Re: [Freesurfer] bbregister error
Hi Charles, can you verify that brainmask.mgz exists for that subject? What do you get if you run stem2fname $SUBJECTS_DIR/$subject/mri/brainmask doug On 3/11/13 4:07 AM, Charles Malpas wrote: Hi Doug, I think I am having the same problem, but only when running on our Red Hut cluster (CentOS 6 was fine). I have attached the terminal output with --debug Many thanks, - Charles On 9 March 2013 03:47, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Salil, can you run fslregister with --debug as the first option, capture the terminal output, and send it to me? thanks doug On 03/07/2013 09:02 PM, Anastasia Yendiki wrote: Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when bbregister invokes fslregister, in this particular line of fslregister: set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol` When run on brainmask.mgz, it returns ERROR: could not determine file. a.y On Wed, 6 Mar 2013, Salil Soman wrote: Thank you for your email. Changing the mask option got me past the error I was having initially, but now I get these new errors: mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis ter.30396/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis ter.30396/fslregister/refvol.fslregister.nii Thank you for your consideration. Best wishes, -S On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu wrote: Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping. a.y -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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. -- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences Department of Medicine (RMH) The University of Melbourne 3010 *Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group** Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.mal...@student.unimelb.edu.au mailto:c.mal...@student.unimelb.edu.au Skype: charles.malpas ___ 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] Binary volume to surface _ mri_vol2surf
Thanks Doug. I can know visualize the resected area using freeview. As the output of mri_vol2surf produces an overlay and not a surface, measurements of area or/and intersection with other outputs from mri_vol2surf are not possible using mris_* functions. What is the best strategy to follow to be able to do simple measurments on these mri_vol2surf outputs ? Transform to surface, but how ? Thanks in advance, Christopher The output of mri_vol2surf is not a surface but an overlay on a surface. You will need to run something like: freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh You'll need to set the threshold to 0.5 in order to see the mask. doug ___ 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] nu_correct: Command not found error
Hi Nick, I had a look in the bin directory and there is a command called 'mri_nu_correct.mni'. Is this the command the script is trying to call? This is the only nu_correct command I could find. I specify v5.2 in the script as there are other versions installed on the clusters. Thanks again for your help! Sinead On 9 March 2013 23:23, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Sinead, Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being careful to run the setup script for just freeview 5.2 and not other packages or versions which might mess-up the perl paths? Nick On Fri, 2013-03-08 at 09:50 +, Sinead Kelly wrote: Dear all, I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. # #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001 mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz... mri_add_xform_to_header -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz INFO: extension is mgz # #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013 For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated. Kind regards, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ 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. -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ 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
[Freesurfer] Definition of anatomical regions
Hi, I have been working on a DBM based method to obtain longitudinal atrophy on some brain data. To quantify ROI, i use aseg.mgz. Several papers talk about Whole Brain, ventricular atrophy but do not actually define what substructures they use? It will be great if somebody can help me get the actual definition of whole brain and ventricles. For ex: WM Hypointensities are part of whole brain?, Since they increase in volume. Thank you , Akshay University of Copehagen ___ 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] nu_correct: Command not found error
Sinead, In your freesurfer directory, is there an 'mni' directory? under that directory is a 'bin' directory where nu_correct should be. Nick Hi Nick, I had a look in the bin directory and there is a command called 'mri_nu_correct.mni'. Is this the command the script is trying to call? This is the only nu_correct command I could find. I specify v5.2 in the script as there are other versions installed on the clusters. Thanks again for your help! Sinead On 9 March 2013 23:23, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Sinead, Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being careful to run the setup script for just freeview 5.2 and not other packages or versions which might mess-up the perl paths? Nick On Fri, 2013-03-08 at 09:50 +, Sinead Kelly wrote: Dear all, I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. # #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001 mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz... mri_add_xform_to_header -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz INFO: extension is mgz # #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013 For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated. Kind regards, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ 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. -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] LME - lme_mass_FDR2 correction doesn't work
Hi Jorge,
I got an error in the correction, and I can't find a way out.
this is the cmd I use:
-
/[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
Qdec = fReadQdec('.../LME.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
ni = [2 2... 2];
X = [ones(length(M),1) M M(:,1).*M(:,2)];
[stats,st] = lme_mass_fit_vw1(X,[1],Y,ni,lhcortex);
CM.C = [0 0 0 1];
fstats = lme_mass_F1(stats,CM);
fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig');
nv = length(stats);
Beta2 = zeros(1,nv);
//Beta//4= zeros(1,nv);//
//for //
//.
