Re: [Freesurfer] Recon error
Can you send the log file?
On 2/10/2021 10:26 AM, Bohorquez Montoya, Luisa wrote:
External Email - Use Caution
Hello Freesurfer
I have been trying to run this subject 3 times (with different
walltime) and I am having the same error. Would you mind please to
explain me what I am doing wrong?
Thank you
subject="$1"
echo $subject
cd /scratch/global/lbohorquez/Freesurfer/"$subject"
export SUBJECTS_DIR=/scratch/global/lbohorquez/Freesurfer/"$subject"
ANATDIR=/scratch/global/lbohorquez/Freesurfer/
OPENMP=12
export OMP_NUM_THREADS=12
recon-all \
-autorecon2 -autorecon3 -subject "$subject" \
-no-isrunning -parallel -openmp 12 \
SUMA-ize with AFNI
echo "Before Suma"
@SUMA_Make_Spec_FS -NIFTI \
-fspath ${SUBJECTS_DIR}/"$subject" \
-sid "$subject"
echo "After Suma"
registration TO MNI
cd ${SUBJECTS_DIR}/"$subject"/SUMA/
@SSwarper -input "$subject"_SurfVol.nii -base
MNI152_2009_template_SSW.nii.gz -subid ssWarp
*Luisa Bohorquez, PhD.*
*Department of Psychiatry,*
*Medical College of Wisconsin.*
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Re: [Freesurfer] Recon Error
Hi Emily no log file attached... cheers Bruce On Tue, 6 Jun 2017, Emily Rogers wrote: > Hello, > > I am trying to implement using Freesurfer segmentation in my analysis for MEG > data. I am trying to segment this structural MRI (1400composite.dcm) and I > keep getting errors. I have attached the log file. Any help is appreciated. > > Thank you, > Emily > > > Emily E. Rogers, MSc > Wake Forest Graduate School of Arts and Sciences > PhD Student, Neuroscience > (336)-906-1103 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Recon Error
Hello, I am trying to implement using Freesurfer segmentation in my analysis for MEG data. I am trying to segment this structural MRI (1400composite.dcm) and I keep getting errors. I have attached the log file. Any help is appreciated. Thank you, Emily Emily E. Rogers, MSc Wake Forest Graduate School of Arts and Sciences PhD Student, Neuroscience (336)-906-1103 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Recon Error
Hi Maura
we are in the process of updating stable6. The existing version has a bug
that causes these crashes. Hopefully we'll have something usable soon
sorry
Bruce
On Wed, 16 Dec 2015, Hamel, Maura K. wrote:
Hi Freesurfer experts,
I’m looking for some help with some recons I tried running yesterday for
about 60 subjects.
The command I submitted was:
recon-all
-i/autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/${subjec
t}/MPRAGE/0*/001.mgz -s ${subject} -all
I have attached the log files, and I’m hoping you can explain the error I
received and what I need to do fix it. Thanks in advance for your help!
FREESURFER_HOME: /usr/local/freesurfer/stable6
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151208
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 4.1.8-1.el6.elrepo.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: tyra
SUBJECTS_DIR:
/autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60
PWD: /autofs/cluster/maury/users/gcoombs/College_Risk
ssh tyra
setenv SUBJECTS_DIR
/autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60
cd /autofs/cluster/maury/users/gcoombs/College_Risk
Best,
Maura Hamel
Clinical Research Coordinator
Psychiatric Neuroimaging Research Program
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th St, Room 2602A
Charlestown, MA 02129
Phone: 617-643-4441
Fax: 617-726-4078
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Re: [Freesurfer] Recon Error
Hello Maura,
Here at the Center we stopeed active development of the stable6 branch
and focused all our development on the dev version. A new stable6 will
be cut soon from dev soon, but in the meantime I have linked the two
together (stable6=dev). So feel free to resubmit your job, as the bug
you encountered has been fixed in the dev branch. You dont need to
change anything on your end.
-Zeke
On 12/16/2015 02:47 PM, Hamel, Maura K. wrote:
> Hi Freesurfer experts,
>
> I’m looking for some help with some recons I tried running yesterday for
> about 60 subjects.
>
> The command I submitted was:
> recon-all -i
> /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/${subject}/MPRAGE/0*/001.mgz
> -s ${subject} -all
>
> I have attached the log files, and I’m hoping you can explain the error
> I received and what I need to do fix it. Thanks in advance for your help!
