Re: [Freesurfer] mris_make_surfaces error with bbr-init-header

R" flag in your autorecon3 command will do the job. best, Andrew From: Sneha Pandya Sent: Tuesday, January 24, 2017 12:49:31 PM To: Hoopes, Andrew; Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header Thank you

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Hi David Try editing the base wm.mgz first instead of editing the long and cross wm files. Rerun autorecon2-wm and autorecon3 for the base dir, then completely rerun the longitudinals. The long surfaces are initialized from the base surfaces, so this could be why your wm fixes seem to have no

Re: [Freesurfer] error message while using autorecon1

Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew From: freesurfer-boun...@nmr

Re: [Freesurfer] error message while using autorecon1

@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1 Hi Colleen, If you source freesurfer, and run:

Re: [Freesurfer] error message while using autorecon1

t found. What do you mean by the methods used to sourced FS? I am using a linux computing cluster to run FS on. Is this what you mean? Thanks, Colleen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hoopes, An

Re: [Freesurfer] Medial Surface Problem

Hi Bronwyn, I tried to replicate your issue using both v5.3 and the current dev environment, but I had no luck. I'm guessing the problem has to do with combining the development binary along with 5.3, so I suggest using the 5.3 version of mris_make_surfaces to fix this. best, Andrew ___

Re: [Freesurfer] Medial Surface Problem

<http://neura.edu.au> [Follow @neuraustralia on twitter]<https://twitter.com/neuraustralia>[Follow NeuRA on facebook]<https://www.facebook.com/NeuroscienceResearchAustralia>[Subscribe to the NeuRA Magazine]<http://www.neura.edu.au/help-research/subscribe> On 29 Jul 201

Re: [Freesurfer] Freesurfer Contrast Issues

Hi Mackenzie, to use ftp, you can run this command to access the server: ftp surfer.nmr.mgh.harvard.edu It will ask you for a login, and you should use "anonymous" as your name. Use your email address when it prompts for a password. To upload a file (ex: file.tar.gz), run these two commands: cd

Re: [Freesurfer] Please unsubscribe me

Sure, you should be unsubscribed now. best, Andrew > On Aug 25, 2017, at 11:29 AM, Micah Rhodes wrote: > > Please unsubscribe me to this email list. > > Thanks. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.ha

Re: [Freesurfer] Error while running recon-all

Hi Ritesh, What operating system and version are you running freesurfer on, ubuntu? Can you also send the fs version build stamp (you can get this by running 'bugr’) best Andrew > On Aug 29, 2017, at 11:41 AM, Ritesh Mahajan > wrote: > > Hello guys, > > I am trying to run recon-all command

Re: [Freesurfer] Freeview aborts under centos6

Hi Markus, What is the output when you run the following: (this will list libraries you have access to) /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so best, Andrew On Sep 15, 2017, at 3:33 AM, Markus Gschwind mailto:markus.gschw...@gmail.com>> wrote: Hi ex

Re: [Freesurfer] Freeview aborts under centos6

!! Markus 2017-09-15 17:49 GMT+02:00 Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>>: Hi Markus, What is the output when you run the following: (this will list libraries you have access to) /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict

Re: [Freesurfer] Freeview aborts under centos6

uceMPI.so.5.6 is not a symbolic link Thanks for your help!! Markus 2017-09-15 17:49 GMT+02:00 Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>>: Hi Markus, What is the output when you run the following: (this will list libraries you have access to) /sbin/ldconfig -N -v $(sed 's/:/ /

Re: [Freesurfer] Freeview Versions

Hi Arkadiy, If you send the buildstamps for your two freesurfer distributions, I can see what the respective versions are. You can print the buildstamp by running the command “bugr” in a sourced fs environment best Andrew On Sep 19, 2017, at 2:25 PM, Maksimovskiy, Arkadiy mailto:amaksimovs...