.//
//end;
//Beta2_Beta//4//_sum = Beta2//+Beta4;//
//mri1 = mri;//
//mri1.vols//z(//4) = 1;//
//fs//_write_Y(Beta2,mri1,'/Beta2.mgh'//);//
//[detvtx,sided_pval,pth//] =
lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);//
//fs_write_Y(sided_pva//l,mri1,//'.../spval.mgh');//
//
//??? Error using //=== reshape//
//To RESHAPE the number of elements must not change.//
//
//Error in ==// fs_write_Y at 21//
//save_mgh(reshape(Y',mri.volsz),//fname,mri.M,mri.mr//_parms);/
-
the cmd: /[detvtx //]/ didn't work, but there was no error message.
I remember in the past this cmd took around 1 day to analyzebut now it
didn't work at all.
/fs_write_Y/ worked fine for Beta, alsothis time I used the /mri//1 //=
mri/ cmd- so the /reshape /error shouldn't be associated with this.
Please help !
best regards,
Alex.
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Re: [Freesurfer] mean thickness covariate, mean area covariate, mri_anatomical_stats for multiple subjects
Hi Laura, If you're looking for another reference that has used this approach, you could see our 2010 paper: http://www.ncbi.nlm.nih.gov/pubmed/20118463 cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Laura M. Tully tully.la...@googlemail.com Date: Saturday, March 9, 2013 5:58 PM To: Anderson M. Winkler wink...@fmrib.ox.ac.uk Cc: free freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mean thickness covariate, mean area covariate, mri_anatomical_stats for multiple subjects Hi Anderson, Thanks, that reference is particularly helpful. Re: the usage of the white versus pial area question - I believe that the default area calculation in freesurfer is the white surface area, so unless one specifies the pial in calculations, the standard surface area output for surface area by parcellation will be white. This suggests the use of the global measurement of white surface area as a covariate would be an appropriate, whereas if one was specifically using pial surface area in the aparc calculations, it may make more sense to use the global measure of pial surface area as a covariate, correct? As for which one to use in analysis, I'm not sure - conceptually it might be that the pial surface area is more sensitive to atrophy but I don't know if that is born out in the data... Laura. On Sat, Mar 9, 2013 at 11:49 AM, Anderson M. Winkler wink...@fmrib.ox.ac.uk wrote: Hi Laura, 1. Is there a paper that I could cite that recommends using mean cortical thickness rather than ICV? If it helps, we used cortical thickness and area as covariate for the respective analysis of regional thickness and area. Brain volume, which is more closely related to ICV, correlates well with area, but not with thickness. We computed a global thickness average by weighting the thickness of each region by their respective areas. The paper is this: http://surfer.nmr.mgh.harvard.edu/ftp/articles/Winkler2010_Neuroimage.pdf 1. Would the same logic be applied to surface area analyses? i.e. would it make more sense to use mean surface area as a covariate in surface area analyses? If so, which mean surface area calculation should be used? mri_anatomical_stats can produce both pial and white matter mean surface area stats. Yes, I think so. It seems more logical to have a global measurement of area in the model than a measurement of brain volume. On the other hand, area and thickness are not correlated one to another (as shown in the paper above and also in Panizzon et al, 2009, in Cereb Cortex). I don't think there is a clear answer on which, pial or white, should be used. I'd probably go with the white, as I think it may be more robust to image quality, but I admit this is a rather weak justification and if the images are good, perhaps the pial could be just as good, despite the fact that it somewhat depends on the white for its construction. 1. Is there a way to run mri_anatomical_stats on multiple subjects at once and write to a tablefile (similar to asegstats2table output)? I think you can use aparcstats2table, then add up all regions in a spreadsheet (or even with awk/gawk). Alternatively, you can use grep to pick the WhiteSurfArea for each hemisphere from the ?h.aparc.stats file for each subject. Hope this helps! All the best, Anderson -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ 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
Re: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work
Hi Alex
The cmd
[detvtx,sided_pval,pth] = lme_mass_FDR2(fstats.pval,fstats.sgn,lhcortex,0.05,0);
only takes a few seconds to finish. Please check if Y, Beta2,
fstats.pval,fstats.sgn, sided_pval
all have the same number of columns.