>
>
> FREESURFER_HOME: /usr/local/freesurfer/stable6
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151208
>
> RedHat release: CentOS release 6.7 (Final)
>
> Kernel info: Linux 4.1.8-1.el6.elrepo.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
> machine: tyra
>
> SUBJECTS_DIR:
> /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60
>
> PWD: /autofs/cluster/maury/users/gcoombs/College_Risk
>
> ssh tyra
> setenv SUBJECTS_DIR
> /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60
> cd /autofs/cluster/maury/users/gcoombs/College_Risk
>
> Best,
>
> *Maura Hamel*
> Clinical Research Coordinator
> Psychiatric Neuroimaging Research Program
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th St, Room 2602A
> Charlestown, MA 02129
> Phone: 617-643-4441
> Fax: 617-726-4078
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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[Freesurfer] recon error
Hi, I got this error while running recon-all : 'imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: mpr2mni305 execution aborted Any idea what could be the cause? Thanks,Xiaomin Yue ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon error
Hi, I got this error while running recon: 'imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: mpr2mni305 execution aborted Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] fsfast question Date: Wed, 26 Mar 2014 17:03:48 -0400 Thanks very much, i will try it. Xiaomin From: cschwie...@mail.rockefeller.edu Date: Wed, 26 Mar 2014 14:56:26 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsfast question you could try to run mkanalysis-sess with -notask and your nuisance regressors specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to save the residuals. maybe that solves your problem? caspar 2014-03-26 14:38 GMT-04:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: No, sorry On 03/26/2014 01:54 PM, Xiaomin Yue wrote: I like to regress out the linear drift, mean, and head motion generated by the motion correction step of fsfast from the raw time course only. Is it possible using fsfast? Xiaomin Date: Wed, 26 Mar 2014 11:28:57 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsfast question Sorry, I don't follow what you are asking. FSFAST does not do any drift removal from the raw data, all of that is in the design matrix doug On 03/26/2014 10:45 AM, Xiaomin Yue wrote: Hi, The analysis necessary to my study is to run some analysis on the raw time course data. Before working on the raw time course data, it is necessary to remove linear drifting, mean, and head motion. Can I just specify those parameters without having conditions in the steps of generating design matrix? If so, what command should be used? Thanks, Xiaomin Yue ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
[Freesurfer] recon error- too many arguments?
Hi, I'm trying to run a recon, but I keep getting the error: too many arguments for the following command: econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i [path to dicom] Any help on this would be excellent! Thanks, M ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon error- too many arguments?
Hi Mia can you send us the actual command and screen output? thanks Bruce On Fri, 15 Jun 2012, Borzello, Mia wrote: Hi, I'm trying to run a recon, but I keep getting the error: too many arguments for the following command: econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i [path to dicom] Any help on this would be excellent! Thanks, M ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon error- too many arguments?
Yes! I attached a screen shot. Thanks! From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, June 15, 2012 11:33 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon error- too many arguments? Hi Mia can you send us the actual command and screen output? thanks Bruce On Fri, 15 Jun 2012, Borzello, Mia wrote: Hi, I'm trying to run a recon, but I keep getting the error: too many arguments for the following command: econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i [path to dicom] Any help on this would be excellent! Thanks, M ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer attachment: freesur.PNG___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon error- too many arguments?
Hi Mia, I think the problem is that you have a space in the path to the dicom. Even though you put a backslash there, I think it is still causing the problem doug On 06/15/2012 01:13 PM, Borzello, Mia wrote: Yes! I attached a screen shot. Thanks! From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, June 15, 2012 11:33 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon error- too many arguments? Hi Mia can you send us the actual command and screen output? thanks Bruce On Fri, 15 Jun 2012, Borzello, Mia wrote: Hi, I'm trying to run a recon, but I keep getting the error: too many arguments for the following command: econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i [path to dicom] Any help on this would be excellent! Thanks, M ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon error- too many arguments?
