Re: [Freesurfer] 'fsaverage' directory
Thank you! sandra, the two fsaverage's that you are using are the same. you can change one of the links to point at the other if you prefer, or continue to use it as-is. it will not affect the results. n. On Tue, 2012-01-10 at 15:10 -0500, swood...@nmr.mgh.harvard.edu wrote: Hi all, We are trying to run exactly the same analysis, particularly the recon-all command, from two different directories. We've found that both directories have '/fsaverage' but that they are sourcing two different links/paths. Why is this and is there a difference in how analysis will be run/processed? The two directories in question are : /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons We have been running everything in /R01BTX_recons, so we want this to be the model. I found out that: /autofs/cluster/ablood/1/miriam/SD_recons already has an fsaverage directory The difference between the fsaverage directories in /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons Are the following: fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons points to: fsaverage - /usr/local/freesurfer/stable5_1_0/subjects/fsaverage and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/miriam/SD_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0/subjects/fsaverage Whereas: fsaverage in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons points to: fsaverage - /usr/local/freesurfer/stable5/subjects/fsaverage and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5/subjects/fsaverage Not sure if: 1. there is a significant difference between these fsaverages and if we need to be using exactly the same fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons as in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons? Thank you! Sandra ___ 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] fmcsm5-all.text ::created when?
Hello, Just a quick question.. when is the file (within the bold subdirectories) fmcsm5(4)-all.txt made? Is it created as a result of running func2roi? Thank you! Sandra ___ 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] fmcsm5-all.text ::created when?
Hi Doug, the file fmcsm4-all.txt, .../bold/tap_lh_long_CD_R01BTX_pat6_sess1_sm4/caud_LH_t3_5_sm4_75thresh. I think tool using the command 'func2roi-sess' produces this file, but I would like to confirm. An example command we use is: func2roi-sess -roidef M6_LH_t6_0_sm5_0thresh -analysis tap_lh_long_aftpat1_sm5 -maskcontrast tap_lh_long_aftpat1_sm5_contrast -labelfile /space/meso/20/users/ablood/SD_botox/SD_botox_recons/SD_aftbotox_pat1_fsfast_recon/label/M6_LH_aftpat1.label -maskthresh 6.0 -masktail pos -maskmap t -s SD_aftbotox_pat1_fsfast -df sessdirfile Thanks! Sandra Hi Sandra, I'm not sure I know what file you are talking about. What is its exact name? doug swood...@nmr.mgh.harvard.edu wrote: Hello, Just a quick question.. when is the file (within the bold subdirectories) fmcsm5(4)-all.txt made? Is it created as a result of running func2roi? Thank you! Sandra ___ 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.
[Freesurfer] problems unpacking diffusion runs
Hello all,
I'm trying to unpack some old data and for a couple of sessions it is
unpacking the wrong run. I just want to unpack the diffusion run. I give
it the correct run number, it see's that number is the diffusion run, but
unpacks another run instead. Here is the command I used:
[purkinje:pat09_sess1_dti] (nmr-stable5.1-env) unpacksdcmdir -src
/space/archive/25/siemens/Allegra-20401-20040831-134936-64 -targ
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti -run 021 dti NII
pat09_sess1_dti.nii -unpackerr
Here is what is spits out:
$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $
/autofs/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti
-src /space/archive/25/siemens/Allegra-20401-20040831-134936-64 -targ
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti -run 021 dti NII