Re: [Freesurfer] Compile problems

Hi Aziz, We store non-text files outside of the repository, have you set up a remote with git annex yet? Instructions are here: https://surfer.nmr.mgh.harvard.edu/fswiki/Freesurfer_github best Andrew On Sep 28, 2017, at 4:10 AM, Aziz Nanthaamornphong mailto:azi...@phuket.psu.ac.th>> wrote: Hi

Re: [Freesurfer] Trouble building 6.0.0 on centos7

Hi Sol, I don't recognize this error, but will look into it. Have you set up the required system libraries and library dependencies described in https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page ? Andrew On Oct 2, 2017, at 5:55 PM, Sol Jerome mailto:s...@utdallas.edu

Re: [Freesurfer] Trouble building 6.0.0 on centos7

al freesurfer RPM Thanks, Sol * Oct 03, 2017, at 15:42:12 PM, Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>> wrote: Hi Sol, I don't recognize this error, but will look into it. Have you set up the required system libraries and library dependencies described in https://surfe

Re: [Freesurfer] Errors on compiling FreeSurfer

Hi Aziz, The centos6-built packages seem to cause issues when building on ubuntu, particularly for tcltk apps. I would ignore this for now, or you could compile tcltk yourself. As a general fix, I’ll work on building a package distribution on ubuntu16 best, Andrew On Oct 9, 2017, at 2:02 AM,

Re: [Freesurfer] Selecting OS for image analysis

Hi Ramesh, Freesurfer is built and developed mainly on centos machines, but ubuntu works fine as well. Here’s some more info: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements best Andrew On Oct 17, 2017, at 7:04 AM, Ramesh Babu mailto:mgrameshbabu2...@gmail.com>> wrote: Dear Expe

Re: [Freesurfer] problem when run qdec

Hi Yawu, Seems like a graphics driver issue. Does running "glxinfo" give the same error? What OS are you using? Andrew > On Oct 24, 2017, at 3:36 AM, Liu Y wrote: > > Dear Experts, > When I run qdec, it showed me error message, any suggestins? > qdec > X Error of failed request: BadValue (

Re: [Freesurfer] lGI mris_fill Error

Hi Arkadiy, This might have to do with SIP, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ Andrew On Oct 27, 2017, at 2:13 PM, Maksimovskiy, Ark

Re: [Freesurfer] mris_decimate missing for Mac

Hi Paula, thanks for pointing this out. It looks like there's an issue with the libs required to build mris_decimate on the current mac build machine. I’ll sort this out, but for now, you can just download and copy ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/OSX/mris_decima

Re: [Freesurfer] mris_jacobian error while running recon-all -make all

Hi Anne, Unfortunately, the “-make all” flag contains a bug in the stable6.0 release. However, this has been fixed in the dev version. This can be quickly fixed if you download this script - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/recon-all.makefile - a

Re: [Freesurfer] problems of testing freesurfer

Hi Danny, The SUBJECTS_DIR variable defines the path to a directory where freesurfer recon data is stored for a particular study. When setting this path variable, you don’t need to include the <> brackets. After sourcing freesurfer, start by making a sample directory and defining your SUBJECTS

Re: [Freesurfer] problems of testing freesurfer

am a beginner. Best Regards, Danny Deng On Nov 8, 2017, at 10:48 AM, Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>> wrote: recon-all -i sample-001.nii.gz -s bert -all ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesur

Re: [Freesurfer] Bug Reporting: recon-all -s 001 exited with ERRORS

Hi Rosalia, What version of perl are you using? Based on this thread from last year - https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-May/045407.html - it seems like this is a known issue with new versions of perl and freesurfer v5.3. Unfortunately, your only two options are to inst

Re: [Freesurfer] error hipp subfields

Hi John, So you've been able to run some subjects successfully through the subfield stream? Can you provide some more information like freesurfer version/buildstamp (run the command ‘bugr') as well as your operating system and version? thanks, Andrew On Nov 13, 2017, at 7:36 AM, John Papatria

Re: [Freesurfer] Freeview Crashes!!

