[Freesurfer] fast_selxavg3.m - ERROR: design is ill-conditioned
I have two sets of identical blocks within each fMRI run, so conditions
{1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this
numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following
output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
...
ntptot = 687, nX = 136, DOF = 551
Saving X matrix to
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat
XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e.,
{1,2,3,4,5,6,7,8,9,10}
so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then
fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541
Saving X matrix to
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat
XCond = 4.33238e+08 (normalized)
ERROR: design is ill-conditioned
1) why does nX increase by 10 in the 2nd case?
2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle 10
separate blocks?
The entire log file in the 2nd case is attached.selxavg3-sess log file
/usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess
-s subj008_10block -analysis improv.10blocks.sm05.lh
$Id: selxavg3-sess,v 1.60 2011/12/09 20:03:03 greve Exp $
uid=8240(preciado) gid=8240(preciado) groups=8240(preciado),160(fsdev),1071(birn),1107(fddev),1576(tbi)
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
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
Wed Oct 23 11:37:06 EDT 2013
preproc-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -a improv.10blocks.sm05.lh -nolog
--
preproc-sess logfile is /dev/null
--
$Id: preproc-sess,v 1.50 2013/01/22 22:08:44 greve Exp $
preciado
setenv FREESURFER_HOME /usr/local/freesurfer/dev
setenv SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
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
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/preproc-sess
-s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -a improv.10blocks.sm05.lh -nolog
Wed Oct 23 11:37:06 EDT 2013
instem f
mc 1 f fmcpr
stc 1fmcpr fmcpr.siemens
sm 0
mask 1 brain
subj008_10block Template -
mktemplate-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -nolog -update
Session: /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
Wed Oct 23 11:37:06 EDT 2013
Detected input format at nii
subj008_10block Update not needed
Run: 014
Wed Oct 23 11:37:06 EDT 2013
subj008_10block 014 Update not needed
Run: 016
Wed Oct 23 11:37:06 EDT 2013
subj008_10block 016 Update not needed
Run: 018
Wed Oct 23 11:37:07 EDT 2013
subj008_10block 018 Update not needed
Wed Oct 23 11:37:07 EDT 2013
mktemplate-sess completed
subj008_10block Mask
mkbrainmask-sess -maskstem brain -fsd bold -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -nolog -update
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
Wed Oct 23 11:37:07 EDT 2013
subj008_10block Update not needed for session-level mask
subj008_10block Update not needed for run 014 mask
subj008_10block Update not needed for run 014 meanval
subj008_10block Update not needed for run 016 mask
subj008_10block Update not needed for run 016 meanval
subj008_10block Update not needed for run 018 mask
subj008_10block Update not needed for run 018 meanval
Wed Oct 23 11:37:07 EDT 2013
mkbrainmask-sess done
subj008_10block Registration -
register-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -dof 6 -per-run -nolog -update
--
register-sess logfile is /dev/null
--
Wed Oct 23 11:37:07 EDT 2013
setenv SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
cd /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/register-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -dof 6 -per-run -nolog -update
freesurfer-Linux-centos6_x86_64-dev-20131015
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
Session: /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
Wed Oct 23 11:37:07 EDT 2013
Run: 014
[Freesurfer] mergecontrasts-sess - Comparisons between subjects
Is it possible to do a conjunction analysis between subjects using one contrast? So far I've been able to do comparisons between contrasts within subjects but not between subjects. Thanks, -Ronny ___ 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] FS-FAST - ERROR: mapping surfaces
Thanks Doug, I did make some manual edits to wm.mgz and brainmask.mgz then reran the subject a couple times using: recon-all -autorecon2-wm -subjid subj007 Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3? Will running 'recon-all -make all -s subj007' do away with my manual edits? -Ronny Hi Ronny, there is a dimension mismatch which usually means that the surfaces for that subject are out of synch, ie, it has not been run through to the end. This often happens when a subject is run all the way through, then edited and re-run but the re-run only runs autorecon1 and autorecon2 but not autorecon3. Try running recon-all -make all -s subj007. You can also just check if the subject is out of synch with vno_match_check subj007 doug On 06/07/2013 11:03 AM, preci...@nmr.mgh.harvard.edu wrote: I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated. -Ronny 1/1 subj007 1/1 subj007 008 lh - Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 - fsaverage) ERROR: mapping surfaces ___ 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] FS-FAST motion correction / register
One of my subjects exhibited motion during the middle time point of one the functional scans. FS-FAST then reads all other time points as having a significant amount of motion because the subject was out of place during the point that is marked as the origin. Is there some way that I can set a different time point? I am worried that there will be some over-correction for motion that isn't really there because my middle time point it out of an anomaly. -Ronny attachment: fsfast.mc.run010.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] FS-FAST motion correction / register
If anything I was thinking of removing the first two time points, as those are going to get nixed anyway. I was hoping it wouldn't come to that but i f that's the only way... -Ronny Hi Ronny, the time point used to as the template is hard-coded to be the middle time point. If this is just the case for one subject, a silly but simple solution is to remove the last two time points from the time series. This will cause the middle time point to shift to an earlier time point. Would this work? doug On 04/10/2013 01:48 PM, preci...@nmr.mgh.harvard.edu wrote: One of my subjects exhibited motion during the middle time point of one the functional scans. FS-FAST then reads all other time points as having a significant amount of motion because the subject was out of place during the point that is marked as the origin. Is there some way that I can set a different time point? I am worried that there will be some over-correction for motion that isn't really there because my middle time point it out of an anomaly. -Ronny ___ 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 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.