pat09_sess1_dti.nii -unpackerr
Thu Sep 29 10:12:31 EDT 2011
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2011/09/29-14:12:31-GMT BuildTimeStamp: Sep
27 2011 05:57:44 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47
greve Exp $ User: swoodman Machine: purkinje Platform: Linux
PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion:
30400
purkinje
Linux purkinje 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011
x86_64 x86_64 x86_64 GNU/Linux
Thu Sep 29 10:12:31 EDT 2011
Log File is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/unpack.log
INFO: Logfile is
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dicomdir.sumfile
INFO: status file is
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/parse.status
Scanning directory Thu Sep 29 10:12:31 EDT 2011
mri_parse_sdcmdir --sortbyrun --d
/space/archive/25/siemens/Allegra-20401-20040831-134936-64 --o
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dicomdir.sumfile
--status
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/parse.status
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74
76 78 80 82 84 86 88 90 92 94 96 98 100
Done scanning Thu Sep 29 10:20:13 EDT 2011
--
1 circle_localizer ok 256 256 3 1 64-1-2.dcm
2 AAScout ok 128 128 128 2 64-2-1.dcm
3t1_mprage_sag ok 256 256 128 1 64-3-1.dcm
4t1_mprage_sag ok 256 256 128 1 64-4-1.dcm
5 ep2d_t1w ok 64 64 30 1 64-5-1.dcm
6t2_HI_RES ok 448 444 30 1 64-6-1.dcm
7 ge_functionals_PACE ok 64 64 30 174 64-7-1.dcm
8 ge_functionals_PACE ok 64 64 30 174 64-8-1.dcm
9 ge_functionals_PACE err 64 64 30 10 64-9-1.dcm
10 ge_functionals_PACE err 64 64 30 10 64-10-1.dcm
11 ge_functionals_PACE ok 64 64 30 174 64-11-1.dcm
12 ge_functionals_PACE ok 64 64 30 174 64-12-1.dcm
13 ge_functionals_PACE ok 64 64 30 174 64-13-1.dcm
14 ge_functionals_PACE ok 64 64 30 174 64-14-1.dcm
15 ge_functionals_PACE ok 64 64 30 174 64-15-1.dcm
16 ge_functionals_PACE ok 64 64 30 174 64-16-1.dcm
17 ge_functionals_PACE ok 64 64 30 174 64-17-1.dcm
18 ge_functionals_PACE ok 64 64 30 174 64-18-1.dcm
19 ge_functionals_PACE ok 64 64 30 174 64-19-1.dcm
20 ge_functionals_PACE ok 64 64 30 174 64-20-1.dcm
21DIFFUSION_HighRes err 128 128 64 70 64-21-1.dcm
22 DIFFUSION_VeryHighRes err 128 128 30 84 64-22-1.dcm
unpacking config --
{021 dti NII pat09_sess1_dti.nii}
---
-
Run 021 -
Thu Sep 29 10:20:13 EDT 2011
021 dti NII pat09_sess1_dti.nii
mri_convert
/space/archive/25/siemens/Allegra-20401-20040831-134936-64/64-17-1.dcm
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017/pat09_sess1_dti.nii
--sdcmlist
/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017/flf -ot nii
--nspmzeropad 3 --in_type siemens_dicom
StartTime: Thu Sep 29 10:12:31 EDT 2011
EndTime: Thu Sep 29 10:20:32 EDT 2011
unpacksdcmdir Done
**and as you see if has decided to copy to run 017 and in that directory
the output files are not correct.
[purkinje:pat09_sess1_dti] (nmr-stable5.1-env) ls
dicomdir.sumfile dti unpack.log
[purkinje:pat09_sess1_dti] (nmr-stable5.1-env) cd dti
[purkinje:dti] (nmr-stable5.1-env) ls
017 seq.info
[purkinje:dti] (nmr-stable5.1-env) cd 017/
[purkinje:017] (nmr-stable5.1-env) ls
flf pat09_sess1_dti.nii pat09_sess1_dti.nii-infodump.dat
The bugreport:
FREESURFER_HOME: /usr/local/freesurfer/stable5_1_0
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514
RedHat
[Freesurfer] unpacking error:: exited abnormally
Hello,
I'm trying to unpack a diffusion run and getting this error, child
process excited abnormally. Anyone encounter this before? Here are the
details:
[purkinje:pat08_sess2_dti] (nmr-stable3-env) unpacksdcmdir -src
/space/archive/181/siemens/TrioTim-35162-20080921-182835-474000 -targ
/cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti -run 6 dti NII
pat08_sess2_dti.nii -unpackerr
Thu Sep 29 10:56:17 EDT 2011
INFO: Logfile is
/cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti/unpack.log
Scanning source directory ...
