01-09 Thread Iglesias Gonzalez, Juan E.
Dear Francesca, Our method cannot reliably segment these thin/faint structures from clinical scans of arbitrary resolution and contrast, which is why they don’t get segmented. If you want to segment the choroid plexus, you could take then intensities under the ventricles and split them into cere

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

2024-01-06 Thread fsbuild
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

2024-01-06 Thread Flemister, Abeoseh B.
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

2024-01-06 Thread Flemister, Abeoseh B.
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

2024-01-05 Thread fsbuild
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

2024-01-05 Thread Flemister, Abeoseh B.
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

2024-01-05 Thread fsbuild
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

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

2024-01-05 Thread Flemister, Abeoseh B.
ciated! Abeoseh Flemister From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: Friday, January 5, 2024 3:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS WARNING: This message has originated from an Ex

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

2024-01-05 Thread Huang, Yujing
This is from your recon-all.log " mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz /usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz mri_convert: extra argument ("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz

Re: [Freesurfer] recon all with optiBET brain mask

2023-12-29 Thread Huang, Yujing
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

Re: [Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

2023-12-29 Thread James Hengenius
External Email - Use Caution Thanks for pointing that out! That seems to be working. Jim On Thu, Dec 28, 2023 at 6:53 PM Huang, Yujing wrote: > This is from Freesurfer wiki - > https://secure-web.cisco.com/1CkNjrY48pCUahVqRgpWm_wWr-VT402BvZ0Y61vf5NBHE08gelDHJOnnrnONbPXLIsRUSgn-e

Re: [Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

2023-12-28 Thread Huang, Yujing
This is from Freesurfer wiki - https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ Q. I have already skull-stripped data. Can I submit it to recon-all? A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data

Re: [Freesurfer] recon-all error - MRISlabel2Mask()

2023-11-22 Thread Douglas N. Greve
yes, sending the full log file will be helpful. My guess is that the surfaces got out of synch (eg, if you had done edits). On 11/21/2023 8:15 PM, Mark Wagshul wrote: External Email - Use Caution Dear Freesurfer experts, Hi. Hoping someone can give me some guidance in how to proceed

Re: [Freesurfer] recon-all error

2023-11-21 Thread Huang, Yujing
NaNs are in your original input image. They are replaced with 0 in the output mri/orig/001.mgz. Doug mentioned “Sometimes SPM will put NaNs in the image to indicate a mask.”. Is that your case? Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Carlos Alcocer Sent: Tuesday, Nov

Re: [Freesurfer] recon-all error

2023-11-19 Thread Douglas N. Greve
And how  did you create 001.mgz? Sometimes SPM will put NaNs in the image to indicate a mask. On 11/17/2023 10:12 AM, Huang, Yujing wrote: Hi Carlos, Can you attach recon-all.log? Best, Yujing *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Carlos Alcocer *Sent:* Thursday,

Re: [Freesurfer] recon-all error

2023-11-17 Thread Huang, Yujing
Hi Carlos, Can you attach recon-all.log? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Carlos Alcocer Sent: Thursday, November 16, 2023 4:57 PM To: Freesurfer support list Subject: [Freesurfer] recon-all error External Email - Use Caution Hi, For some of m

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

2023-11-13 Thread Iglesias Gonzalez, Juan E.
Dear Pauline, Thanks for the interest in our new pipeline! You can only run one scan at the time (but that scan may be of any resolution / contrast). Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lieshout, P.B. van (Pau

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

2023-09-28 Thread fsbuild
  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

2023-09-26 Thread fsbuild
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

2023-09-26 Thread Sorby-Adams, Annabel
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

2023-09-26 Thread Iglesias Gonzalez, Juan E.
External Email - Use Caution Dear Julian, I believe this is a problem with SynthSeg not being compatible with the new microprocessor in MAC computers. Our software engineers are looking into solutions to this. Sorry for the inconvenience, Eugenio -- Juan Eugenio Iglesias http://

