Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Trac Stats
by Anastasia Yendiki 15 Aug '13

15 Aug '13

I didn't suggest taking it off, I meant make sure that the '/' is there, because the error message suggested to me that a '/' was missing from a filename listed IN that text file. Check your original error message. On Thu, 15 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > I took off the '/' before the autofs, but then it gave me a different > problem. > > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ > recons] : tractstats2table --load-pathstats-from-fileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re > cons/Forceps_Major_CC.list.txt --overall --tablefileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re > cons/Forceps_Major_CC.All.table > > ERROR: the fileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re > cons/Forceps_Major_CC.list.txt doesnt exist > > Actually it does exist. > > thanks, > > Alan > > > On Thu, Aug 15, 2013 at 2:40 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Is it really autofs without the '/' in front? > > On Thu, 15 Aug 2013, Alan Francis wrote: > > Hi Anastasia: > > Sorry to bother you again. I am trying to extract trac > stats from the FS > data. When I run the following script, it gives me an > error message: > > csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5 > .3_Data/diffusion_ > recons] : tractstats2table--load-pathstats-from-file/autofs/space/dali_003/users/BW_project_DTI/FreeS > urfer_5.3_Data/diffusion_r > econs/Forceps_Major_CC.list.txt --overall--tablefile/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/ > diffusion_r > econs/Forceps_Major_CC.All.table > > Parsing the .stats files > > ERROR: The statsfileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusio > n_re > cons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt > is not found > or is too small to be a valid statsfile > > However, when I manually checked the pathstats.overall.txt, the > data is > physically there. Am I doing something wrong? > > thanks so much, > > Alan > > > > > 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. > > > >

2 3

create label from cluster obtained with mri_glm-fit-sim
by Garikoitz Lerma-Usabiaga 15 Aug '13

15 Aug '13

Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster? If I use mri_binarize or mri_cor2label is not working (I understand that the clusters are not stored as individual vertexes in the .mgh file but I don't know what the format is. Thanks in advance! Gari PD: I am on a VPN and tksurfer is not working for manually creating a label with the contour of the cluster.

3 5

Trac Stats
by Alan Francis 15 Aug '13

15 Aug '13

Hi Anastasia: Sorry to bother you again. I am trying to extract trac stats from the FS data. When I run the following script, it gives me an error message: csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : tractstats2table --load-pathstats-from-file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/Forceps_Major_CC.list.txt --overall --tablefile /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/Forceps_Major_CC.All.table Parsing the .stats files ERROR: The stats file autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt is not found or is too small to be a valid statsfile However, when I manually checked the* pathstats.overall.txt, *the data is physically there. Am I doing something wrong? thanks so much, Alan

2 1

Bus error for tkmedit and tksurfer
by ye tian 15 Aug '13

15 Aug '13

Dear Freesurfers, Tkmedit and tksurfer both return "Bus error" for me. I can even have a glimpse of the surfaces before tksurfer collapses on me. I checked the archive http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19422.html I don't think disc space is an issue for me since the freesurfer is installed and run on a portable hard drive with >600GB of free space. Thank you very much for your help in advance! Sincerely, Ye