Re: [Freesurfer] Problem with aseg - Other segmentations fine
Yes, the white surface is actually pretty good all around. I am actually concerned about how the conditions that created the poor aseg segmentation would impact any subcortical analysis. I am not entirely clear what the impact of this segmentation could be and how (besides a voxel by voxel correction) to fix it. -Ronny Hi Ronny the white surface seems like it is in the right place most of the time, isn't it? That's why we use it for morphometry more than the aseg where we can use either cheers Bruce On Tue, 2 Apr 2013, preci...@nmr.mgh.harvard.edu wrote: I am having a bit of a problem the aseg on this subject. (See 2013.03.22.cor108.aseg.jpg attached) It is way overestimating the white matter bilaterally. The problems are about this bad for about 20 or more slices so editing manually seems like... a less than efficient proposition. Any thoughts on how to fix this programmatically? For reference, I have a attached some other images with no segmentation and using the Desikan-Killiany atlas (aparc+aseg) and the Destrieux atlas (aparc.a2009s+aseg) which look fine. Thanks, -Ronny ___ 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] Underestimated Pial surface - after deleting problematic voxels
mri_info for both attached. Interestingly enough, brain.finalsurfs.manedit.mgz is significantly larger in size. If it was a copy of the other, shouldn't it be the same size? Also, brain.finalsurfs.manedit.mgz shows a time/date stamp from the last time I edited it and brain.finalsurfs.mgz has a time/date stamp from the last time I executed recon-all -autorecon-pial... -rw-rw-r-- 1 preciado birn 1416877 Mar 26 22:23 brain.finalsurfs.manedit.mgz -rw-rw-r-- 1 preciado birn16605 Mar 27 09:39 brain.finalsurfs.mgz A more basic question, I am assuming that -autorecon-pial defaults to using brain.finalsurfs.manedit.mgz and then proceeds to use brain.finalsurfs.mgz if there is no manual edit volume, is that correct? -Ronny well, something is really wrong. Did you happen to change the voxel type of brain.finalsurfs.mgz? Can you run mri_info on it and send us the results? If not, then upload the tarred and gzipped subject dir and I'll take a look. I don't think it will be hard to fix On Thu, 28 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: A) Log attached. B) That was my next step but I wanted to check first to see if there was something obvious I was missing. I actually ran recon-all -autorecon-pial -subjid subject_name twice. I thought the first time, that it was the result of some process failing/not completing along the way without entirely crashing freesurfer. I ran it again in the hopes that it was some crazy fluke but the result is exactly the same. -Ronny eek, that's pretty bad. No idea why that would happen. Can you send us the recon-all.log? If you rerun with the original brain.finalsurfs.mgz does it restore good surfaces? On Thu, 28 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello Freesurfers, I ran recon-all on a subject's structural data like so: recon-all -autorecon-all -subjid subect_name The resulting pial surface looked pretty good except that there were a few voxels of dura and cerebellum that were included in the pial surface. not a big deal. I deleted some voxels of dura from brainmask.mgz and deleted voxels of from the cerebellum by creating and saving a copy of brain.finalsurfs.mgz. /subject_name/mri/ cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then I ran recon all to regenerate the pial surface: recon-all -autorecon-pial -subjid subject_name The results from the pial surface redrawing are now totally wrong and completely underestimated. The weird thing is that it looked perfectly fine before and removing some problematic voxels caused this result. Any insights as to how/why this occurred and how to fix it? Images of the AFTER picture attached. Thanks! -Ronny brain.finalsurfs.mgz.mri_info Description: Binary data brain.finalsurfs.manedit.mgz.mri_info Description: Binary data ___ 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
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] tkregister2 error
Dear list, I'm having problems with the tkregister2 command, I input the following command: tkregister2 --mov ~/Desktop/input/*_d/mri/rawavg.mgz --noedit --s *_d --regheader --reg ~/Desktop/input/*_d/mri/register.dat Where I'm setting the directory of my subjects, and I get the following output /Desktop/input/*_d/mri/register.dat /usr/local/freesurfer/tktools/tkregister2.bin: No match. However, when I try a similar command with the sample data from bert (And after adjusting the subject folder settings) It works fine. I ran out of ideas on how to fix it, does anybody have any clue of what can I do? Thanks a lot for your help Regards ___ 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.