What is the output of: ldd `which freeview.bin` thanks, Andrew On Nov 10, 2017, at 8:52 AM, Ruopeng Wang mailto:rpw...@nmr.mgh.harvard.edu>> wrote: What version of freesurfer did you run? It looks like the issue is related to incompatible/missing libraries. Ruopeng On Nov 10, 2017, at 7:18 A

Re: [Freesurfer] "error parsing license file, expected 4 values" with amygdala segmentation

Hi Carl, How many lines of text exist in your license file? Andrew On Nov 9, 2017, at 8:18 AM, Carl Anderson mailto:remfr...@gmail.com>> wrote: Hi Everyone, I'm running freesurfer-Darwin-OSX-dev-20171107-ec5ce3a I seem to get the line "error parsing license file, expected 4 values" occuring fr

Re: [Freesurfer] data conversion

Hi Danny, If you want to cd into SUBJECTS_DIR, just run: export SUBJECTS_DIR=/downloads/buckner_data/tutorial_subjs cd $SUBJECTS_DIR “cd $downloads/buckner_data/tutorial_subjs” isn’t a valid command if you haven’t set a variable named “downloads" Andrew > On Nov 23, 2017, at 4:00 AM, Danny De

Re: [Freesurfer] medial wall label in Freesurfer 6

Hi Sofia, Another user seems to be experiencing a similar issue right now. How many subjects are you trying to average? I haven’t been able to replicate this, so it might require uploading some subjects. Can you send the make_average_volume.log? best, Andrew On Nov 27, 2017, at 10:16 AM, Sofi

Re: [Freesurfer] MacOS Sierra 10.12.5 dyld lazy symbol binding error

Hi Kelly, This might have to do with SIP being enabled, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, Andrew On Nov 27, 2017, at 6:33 PM,

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

I’ve tested a few different (large) sets of subject data and still been unable to replicate this problem, so tough to say what’s causing it. Are you using the make_average_subject 6.0.0-patch? Have you also tried running the command with a subgroup containing the other 56 subjects (maybe it’s a

Re: [Freesurfer] error: dyld: lazy symbol binding failed

Hi Stephan, This probably has to do with SIP being enabled, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, Andrew On Nov 29, 2017, at 1:

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

The make_average_subject patch can be downloaded here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ The readme file contains some instructions. This patch will definitely fix your recon-all error, but I don’t think it’s related to the labeling issue. Though, it’s worth a t

Re: [Freesurfer] license file error

Hi Ri, It looks like there might be an issue with the license saved at /Applications/freesurfer6/.license. Try overwriting this file with your license.txt best, Andrew On Nov 29, 2017, at 6:23 PM, Ritobrato Datta mailto:ridatpennc...@gmail.com>> wrote: Hi All, I am using Mac OS X Sierra an

Re: [Freesurfer] Trouble building 6.0.0 on centos7

ilddir/build/BUILD/freesurfer-6.0.0/freeview' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0' > make: *** [all] Error 2 > > > > Thanks, > Sol > > * Oct 05, 2017, at 19:54:55 PM, Hoopes, Andrew &g

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Okay, can you upload the compressed average subject to our ftp server (https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) and I will take a look? thanks, Andrew On Nov 30, 2017, at 12:30 PM, M del Mar Velasco mailto:melly_2...@hotmail.com>> wrote: Hi, I have installed the patch and i

Re: [Freesurfer] error hipp subfields

roblem. John On Mon, Nov 13, 2017 at 9:07 PM, Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>> wrote: Hi John, So you've been able to run some subjects successfully through the subfield stream? Can you provide some more information like freesurfer version/buildstamp (run the comman