3 4

Antw: Re: [tracula] error running trac-all -prep
by Borsodi Florian 15 Aug '13

15 Aug '13

Hi Anastasia I ran the command you sent me and it runs without any errors. I also attached the command line for you. Furthermore i ran data with 12 diffusion directions and i keep getting the same kind of problems. sincerely Florian >>> Anastasia Yendiki 02.08.13 19.59 Uhr >>> Hi Florian - Can you please run this command directly on the command line and see if there are any errors? flip4fsl /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz Thanks, a.y On Fri, 2 Aug 2013, Borsodi Florian wrote: > Hi Anastasia > > Thank you for your answer. > > Yes, those files exist. > I also extracted the bvec an bval files with anotther software then dcm2nii > and i keep getting the same kind of error. > Also, about the 6 diffusion direction, those data i sent you, are just > testdata for running tracula. > > sincerely > Florian > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr >>> > > Hi Florian - Do these files exist? > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals > > > The format of the bvecs and bvals that you sent seems fine, but (and this > has nothing to do with the error you're getting) I have to warn you that > you may not be able to get good results running probabilistic tractography > on this data. It looks like you're acquiring the same 6 diffusion > directions, repeated 8 times. Six directions is the absolute minimum for > reconstructing the tensor model, but will probably not be sufficient for > the crossing fiber model that bedpostx reconstructs (and is used by > tracula). Your scan time is better spent acquiring 48 different > directions, rather than the same 6 directions 8 times. > > a.y > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > Hello, > > > > I have been trying to run tracula on my data and i keep getting the same > > kind of error repeatedly. > > For my imput I am using dicoms from a Siemens scanner with a stadard > > diffusion protocol. However, tracula cannot read the bvec and bval data > out > > of the dicom header. Therefore, I implemented bvec and bval files into the > > config file. > > After doing so, I got the error which says that tracula cannot find the > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > I have tried many options, but still cannot find a solution. > > I am hoping to get some troubleshooting help. > > > > I have atteched my log- and config- files, as well as my bvec and bval > > files. > > To uphold patient confidentiality, I have encode the name patient's data > as > > "AAAAAA". > > > > I believe the problems are the bvec and bval files or their structures. > The > > log-file lete me assume this, especially the lines 202 - 205, 264 - 268 > and > > 1480 - 1484. > > > > Thank you in advance for your help, and your speedy response. > > > > With kind regards, > > > > Florian Borsodi > > Department of Neurology > > Medical University of Graz > > > > > > > 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Re: [Freesurfer] Preproc
by Anastasia Yendiki 15 Aug '13

15 Aug '13

Hi Alan - This appears to be the same error message as the one for subject 118 that you sent yesterday. So I'd try here whatever you did to fix that one. a.y On Wed, 14 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > Sorry to bother you again. Another of my brains gave an error message. I > have enclosed the trac-all log as an attachment. > > Thanks ever so much for your help, > > Alan > >

2 1

fcseed-sess error
by O S 15 Aug '13

15 Aug '13

Dear Support, I am trying to use fcseed-sess to create a ventricle and CSF regressor for my resting state analysis. I have encountered an error running fcseed-sess. fcseed-config -vcsf -fsd Bold1 -mean -cfg vcsf_bold1_config -overwrite works, but then the following command fails: fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite The above command worked for half my subjects and had the below error for half with no discernible pattern. I've run it on jizo as well as my home machine with the same error. Cut-and-paste the following info into your FreeSurfer problem report: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.4 (Final) Kernel info: Linux 2.6.32-358.2.1.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: jizo SUBJECTS_DIR: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs PWD: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs ssh jizo setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs --------------------------------------------------------------------- I would appreciate any help. Let me know if anything is unclear. Thank! Best, Omar Error Message ************* [jizo:fc_fs] (nmr-stable53-env) fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite Logfile is /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/log/fcseed-sess.vcsf_bold1_config.log.AC30_1319 Wed Aug 14 11:31:50 EDT 2013 Linux jizo 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs /usr/local/freesurfer/stable5_3_0/fsfast/bin/fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Wed Aug 14 11:31:50 EDT 2013 Linux jizo 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs /usr/local/freesurfer/stable5_3_0/fsfast/bin/fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 mri_label2vol --seg /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/mri/aparc+aseg.mgz --reg /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat --temp /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/template.nii.gz --fillthresh .95 --o /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz --pvf /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz PVF /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/template.nii.gz Outut Volume: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz Registration File: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat Fill Threshold: 0.95 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.167 -0.000 12.500; 0.000 0.000 0.000 1.000; Template Voxel Volume: 58.5938 nHits Thresh: 55.6641 Loading registration from /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat RegMat: -------- -0.106 0.977 -0.185 7.376; -0.994 -0.104 0.019 -0.687; -0.000 0.186 0.983 -23.526; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- 0.034 -0.313 0.059 29.640; 0.000 -0.059 -0.314 39.528; -0.166 -0.017 0.003 12.385; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 1120 (0 filled) ASeg2Vol: done PVF /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz Computing PVF 58.5938 mri_binarize --i /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz --o /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz --match 4 --match 5 --match 43 --match 44 --match 31 --match 63 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs cmdline mri_binarize --i /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz --o /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz --match 4 --match 5 --match 43 --match 44 --match 31 --match 63 sysname Linux hostname jizo machine x86_64 user osinglet input /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz Binarizing based on matching values nMatch 6 0 4 1 5 2 43 3 44 4 31 5 63 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_segstats --i /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz --seg /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz --id 1 --sum /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/junk.sum --avgwfvol /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz --seg /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz --id 1 --sum /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/junk.sum --avgwfvol /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh sysname Linux hostname jizo machine x86_64 user osinglet UseRobust 0 Loading /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz Loading /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz Voxel Volume is 58.5938 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh Segmentation fault (core dumped)