Re: [Freesurfer] Recon-all completed without error in 10 seconds

2023-09-13 Thread Alan Francis
External Email - Use Caution Hello Lauren: Open the sR0391178-0002-1-000208-01.nii.gz file using freeview and see if the whole 3D brain is in place. This should give you a clue as to why this occurred. best, Alan On Wed, Sep 13, 2023 at 1:02 PM Lauren Stephens wrote: >

Re: [Freesurfer] Recon-all completed without error in 10 seconds

2023-09-13 Thread Huang, Yujing
Sent: Wednesday, September 13, 2023 2:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds External Email - Use Caution Hi Yujing, Thank you, that did work! Follow up question: Why would the code I used above, successfully generate the re

Re: [Freesurfer] Recon-all completed without error in 10 seconds

2023-09-13 Thread Boa Sorte Silva, Narlon
External Email - Use Caution I think you need to pass the flag ‘-all’ in the command line. recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-1-000208-01.nii.gz -all Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/CLEA

Re: [Freesurfer] Recon-all completed without error in 10 seconds

2023-09-13 Thread Lauren Stephens
support list Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds External Email - Use Caution Hi Lauren, You will also need to specify ‘-all’ to recon-all. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Lauren Stephens Sent

Re: [Freesurfer] Recon-all completed without error in 10 seconds

2023-09-13 Thread Huang, Yujing
External Email - Use Caution Hi Lauren, You will also need to specify '-all' to recon-all. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Lauren Stephens Sent: Wednesday, September 13, 2023 2:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfe

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

2023-08-25 Thread Matthew Lynch
External Email - Use Caution Recon-all-clinical worked consistently with 32 Gb RAM. I used WSL Ubuntu with 26Gb allocated to WSL before it would use swap. I watched one run, and it used total physical and swap memory of about 28 Gb. With 16Gb RAM it worked on about 75% of scans.

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

2023-08-19 Thread fsbuild
External Email - Use Caution  Thanks for the updates.  Not that it will likely help with the memory underrun, but it should be straightforward to update Freesurfer from 7.2.0 to 7.4.1 in the VM from the command line. You can use the Firefox browser in the VM to download the 7.4.1

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

2023-08-19 Thread Matthew Lynch
External Email - Use Caution Thank you fsbuild for the suggestions. Unfortunately it still does not work. I did not try the virtual machine, because I could only find version 7.2.0 ova file on the freesurfer website. It appears the 7.4.0 version does not yet have a virtual machi

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

2023-08-13 Thread Matthew Lynch
External Email - Use Caution The method I mentioned before does not always work. It worked for all but about 3 scans out of approximately 30. There are some scans for which the "committed memory" caps at about 23 Gb in the task manager and then either the out of memory error occu

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

2023-08-10 Thread fsbuild
External Email - Use Caution  Hello Matthew, Thanks for this info. If it is not too much work, just wondering if you could make a rough estimate or compute an average for the *total*memory* in use = (size of physical RAM in use by synthseg + size of all swap files resident on dis

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

2023-08-10 Thread Matthew Lynch
External Email - Use Caution Here is some additional follow up. I was able to get recon-all-clinical working in Ubuntu in WSL on a 16 Gb machine by increasing the swap and memory allowed in WSL. This is done through the .wslconfig file which is located in the %USERPROFILE% folder

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

2023-07-29 Thread Matthew Lynch
External Email - Use Caution I was able to get recon-all-clinical working with 16 Gb computer. I thought the problem might be Windows hogging memory, so I created a live persistent USB install of lubuntu, using lubuntu 22 as a low resource distro in order to minimize memory usage,

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

2023-07-13 Thread Matthew Lynch
External Email - Use Caution I do not have access to a computer with more RAM. I can run recon-all with 1mm T1 images without any problems. How much RAM would recon-all-clinical be expected to need? Does it require less RAM if it uses the GPU instead of CPU? On Thu, Jul 13, 202

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

2023-07-13 Thread Fischl, Bruce R.,PHD
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

Re: [Freesurfer] recon-all ends with error

2023-06-29 Thread Huang, Yujing
External Email - Use Caution It looks like you started recon-all by copying in mri/orig/001.mgz. I saw multiple runs of recon-all that were run on top of each other. Can you try to restart clean by providing the input on the command line ‘recon-all -s -I -all’? Best, Yujing

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