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Thanks, I just received it - I’ll take a look Andrew On Dec 1, 2017, at 5:10 AM, M del Mar Velasco mailto:melly_2...@hotmail.com>> wrote: Hello, I have upload the data. Recipient mail was ahoo...@mgh.harvard.edu. Please, check you have received it. Thanks very

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, I think I’ve found the cause - it’s due to a small bug in make_average_surface. I should have a fix for you soon (today or tomorrow). best, Andrew > On Dec 7, 2017, at 3:47 PM, M del Mar Velasco wrote: > > Hi, > > Have you take a look at our data? Have you find any possible caus

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

issues persist. best, Andrew On Dec 7, 2017, at 3:54 PM, Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>> wrote: Hi M del Mar, I think I’ve found the cause - it’s due to a small bug in make_average_surface. I should have a fix for you soon (today or tomorrow). best, Andrew On Dec 7, 2017, a

Re: [Freesurfer] A note about the Freesurfer license file

Hi Mike, Is it possible that freesurfer is reading the wrong license file? What are you naming the new license as? FS could be reading a hidden “.license” file in FREESURFER_HOME instead. best, Andrew > On Dec 7, 2017, at 4:35 PM, Angstadt, Mike wrote: > > I am getting this same glibc messa

Re: [Freesurfer] Issue with Freesurfer installation

Hi Scott, It looks like "/Users/scottpruett/sample-001.mgz" doesn’t exist because your cp command never ran (you have to specify a destination). Try: cp $FREESURFER_HOME/subjects/sample-001.mgz . best, Andrew On Dec 14, 2017, at 4:00 PM, Pruett, Scott mailto:brandon_pru...@brown.edu>> wrote:

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, Okay, I just updated the script at https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface. Let me know if the issue continues. best, Andrew On Dec 22, 2017, at 9:25 AM, M del Mar Velasco mailto:melly_2...@hotmail.com>> wrote: Hi, I am sorry for i

Re: [Freesurfer] the comand of 'segmentHA_T1_long.sh' is not found

Hi Gallen, segmentHA_T1_long.sh is only available in the freesurfer dev version. Also, if you’re getting the glibc license error while using the martinos freesurfer distribution, I will message you directly to sort this out. best, Andrew On Dec 22, 2017, at 3:11 PM, Gong, Liang mailto:lgo...@

Re: [Freesurfer] OpenGL link errors

Hi, I’ve responded to your issue via the GitHub page, but I’ll post my response here for the records: It looks like your compilation is missing the -lGLU -lGL library flags. You should check mris_show/Makefile to make sure that GL_LIBS and GLU_LIBS have been set: grep -e GLU_LIBS -e GL_LIBS mr

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

Hi Carme, segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev best, Andrew On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal mailto:carme.ur...@gmail.com>> wrote: Dear FreeSurfer users, I wanted to run the new script that segments the h

Re: [Freesurfer] asegstats2table error message

Hi, This is a bug introduced by python3, you must run this script with python2 by either modifying the first line to say: #!/usr/bin/env python2 or by running: python2 $FREESURFER_HOME/bin/asegstats2table --subjects baseline 12m 24m 36m --meas volume --tablefile aseg_stats.txt best, Andrew O

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed, You can download a new, free license for v6.0 directly from here: http://surfer.nmr.mgh.harvard.edu/registration.html best, Andrew On Jan 9, 2018, at 9:11 AM, m.ba...@uliege.be wrote: Dear Bruce, Many thanks for you answer! I am trying to rerun the cor

Re: [Freesurfer] Hippocampal segmentation flips on the left side

I think this is related to a matlab incompatibility. Can I see a copy of the log? Andrew > On Jan 11, 2018, at 12:09 PM, Iglesias Gonzalez, Eugenio > wrote: > > Dear Lauri, > Your problem is that GLIBCXX_3.4.15 was not found by kvlApplyTransform, so > the left model was not successfully flip

Re: [Freesurfer] FreeSurfer LocalGI error

Hi Manoj, This probably has to do with SIP being enabled, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, Andrew On Jan 16, 2018, at 2:59

Re: [Freesurfer] recon-all exited with error

Hi Trisanna, Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue. best, Andrew On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much mailto:trisanna.sprung-m...@mail.mcgill.ca>> wrote: Sorry, Bruce. ignore my last email. Not sure what happened there.