2 1

Correction multiple comparisons for parcelated areas
by Anita van Loenhoud 15 Aug '13

15 Aug '13

Dear FreeSurfers, I’m comparing two groups (patients (N=45) and controls (N=93)) on cortical thickness using 34 parcelated areas in each hemisphere (i.e. 68 areas in total). When correcting for multiple comparisons using Bonferroni, only one area remains significant. Bonferroni is quite conservative (alpha needs to be lower than 0.05/68= 0.000735). Could you recommend any other, more lenient correction statistics for my data? In a search through the literature, I encountered adjusted Bonferroni or Benjamini-Hochberg as alternatives. Do you think these would be useful statistics, or have I missed other, more appropriate ones? Thanks a lot, Anna

3 2

Finding a reference..
by jh kim 15 Aug '13

15 Aug '13

Dear experts Just a simple question. Is there a published study that showed a superiority of cortical thickness analysis (i.e., FreeSurfer) over VBM approach in assessing cortical grey matter changes in brain disorders? If so, please let me know. Thanks in advance for your help. Kim

1 0

Fwd: FS version
by Cristian Paz 15 Aug '13

15 Aug '13

---------- Forwarded message ---------- From: Cristian Paz <pazcristian99(a)gmail.com> Date: 2013/8/14 Subject: Re: [Freesurfer] FS version To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Thank you for your reply! now - on the third try, I left it for three hours without checking and now it is actually running fiurther. great! what types of problem do I risk if if I use different versions? Will it be correct if it successfully runs or could there be errors? best, Cris 2013/8/14 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > how long do you wait? In general it's a bad idea to mix version > > Bruce > > > > On Wed, 14 Aug 2013, Cristian Paz wrote: > > because every time I try to run >> >> recon-all -autorecon-pial -s 101 >> it seems to hang up here and nothing more happens : >> >> >> ______________________________**______________________ >> #@# Sphere lh Wed Aug 14 14:42:06 CEST 2013 >> /media/Secure_HDD/patients/**101/scripts >> >> mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere >> >> setting seed for random number genererator to 1234 >> $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ >> reading original vertex positions... >> unfolding cortex into spherical form... >> surface projected - minimizing metric distortion... >> ______________________________**________________________ >> >> Could this have to do with FreeSurfer version maybe? >> >> Cris >> >> >> 2013/8/14 Cristian Paz <pazcristian99(a)gmail.com> >> Dear experts! >> >> I have a question. >> >> I have run recon-all on a cluster , and I am editing on my local >> machine. I just checked the versions and I see that I have: >> >> freesurfer-x86_64-redhat-**linux-gnu-stable5-20110522 at the computing >> cluster and >> >> freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 on my local >> computer.... >> >> Is this a problem? >> >> Thank you very much for your help. >> >> Kind regards Cris >> >> >> >> >> > > 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<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. >

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