INFO: summary file is
/cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti/dicomdir.sumfile
INFO: status file is
/cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti/parse.status
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74
76 78 80 82 84 86 88 90 92 94 96 98 100
Done scanning Thu Sep 29 11:03:30 EDT 2011
--
1localizer ok 512 512 3 1 474000-01-02.dcm
2 AAScout ok 128 128 128 2 474000-02-01.dcm
3T1_MPRAGE_sag ok 256 256 128 1 474000-03-01.dcm
4T1_MPRAGE_sag ok 256 256 128 1 474000-04-01.dcm
5DIFFUSION_HighRes err 128 128 64 24 474000-05-01.dcm
6DIFFUSION_HighRes err 128 128 64 70 474000-06-01.dcm
7DIFFUSION_HighRes ok 128 128 64 1 474000-07-01.dcm
8DIFFUSION_HighRes ok 128 128 64 1 474000-08-01.dcm
9DIFFUSION_HighRes ok 128 128 64 1 474000-09-01.dcm
10DIFFUSION_HighRes ok 128 128 64 1 474000-10-01.dcm
11DIFFUSION_HighRes ok 128 128 64 1 474000-11-01.dcm
12DIFFUSION_HighRes ok 128 128 1 64 474000-12-01.dcm
13 ep2d_t1w ok 64 64 30 1 474000-13-01.dcm
14 PASL ok 64 64 16 133 474000-14-01.dcm
15 PASL err 64 64 16 1 474000-15-01.dcm
16 PASL err 64 64 16 1 474000-16-01.dcm
17 PASL ok 64 64 16 133 474000-17-01.dcm
18 PASL err 64 64 16 1 474000-18-01.dcm
19 PASL err 64 64 16 1 474000-19-01.dcm
20 ge_functionals ok 64 64 30 126 474000-20-01.dcm
21 ge_functionals ok 64 64 30 174 474000-21-01.dcm
22 ge_functionals ok 64 64 30 174 474000-22-01.dcm
23 ge_functionals ok 64 64 30 128 474000-23-01.dcm
24 ge_functionals ok 64 64 30 126 474000-24-01.dcm
25 ge_functionals ok 64 64 30 174 474000-25-01.dcm
26 T2_TSE_Axial_HiRes ok 256 256 30 1 474000-26-01.dcm
unpacking config --
{6 dti NII pat08_sess2_dti.nii}
---
-
Run 6 -
Thu Sep 29 11:03:30 EDT 2011
6 dti NII pat08_sess2_dti.nii
INFO: this run has an error, but trying anyway
ERROR: mri_convert
child process exited abnormally
[purkinje:pat08_sess2_dti] (nmr-stable3-env) bugr
Cut-and-paste the following info into your FreeSurfer problem report:
-
FREESURFER_HOME: /usr/local/freesurfer/stable3
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v3.0.5-20070714
RedHat release: CentOS release 5.5 (Final)
Kernel info: Linux 2.6.18-194.32.1.el5 x86_64
NMR Center info (/space/freesurfer exists):
machine: purkinje
SUBJECTS_DIR: /space/sake/3/users/inverse/subjects
PWD: /autofs/cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti
Thank you for any help!!
Sandra
___
Freesurfer mailing list
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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] bedpostx changes in past 2 years?
Hi all, We always run bedpostx in the developement (nmr-dev-env) environment, and after some digging around, we've noticed some differences in outputs between 2008 and now. Has anything changed with bedpostx in dev environment since 2008, that would effect data and/or analysis? There seem to be more log files in the bedpostx log directory in the sessions that were run more recently. So this is mainly why we are wondering if something has changed in the bedpostx program between October 2008 and October 2009 that affects the tractography data. Thank you! Sandra ___ 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] repeated measures ANOVA
Hello all, We would like to analyise our repeated measures DTI data using an ANOVA. We are wondering if someone might have experience running AVOVA's on 3D data? Is there a particular tool used or did you use MATLAB for this type of analysis? Thank you, Sandra Sandra Woodman Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital ___ 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] freeview
Hello all! I have a question regarding using freeview. When doing a 3D rengering of t-maps, there is a setting that allows you to view clusters with peak t scores. When we do this peak t scores are included in two clusters. We wish to only show ONE cluster for an image we are creating. How does one get rid of a cluster, ie only show the one of interest? Thank you! Sandra ___ 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] DTI bvecs/bvals question
Hello all, We have a question regarding DTI data we aquired a few years ago (2005-2006). For those of you who use DTI sequences, 1.) Do you use normalized bvals/bvecs files or do you use the files that come direct from the scanner for each individual subject? 2.) When scanning on either bay 3 or 4, are the same bval/bvecs files used? ie is there a difference between magnets when using the same sequence? Thanks for your help! Sandra ___ 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] preproc-sess error
Hello everyone, I keep encountering the same error when running some preprocessing steps (spatial smooting part). I run the command line: preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 And I encounter this error: ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed Any help/advice would be much appreciated! Thanks, Sandra ___ 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] preproc-sess error
Additional info: FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v3.0.5-20070714 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 NMR Center info (/space/freesurfer exists): Does this give you the info you're looking for? Thanks, Sandra which version are you using? swood...@nmr.mgh.harvard.edu wrote: Hello everyone, I keep encountering the same error when running some preprocessing steps (spatial smooting part). I run the command line: preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 And I encounter this error: ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed Any help/advice would be much appreciated! Thanks, Sandra ___ 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.
[Freesurfer] spmregister error
Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@partners.org ___ 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] spmregister error
That seems to now work with those changes. Thanks so much to Adam and Doug! Sandra Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last row in the FreeSurfer FAST section, under the line beginning with clear. Hope that helps! -Adam Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@partners.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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.