Best
-Jorge
De: Alex Hanganu al.hang...@yahoo.ca
Para: Jorge L. Bernal-Rusiel jber...@nmr.mgh.harvard.edu; FS Mailing List
Freesurfer@nmr.mgh.harvard.edu
Enviado: Lunes 11 de marzo de 2013 10:53
Asunto: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work
Hi Jorge,
I got an error in the correction, and I can't find a way out.
this is the cmd I use:
-
[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
Qdec = fReadQdec('.../LME.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
ni = [2 2... 2];
X = [ones(length(M),1) M M(:,1).*M(:,2)];
[stats,st] =
lme_mass_fit_vw1(X,[1],Y,ni,lhcortex);
CM.C = [0 0 0 1];
fstats = lme_mass_F1(stats,CM);
fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig');
nv = length(stats);
Beta2 = zeros(1,nv);
Beta4= zeros(1,nv);
for
.
.
end;
Beta2_Beta4_sum = Beta2+Beta4;
mri1 = mri;
mri1.volsz(4) = 1;
fs_write_Y(Beta2,mri1,'/Beta2.mgh');
[detvtx,sided_pval,pth] =
lme_mass_FDR2(fstats.pval,fstats.sgn,lhcortex,0.05,0);
fs_write_Y(sided_pval,mri1,'.../spval.mgh');
??? Error using === reshape
To RESHAPE the number of elements must not change.
Error in == fs_write_Y at 21
save_mgh(reshape(Y',mri.volsz),fname,mri.M,mri.mr_parms);
-
the cmd: [detvtx ] didn't work, but there was no error message. I remember
in the past this cmd took around 1 day to analyzebut now it didn't work at all.
fs_write_Y worked fine for Beta, alsothis time I used the mri1 = mri cmd- so
the reshape error shouldn't be associated with this.
Please help !
best regards,
Alex.
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Re: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work
Hi Jorge,
I see now:
/Y, Beta2, sided_pval/ - have the same number of columns
/fstats.pval/ and /fstats.sgn/ were not generated (or they are not in
the workspace) !
a.
Le 3/11 11:53, jorge luis a écrit :
Hi Alex
The cmd
/[detvtx,sided_pval,pth//] =
lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);//
/
only takes a few seconds to finish. Please check if /Y, Beta2,
fstats.pval/,/fstats.sgn,/ /sided_pval
/
all have the same number of columns.
Best
-Jorge
*De:* Alex Hanganu al.hang...@yahoo.ca
*Para:* Jorge L. Bernal-Rusiel jber...@nmr.mgh.harvard.edu; FS
Mailing List Freesurfer@nmr.mgh.harvard.edu
*Enviado:* Lunes 11 de marzo de 2013 10:53
*Asunto:* [Freesurfer] LME - lme_mass_FDR2 correction doesn't work
Hi Jorge,
I got an error in the correction, and I can't find a way out.
this is the cmd I use:
-
/[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
Qdec = fReadQdec('.../LME.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
ni = [2 2... 2];
X = [ones(length(M),1) M M(:,1).*M(:,2)];
[stats,st] = lme_mass_fit_vw1(X,[1],Y,ni,lhcortex);
CM.C = [0 0 0 1];
fstats = lme_mass_F1(stats,CM);
fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig');
nv = length(stats);
Beta2 = zeros(1,nv);
//Beta//4= zeros(1,nv);//
//for //
//.
.//
//end;
//Beta2_Beta//4//_sum = Beta2//+Beta4;//
//mri1 = mri;//
//mri1.vols//z(//4) = 1;//
//fs//_write_Y(Beta2,mri1,'/Beta2.mgh'//);//
//[detvtx,sided_pval,pth//] =
lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);//
//fs_write_Y(sided_pva//l,mri1,//'.../spval.mgh');//
//
//??? Error using //=== reshape//
//To RESHAPE the number of elements must not change.//
//
//Error in ==// fs_write_Y at 21//
//save_mgh(reshape(Y',mri.volsz),//fname,mri.M,mri.mr//_parms);/
-
the cmd: /[detvtx //]/ didn't work, but there was no error
message. I remember in the past this cmd took around 1 day to
analyzebut now it didn't work at all.
/fs_write_Y/ worked fine for Beta, alsothis time I used the
/mri//1 //= mri/ cmd- so the /reshape /error shouldn't be
associated with this.
Please help !
best regards,
Alex.