Re: [Freesurfer] recon-all exited with error

y successfully changed. ftp> quote PASV 227 Entering Passive Mode (132,183,202,158,147,251). ftp> put icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection. On Wed, Jan 17, 2018 at 5:5

Re: [Freesurfer] recon-all exited with error

st wanted to make sure that my recipient email would be the FreeSurfer support list. Trisanna On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>> wrote: Hi Trisanna, Okay - if your file is less than 2GiB, I suggest sending your data via the Martinos file drop

Re: [Freesurfer] Hippocampal segmentation flips on the left side

for now: export LD_PRELOAD=/usr/lib64/libstdc++.so.6 # (with bash) or setenv LD_PRELOAD /usr/lib64/libstdc++.so.6 # (with tcsh) best Andrew On Jan 11, 2018, at 2:43 PM, Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>> wrote: I think this is related to a matlab incompatibility. Can I

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, I think I’ve discovered the source of this issue. It’s tough to troubleshoot it without access to the subject set, but I think I have a working fix. The patch link (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface) is updated with the new sc

Re: [Freesurfer] Anatomical ROI analysis

Hi Ting, this is a bug introduced by python3, you must run this script with python2 by either modifying the first line to say: #!/usr/bin/env python2 or by running: python2 $FREESURFER_HOME/bin/asegstats2table --subjects 004 021 040 067 080 092 --segno 11 17 18 --tablefile aseg.vol.table best,

Re: [Freesurfer] Which Dev Version is Best?

Hi Arkadiy, You should use the OSX-ElCapitan dev version, it’s the most up-to-date and contains new patches. We’ve recently upgraded the mac dev builds from OS X Lion (10.7) to El Capitan (10.11), so you’re in the clear if you’re using Sierra (10.12). This is a relatively recent change, so let

Re: [Freesurfer] Which Dev Version is Best?

upgrade back up based on your info- might you have any suggestions for how to fix the “cocoa” problem? Thanks again, Arkadiy From: "Hoopes, Andrew" Date: Monday, January 22, 2018 at 2:45 PM To: "Maksimovskiy, Arkadiy" , Freesurfer support list Subject: Re: [Freesurfer] Wh

Re: [Freesurfer] Which Dev Version is Best?

all of your help and info. -Arkadiy From: "Hoopes, Andrew" mailto:ahoo...@mgh.harvard.edu>> Date: Monday, January 22, 2018 at 3:21 PM To: "Maksimovskiy, Arkadiy" mailto:amaksimovs...@mclean.harvard.edu>>, Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Hippocampus Subfield analysis error

Hi Hannah, What kind of environment are you running this in? These errors make it seem like you do not have a PATH variable set at all. Are you using bash? and what operating system? best Andrew > On Jan 22, 2018, at 4:06 AM, Iglesias Gonzalez, Eugenio > wrote: > > Hi Hannah, > This seems

Re: [Freesurfer] segmentHA_T2.sh

Hi Eva, I believe this should be fixed in the most recent El Capitan dev version. Let me know if the issue persists. best Andrew On February 1, 2018 at 7:02:19 AM, Iglesias Gonzalez, Eugenio (e.igles...@ucl.ac.uk) wrote: We are looking into all this. We’ll have up

Re: [Freesurfer] Wm.mgz editing

Hi Emily, Another user had this problem recently, and we weren’t able to resolve it. For now, if your upload is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) Let me know