bingo! thanks a lot! m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, June 15, 2012 1:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon error- too many arguments? Hi Mia, I think the problem is that you have a space in the path to the dicom. Even though you put a backslash there, I think it is still causing the problem doug On 06/15/2012 01:13 PM, Borzello, Mia wrote: Yes! I attached a screen shot. Thanks! From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, June 15, 2012 11:33 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon error- too many arguments? Hi Mia can you send us the actual command and screen output? thanks Bruce On Fri, 15 Jun 2012, Borzello, Mia wrote: Hi, I'm trying to run a recon, but I keep getting the error: too many arguments for the following command: econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i [path to dicom] Any help on this would be excellent! Thanks, M ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: freesurfer recon error
Have you tried including the flag -cw256 with the recon-all command? On Tue, Jul 5, 2011 at 10:18, Sarah Rappaport - UoB` sjr...@bham.ac.ukwrote: Hi!, I am new to FreeSurfer and I am having some difficulty with the T1 reconstruction. My MRI files were Par Rec and converted to nii. I successfully converted the nii file to mgz but had errors when running the recon -all command (see screen print attached). I have tried re-exporting the files in case there was an inital error at this stage but it returned the same error. I would appreciate any help with this. thanks Sarah ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Recon error
Hi Michele, this means that the computed talairach transformation was deemed to be unlikely and therefore possibly wrong. This usually occurs when the input volume is in the incorrect orientation. Did you convert to analyze format at any time? If you bring the orig.mgz up in tkmedit are the orientations correct? That is, does the sagittal view look sagittal, etc...? It's also possible that the tal is correct but the suject was in an unusal orientaton. If you visually inspect the tal and it's correct and the orientation are correct, then use the -notal-check flag to skip checking. cheers Bruce On Tue, 29 Jun 2010, Michele Placci wrote: Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the University of Padua with a degree in Mathematics. I'm trying to use FreeSurfer for analyze a 3D image MRI, NIFTI format (converted from DICOM) to calculate brain volume. I ran recon-all -autorecon1 -autorecon2 -subjid ...file with extension.mgz, after the conversion with mri_convert from a unique file .nii and I obtained the errors that you can see in the attachments. Any suggestion? Thank you in advance. Michele. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Recon error: Talairach Failure Detection
Hi, I'm getting an error trying to run a reconstruction. I'm working on multnomah and my subjects directory is: /autofs/space/multnomah_002/users/Cashlab/ *I'm using the following command:* [multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG15_SurferOutput -i MG15/MG_15_SPGR/1.2.840.113619.2.176.3596.6688992.17364.1172489897.387.dcm *I get the following error:* #...@# Talairach Failure Detection Sun Dec 13 11:51:46 EST 2009 /autofs/space/multnomah_002/users/Cashlab/MG15_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0308, pval=0.0034 threshold=0.0050) Linux multnomah 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sun Dec 13 11:51:46 EST 2009 *My environment information is:* freesurfer-Linux-centos4-stable-v4.5.0-20091124 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current Any help will be appreciated! Thanks, Rodrigo Zepeda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon error: Talairach Failure Detection
Hi Rodrigo, first check the talairach registration to see whether it really failed or not -- the automatic checker is often a bit conservative. If it did, then you can fix it by hand. If it did not, then you can re-run recon-all with -notal-check. doug Rodrigo Zepeda wrote: Hi, I'm getting an error trying to run a reconstruction. I'm working on multnomah and my subjects directory is: /autofs/space/multnomah_002/users/Cashlab/ *I'm using the following command:* [multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG15_SurferOutput -i MG15/MG_15_SPGR/1.2.840.113619.2.176.3596.6688992.17364.1172489897.387.dcm *I get the following error:* #...@# Talairach Failure Detection Sun Dec 13 11:51:46 EST 2009 /autofs/space/multnomah_002/users/Cashlab/MG15_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0308, pval=0.0034 threshold=0.0050) Linux multnomah 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sun Dec 13 11:51:46 EST 2009 *My environment information is:* freesurfer-Linux-centos4-stable-v4.5.0-20091124 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current Any help will be appreciated! Thanks, Rodrigo Zepeda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recon error
Hi, I'm getting an error trying to run a reconstruction. I'm working on multnomah and my subjects directory is: /autofs/space/multnomah_002/users/Cashlab/ I'm using the following command: [multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG25_SurferOutput -i MG25/MRI/1.3.12.2.1107.5.2.30.26039.3.2007081618514610873067809.dcm I get the following error: writing labeled volume to aseg.auto_noCCseg.mgz... ERROR: opening pipe gzip -f -c aseg.auto_noCCseg.mgz, errno = 12 Cannot allocate memory mri_ca_label: MRIwrite(aseg.auto_noCCseg.mgz) failed My environment information is: freesurfer-Linux-centos4-stable-v4.5.0-20090823 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /autofs/space/multnomah_002/users/Cashlab MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current Any help will be appreciated! Thanks, Rodrigo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon error