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Re: [Freesurfer] Binary volume to surface _ mri_vol2surf
Hi Christopher, I'm not sure I understand your question. What do you mean by simple measurements? doug On 3/11/13 10:59 AM, Christopher wrote: Thanks Doug. I can know visualize the resected area using freeview. As the output of mri_vol2surf produces an overlay and not a surface, measurements of area or/and intersection with other outputs from mri_vol2surf are not possible using mris_* functions. What is the best strategy to follow to be able to do simple measurments on these mri_vol2surf outputs ? Transform to surface, but how ? Thanks in advance, Christopher The output of mri_vol2surf is not a surface but an overlay on a surface. You will need to run something like: freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh You'll need to set the threshold to 0.5 in order to see the mask. doug ___ 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] Permission denied - could not open lh.BA3b.thresh.label
Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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] Permission denied - could not open lh.BA3b.thresh.label
Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://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 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] Permission denied - could not open lh.BA3b.thresh.label
It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface So looks like lh.BA3a.thresh.label ran just fine, but not lh.BA3b.thresh.label. This ran as part of recon-all and failed in the middle of executing that script so I hadn't even tried to run it any other way (without *.thresh.*) That said, I just ran the problematic piece line of code and it all of a sudden works just fine... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface Any reason why it wouldn't have worked Friday near 7pm and works not? -Ronny Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://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 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] Permission denied - could not open lh.BA3b.thresh.label
Probably a network glitch? I'd try restarting it and seeing if the error persists. On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface So looks like lh.BA3a.thresh.label ran just fine, but not lh.BA3b.thresh.label. This ran as part of recon-all and failed in the middle of executing that script so I hadn't even tried to run it any other way (without *.thresh.*) That said, I just ran the problematic piece line of code and it all of a sudden works just fine... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface Any reason why it wouldn't have worked Friday near 7pm and works not? -Ronny Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://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 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] Permission denied - could not open lh.BA3b.thresh.label
I am thinking that that's possible. Same command with same type of parameters executed successfully before the failure, and now previously failed command is working. I will try it again... Thanks for the input. -Ronny Probably a network glitch? I'd try restarting it and seeing if the error persists. On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface So looks like lh.BA3a.thresh.label ran just fine, but not lh.BA3b.thresh.label. This ran as part of recon-all and failed in the middle of executing that script so I hadn't even tried to run it any other way (without *.thresh.*) That said, I just ran the problematic piece line of code and it all of a sudden works just fine... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface Any reason why it wouldn't have worked Friday near 7pm and works not? -Ronny Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://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 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
[Freesurfer] Extract pial surface
Hi Freesurfers, I would like to extract the whole pial surface of a brain volume. I already done the segmentation and i have ( rh.pial and lh.pial surfaces). Does it exist a way to get the whole pial surface without separation? Thanks. VP ___ 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] surface area mesurment and qatools
Hi What would be the best way to measure cortical surface either the white surface area or pial surface? Is the total surface area calculated by mris_anatomical the same pial surface? When using QA tool which article should I cite? Knut J ___ 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] Extract pial surface
VP, the recon-all stream produces ?h.ribbon.mgz and ribbon.mgz files which are based on the surfaces, so that is your best option. Nick On Mon, 2013-03-11 at 15:28 -0400, Valtina Pouegue wrote: Hi Freesurfers, I would like to extract the whole pial surface of a brain volume. I already done the segmentation and i have ( rh.pial and lh.pial surfaces). Does it exist a way to get the whole pial surface without separation? Thanks. VP ___ 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] qdec question
Hello! I am running qdec group analysis on my patient data and have one very important question. I am studying the differences between two Epilepsy subtypes. Each one of my patients has a hemisphere of onset, either Left or Right, that I would like to use in looking for differences between ipsilateral and contralateral hemispheres. However, ipsilateral patients need to be grouped together, but qdec only allows me to visualize left or right hemispheres separately. Is there a way to combine left hemispheres with right hemispheres in an attempt to study grey matter thickness in hemispheres ipsilateral to seizure onset? [Because the ipsilateral hemisphere is the right hemisphere for some patients and left hemisphere for others]. For example, is it possible to somehow flip the right hemisphere such that ipsilateral hemispheres align together? Thank you in advance for your help, Kristina Nalbandian ___ 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] qdec question
Hello! I am running qdec group analysis on my patient data and have one very important question. I am studying the differences between two Epilepsy subtypes. Each one of my patients has a hemisphere of onset, either Left or Right, that I would like to use in looking for differences between ipsilateral and contralateral hemispheres. However, ipsilateral patients need to be grouped together, but qdec only allows me to visualize left or right hemispheres separately. Is there a way to combine left hemispheres with right hemispheres in an attempt to study grey matter thickness in hemispheres ipsilateral to seizure onset? [Because the ipsilateral hemisphere is the right hemisphere for some patients and left hemisphere for others]. For example, is it possible to somehow flip the right hemisphere such that ipsilateral hemispheres align together? Thank you in advance for your help, Kristina Nalbandian ___ 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.