Re: [Freesurfer] Problems running LGI

Hi Dusan, I’ll take a look at this and get back to you soon. I think this issue is related to the matlab version. best Andrew On February 10, 2018 at 4:27:11 PM, Dusan Hirjak (dusanhir...@hotmail.com) wrote: Dear Freesurfer Experts, I am currently trying to

Re: [Freesurfer] Problems running LGI

, Andrew On February 12, 2018 at 10:28:09 AM, Hoopes, Andrew (ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>) wrote: Hi Dusan, I’ll take a look at this and get back to you soon. I think this issue is related to the matlab version. best Andrew On February 10, 2018 at 4:27:11 PM,

Re: [Freesurfer] IndexError: list index out of range

Hi Sara and Arkadiy, What version of python2 are you using? python --version thanks Andrew On February 13, 2018 at 10:16:34 AM, Makaretz, Sara Johanna (smakar...@mgh.harvard.edu) wrote: *I also got this error when I ran w/ python 2: python2 $FREESURFER_HOME

Re: [Freesurfer] IndexError: list index out of range

Python 2.7.3 -- EPD 7.3-1 (64-bit) Sara From: Hoopes, Andrew Sent: Thursday, February 15, 2018 3:56:22 PM To: Makaretz, Sara Johanna; Freesurfer support list Subject: Re: [Freesurfer] IndexError: list index out of range Hi Sara and Arkadiy, What version of pytho

Re: [Freesurfer] Error in running make_average_subject

Hi Janani, We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ The second part of the readme file in that directory provides instructions for resolving this. best Andrew On February 19, 2018 at 9:40:22 AM, M Janani (janan...@hcl.com

Re: [Freesurfer] Error in running make_average_subject

u Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64 recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018 I've attached the recon-all.log file. Any help would be greatly appreciated. Best, Scott On Tue, Feb 20, 2018 at 10:25 AM, Hoopes, Andrew

Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

Hi Davide, Yes, the centos6 freesurfer6.0 download is compatible with centos7 best Andrew On February 20, 2018 at 5:59:04 PM, Vanzo, Davide (davide.va...@vanderbilt.edu) wrote: Hello, According from few messages in this mailing list, FreeSurfer 6.0.0 shou

Re: [Freesurfer] Freeview update on Mac

Hi Sarah, I updated the wiki page. We actually just put up a standalone, dev freeview app today. best Andrew On February 27, 2018 at 11:38:57 AM, Sarah Cole (coleashle...@gmail.com) wrote: Hi Doug/Zeke, Could you please update the page for freeview update on M

Re: [Freesurfer] FSdev compilation error

Hi Victor, Can you send over the config.log? Also, it’s probably worth noting that the cuda dev builds are currently failing due to recent mrisurf.c changes (working on fixing this now), so if you’re trying to resolve this as soon as possible, it might make sense to checkout and build an older

Re: [Freesurfer] Installation problem

Hi Neda, What’s going on exactly? Is the source command hanging or is it repeatedly printing the freesurfer startup message? best Andrew On March 7, 2018 at 3:03:38 AM, Neda Mohammadi (n55moham...@gmail.com) wrote: Dear Expert, I tried to install Freesurfer on

Re: [Freesurfer] hew hippocampal and amygdala subfields

Hi Thomas, I have a feeling this issue has been fixed in recent updates, but I’ll need some more info to troubleshoot. Can you send the buildstamp (using the bugr command) for this FS dev version as well as the platform and version of the system you're running it on? thanks Andrew On March 1

Re: [Freesurfer] FSdev compilation error

ig.log I will try to build an older version too. Thank you -- Best regards Victor Hansen IT support Neurological Research Unit, Rigshospitalet nru.dk On Wed, 2018-03-07 at 17:45 +, Hoopes, Andrew wrote: Hi Victor, Can you send over the config.log? Also, it’s probably worth noting that the cu

