Hello Eduard,
It looks to me like the application freesurfer/BrainstemSS/mac_osx/segmentSubject.app needs to be run via the script freesurfer/BrainstemSS/mac_osx/run_SegmentSubject.sh which sets the path to pick up the Matlab library libmwcpp11compat.dylib.
While I think we have that library in house because we have a Matlab license, you would need to have a Matlab distribution or download their runtime environment in order to get that library for segmentSubject.app to run.
- rob
On Oct 3, 2018, at 3:50 PM, Vasile, Eduard EVASILE@mgh.harvard.edu wrote:
Hi,
Coming back with an update from the previous email. I installed it but it tells me that it cannot be open because of a problem and then I get the above error. The version is 6.0. Is there a place where I can come with my laptop and see what is the problem?
Process: prelaunch [1300] Path: /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch Identifier: segmentSubject Version: 1 Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: prelaunch [1300] User ID: 501
Date/Time: 2018-10-03 15:47:11.569 -0400 OS Version: Mac OS X 10.13.6 (17G2307) Report Version: 12 Bridge OS Version: 3.0 (16P375) Anonymous UUID: C3615BC6-2956-15B2-00D8-9F435B158DB0
Sleep/Wake UUID: 2988BAC2-9FC2-422B-AF82-6F0576A1E894
Time Awake Since Boot: 3200 seconds
System Integrity Protection: enabled
Crashed Thread: 0
Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY
Termination Reason: DYLD, [0x1] Library missing
Application Specific Information: dyld: launch, loading dependent libraries
Dyld Error Message: Library not loaded: @rpath/libmwcpp11compat.dylib Referenced from: /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch Reason: image not found
Binary Images: 0x100000000 - 0x100000ff7 +segmentSubject (1) <BF09BC5D-285F-35DE-BE47-E8F723B03986> /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch 0x105013000 - 0x10505dacf dyld (551.4) <8A72DE9C-A136-3506-AA02-4BA2B82DCAF3> /usr/lib/dyld
Kind regards Eduard
On 10/3/18, 12:00 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu> wrote:
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1. Re: Error during decompression of DICOM JPEG compressed series (Greve, Douglas N.,Ph.D.) 2. Re: Error during decompression of DICOM JPEG compressed series (Dicamillo, Robert) 3. Re: Error during decompression of DICOM JPEG compressed series (Greve, Douglas N.,Ph.D.) 4. Mac OS free surfer instalation (Vasile, Eduard) 5. Re: Mac OS free surfer instalation (Hoopes, Andrew) 6. Re: amygdala segmentation atlas influence (Iglesias Gonzalez, Eugenio) 7. Deadline approaching: PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center G?ttingen (Caspar M. Schwiedrzik) 8. Re: Overlay electric field distribution on pial surface (Meusen - Klooster, D.C.W.) 9. Re: Overlay electric field distribution on pial surface (Bruce Fischl) 10. output values of vertices on surface into a textfile (Sims, Sara A)
Message: 1 Date: Tue, 2 Oct 2018 17:00:09 +0000 From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 9b313c16-98ba-9434-e1a9-85febbbd28d3@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Sorry, I meant to change your default shell. That command is being run using the system() command from inside of a c-program, which undoubtedly starts your default shell. Just see if it works.
On 10/02/2018 10:36 AM, k3ops@free.fr wrote:
External Email - Use CautionI am using bash shell but I tried with many others as mentioned in my first post (zsh, tcsh, csh, sh) and nothing worked so far...
----- Mail original ----- De: "Douglas N. Greve,Ph.D." DGREVE@mgh.harvard.edu ?: freesurfer@nmr.mgh.harvard.edu Envoy?: Mardi 2 Octobre 2018 15:18:14 Objet: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series
What shell are you using? Try using cshell or tcshell to see if it works.
On 10/2/18 4:56 AM, k3ops@free.fr wrote:
External Email - Use CautionHi FS team,
I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. I am facing an issue with a JPEG compressed DICOM series that I am not able to precess, I always get the following error during "mri_convert" procedure (before calling recon-all), I also wrote the last command that produces this error:
fsdcmdecompress --i freesurfer_18/6858304 --o /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out sh: 1: Syntax error: Bad fd number
After some investigations, it looks it is related to the way standard outputs are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file (which is missing by the way). It looks like ">&" redirection is not a correct syntax in bash (the shell I am using), so I tried with others but unfortunately none of them worked so far (zsh, tcsh, csh, sh).
Do you have any recommendation for the way to use "mri_convert" tool? or any other tool that could convert DICOM to nifty efficiently?
Thanks for your feedbacks.
Regards, Florent
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Message: 2 Date: Tue, 2 Oct 2018 17:43:26 +0000 From: "Dicamillo, Robert" RDICAMILLO@mgh.harvard.edu Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 8A4D4B9A-2E49-445A-A616-C74122B3A599@nmr.mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
It may be complaining about >& for redirection. Try using 2>&1 instead.
On Oct 2, 2018, at 4:56 AM, k3ops@free.frmailto:k3ops@free.fr wrote:
sh: 1: Syntax error: Bad fd number