Looks like that is a pretty weak computer. Can you run it on a stronger computer? Rodrigo Zepeda wrote: Hi, I'm getting an error trying to run a reconstruction. I'm working on multnomah and my subjects directory is: /autofs/space/multnomah_002/users/Cashlab/ I'm using the following command: [multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG25_SurferOutput -i MG25/MRI/1.3.12.2.1107.5.2.30.26039.3.2007081618514610873067809.dcm I get the following error: writing labeled volume to aseg.auto_noCCseg.mgz... ERROR: opening pipe gzip -f -c aseg.auto_noCCseg.mgz, errno = 12 Cannot allocate memory mri_ca_label: MRIwrite(aseg.auto_noCCseg.mgz) failed My environment information is: freesurfer-Linux-centos4-stable-v4.5.0-20090823 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /autofs/space/multnomah_002/users/Cashlab MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current Any help will be appreciated! Thanks, Rodrigo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon error
Thanks. I tried running it on oct and I'm getting another error earlier on recon process. The subjects directory is: /homes/11/rzepeda/Recon I'm using the following command: [oct:~/Recon] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG25_SurferOutput -i MG25/MRI/1.3.12.2.1107.5.2.30.26039.3.2007081618514610873067809.dcm I get the following error: $Id: gauss_4dfp.c,v 1.2.2.1 2009/05/15 21:44:49 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1gauss_4dfp: talsrcimg_g11.4dfp.img write error ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=255 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Is this related to the same problem as before or is it something different? I was surprised that multnomah wasn't able to handle that recon, I've run many recons there and never had this problem. Thank you! Rodrigo On Wed, Aug 26, 2009 at 1:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Looks like that is a pretty weak computer. Can you run it on a stronger computer? Rodrigo Zepeda wrote: Hi, I'm getting an error trying to run a reconstruction. I'm working on multnomah and my subjects directory is: /autofs/space/multnomah_002/users/Cashlab/ I'm using the following command: [multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG25_SurferOutput -i MG25/MRI/1.3.12.2.1107.5.2.30.26039.3.2007081618514610873067809.dcm I get the following error: writing labeled volume to aseg.auto_noCCseg.mgz... ERROR: opening pipe gzip -f -c aseg.auto_noCCseg.mgz, errno = 12 Cannot allocate memory mri_ca_label: MRIwrite(aseg.auto_noCCseg.mgz) failed My environment information is: freesurfer-Linux-centos4-stable-v4.5.0-20090823 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /autofs/space/multnomah_002/users/Cashlab MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current Any help will be appreciated! Thanks, Rodrigo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recon Error Message
Hi guys, I also have another question: I am getting the following error message when I run recon-all with a few of my images: Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux meddhcp202-30.dhcp.med.ualberta.ca 2.6.18-92.1.13.el5 #1 SMP Thu Sep 4 03:51:21 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Nov 7 21:17:02 MST 2008 Does anybody have an answer as to why this may be happening? Thanks Alexa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon Error Message
can you send us the recon-all command line? On Wed, 12 Nov 2008, Alexa Nardelli wrote: Hi guys, I also have another question: I am getting the following error message when I run recon-all with a few of my images: Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux meddhcp202-30.dhcp.med.ualberta.ca 2.6.18-92.1.13.el5 #1 SMP Thu Sep 4 03:51:21 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Nov 7 21:17:02 MST 2008 Does anybody have an answer as to why this may be happening? Thanks Alexa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon error
Ilana, use: tkregister2 --s (subjid) --fstal note that the talairach alignment can fail for a number of reasons. a catastrophic one would be if the direction cosines in the input file are all wrong (coronal, saggital, horizontal wrong). or it could be that the subject was just scanned in an odd position, in which case using tkregister2 to manually adjust might be appropriate. or you can ignore the tal check with the -no-talcheck flag, but downstream processing may fail. Nick On Sun, 2008-08-10 at 11:53 -0400, Ilana Hairston wrote: Hi there, I am new to free surfer, and am trying to analyse brains of kids ages 8-11. running recon1 i get the following error message: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Looking at past mailings seems you recommended checking the registry. However, during recon no file called ???.dat was created as far as i can tell, and without specifying --reg i get the error: ___$ tkregister2 --s C2647 --mov C2647_070809cv.img INFO: no target volume specified, assuming FreeSurfer orig volume. ERROR: no registration file specified thanks, ilana -- You must believe in free will; there is no choice. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon error
it is in the mri dir: /Users/frederickpowell/freesurfer/subjects/011106RJ/mri/nu.mgz On Thu, 1 Jun 2006, Frederick Powell wrote: gunzip: /Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz.gz: No such file or directory mghRead(/Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz, -1): read error I went into my subjects directory and to the subject that I ran with the error and received the above. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