Re: [Freesurfer] Installation problem

| sort thanks, Andrew From: Neda Mohammadi Date: Sunday, March 11, 2018 at 6:30 AM To: "Hoopes, Andrew" Cc: FS Help Subject: Re: [Freesurfer] Installation problem Hi Andrew, Thanks for your reply. It repeat the freesurfer startup message . freesurfer-Linux-centos6_x86_64-

Re: [Freesurfer] Problem running mri_convert

Hi Jay, as a temporary fix for 6.0, I would suggest disabling SIP and rerunning: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best Andrew From: on behalf of Jay Edelman Reply-To: FS Help Date: Thursday, March 22, 2018 at 10:02 PM To: FS Help Subject:

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Anna, Unfortunately, we’re not able to build the dev code right now due to a compile error, but this should get sorted out within the next day or two, so I can help you out with getting this new mri_normalize then best Andrew From: on behalf of Anna Daniels Reply-To: FS Help Date: Monda

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

9, 2018, at 2:31 PM, Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>> wrote: Hi Anna, Unfortunately, we’re not able to build the dev code right now due to a compile error, but this should get sorted out within the next day or two, so I can help you out with getting this new mri_normali

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Anna, You can download the new mri_normalize from this link - https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_normalize To get it into your FS installation, first set executable permissions and then move it into your $FREESURFER_HOME/bin directory (sudo

Re: [Freesurfer] unable to open freeview

Hi Darko, how are you sourcing freesurfer? And what is the output of running “which freeview” and “which freeview.bin”? best, Andrew From: on behalf of Darko Komnenić Reply-To: FS Help Date: Tuesday, April 17, 2018 at 11:17 AM To: FS Help Subject: [Freesurfer] unable to open freeview Dear

Re: [Freesurfer] unable to open freeview

following line right before the call to “freeview.bin $argv”: echo $PATH and send the output over. best Andrew From: Darko Komnenić Date: Tuesday, April 17, 2018 at 11:35 AM To: "Hoopes, Andrew" Cc: FS Help Subject: Re: [Freesurfer] unable to open freeview Hi Andrew, FreeSurfe

Re: [Freesurfer] unable to open freeview

also be helpful if you add another “echo $PATH” line right below the “#!/bin/tcsh -ef” in the freeview script best Andrew From: Darko Komnenić Date: Tuesday, April 17, 2018 at 12:36 PM To: "Hoopes, Andrew" Cc: FS Help Subject: Re: [Freesurfer] unable to open freeview Hi Andrew,

Re: [Freesurfer] unable to open freeview

called? You don’t want that “Linuxbrew directory detected…” error in your PATH variable From: Darko Komnenić Date: Tuesday, April 17, 2018 at 1:21 PM To: "Hoopes, Andrew" Cc: FS Help Subject: Re: [Freesurfer] unable to open freeview Hi Andrew, OK, so here is what happened: After addin

Re: [Freesurfer] unable to open freeview

Are you using a bash shell? If you are, there should be a file located at ~/.bashrc (it’s a hidden file in your home folder) Andrew From: Darko Komnenić Date: Tuesday, April 17, 2018 at 2:24 PM To: "Hoopes, Andrew" Cc: FS Help Subject: Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

Hi Richard, thanks for pointing this out – I’ll take a look into it. best Andrew From: on behalf of "Jones, Richard" Reply-To: FS Help Date: Thursday, April 19, 2018 at 9:49 AM To: FS Help Subject: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305 I ran the command shown belo

Re: [Freesurfer] unable to open freeview

Darko Komnenić Date: Thursday, April 19, 2018 at 6:54 AM To: "Hoopes, Andrew" Cc: FS Help Subject: Re: [Freesurfer] unable to open freeview An update, in the .bash_profile file, there is a line about linuxbrew. Do you recommend that I remove it? Sending the file attached. Best, Darko On

Re: [Freesurfer] unable to open freeview

PM To: "Hoopes, Andrew" Cc: FS Help Subject: Re: [Freesurfer] unable to open freeview Hi Andrew, I commented out the last two lines, and the same error message still appears. Please let me know if you have any other suggestions. Thanks! Best, Darko On Thu, Apr 19, 2018 at 6:08

Re: [Freesurfer] recon all error mpr2mni305

Hi Richard, it seems this was caused by a minor update to our mac build machine. These libraries should be correctly linked now in the most recent dev build (updated a few minutes ago). Let me know if you still have issues best, Andrew On 4/19/18, 2:39 PM, "freesurfer-boun...@nmr.mgh.harvard.ed

Re: [Freesurfer] V6 Stable OSX software error - multistrip flag

Hi Matt, this issue should be fixed in the freesurfer development version, but as a temporary fix to get things working in v6, I would suggest disabling SIP and rerunning: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best Andrew From: on behalf of Matth

Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

I’m not sure. How long do these runs usually take Eugenio? I’m noticing that the process only used 9% of the cpu, which is odd since it ran for 10+ hours Andrew From: "Iglesias Gonzalez, Eugenio" Date: Tuesday, May 8, 2018 at 4:18 AM To: FS Help Cc: "Hoopes, Andrew" Subj

Re: [Freesurfer] SIP disabled, fs_update run, still getting "dyld: lazy symbol binding failed" from within MATLAB

Hi Fred, you mention that the fs environment variables are accessible within MATLAB, but is freesurfer fully sourced in your MATLAB environment? I’m guessing this is an issue with your DYLD_LIBRARY_PATH not being set correctly. You should check to see if the DYLD_LIBRARY_PATH env variable in you

Re: [Freesurfer] Recon-all exited with errors

Hi Ryan, this issue should be fixed in the freesurfer development version, but as a temporary fix to get things working in v6, I would suggest disabling SIP and rerunning: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best Andrew From: on behalf of Ryan

Re: [Freesurfer] niiWrite(): error opening file tmp.nii

Hi Konstantina, you have to set SUBJECTS_DIR equal to an actual directory path in your filesystem, the “” is just a placeholder. Best, Andrew From: on behalf of Konstantina Skolariki Reply-To: FS Help Date: Monday, July 9, 2018 at 10:30 AM To: FS Help Subject: Re: [Freesurfer] niiWrite(): er

Re: [Freesurfer] mris_ca_label seed

Hi Rosemary, the seeds for those commands are set from recon-all. The individual binaries do not seed themselves with a default value, so it’s expected that mris_ca_label produces inconsistent results when run independently (and without the -seed flag). The algorithm processes the surface verti

Re: [Freesurfer] Surface editing: recon-all exited with errors

Hi Eli, the -make all flag contains a bug in the 6.0 release. This can be fixed if you download this script - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/recon-all.makefile - and overwrite the current $FREESURFER_HOME/bin/recon-all.makefile Let me know if yo

Re: [Freesurfer] mris_register segmentation fault while running recon-all with -cm option on a scan with .6mm isotropic voxels

Hi Francois, this is an mris_register bug from last month that should be fixed in the most recent dev distribution. best, Andrew From: on behalf of "Lalonde, Francois (NIH/NIMH) [E]" Reply-To: FS Help Date: Tuesday, August 7, 2018 at 2:33 PM To: FS Help Subject: [Freesurfer] mris_register s

Re: [Freesurfer] Untar and sh files in dev version

Hi K, your original error is usually due to an incomplete download. You might want to try redownloading and untaring again Best, Andrew From: on behalf of Schumman Resonance Reply-To: FS Help Date: Saturday, August 11, 2018 at 9:24 AM To: FS Help Subject: Re: [Freesurfer] Untar and sh files

Re: [Freesurfer] Stats2table_bash.sh script

asegstats2table is a python2 script, and you are likely running it with python3. Try running the script with “python2” prepended to the command: python2 asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats --all-segs --tablefile wmparc_stats.txt best, Andrew From: o

  1   2   3   4   >