Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

Re: [Freesurfer] fcseed-sess error
by Omar Singleton 24 Aug '13

24 Aug '13

Sorry about that. I must have clicked 'reply' by mistake rather than 'reply all'. I wouldn't want to deprive anyone of the opportunity to help me resolve this issue. --The issue-- I looked at the segmentation in tkmedit and the labels for the ventricles showed up the same as in subjects that worked. I checked registration by eye and used this command from the tutorial: tkregister-sess -s AC30_1319 -fsd Bold1 -per-run -bbr-sum Which output: AC30_1319 001 0.4437 I'm not sure what the problem is with these subjects. Is there another way I should check the data? Any suggestions? -Omar > Hi Omar, can you post questions to the list instead of us personally? > thanks! > doug > > On 08/19/2013 09:41 AM, Omar Singleton wrote: >> Hi Doug, >> >> Thanks for the help. I looked at the segmentation in tkmedit and the >> labels for the ventricles showed up the same as in subjects that worked. >> I >> checked registration by eye and used this command from the tutorial: >> >> tkregister-sess -s AC30_1319 -fsd Bold1 -per-run -bbr-sum >> >> Which output: >> >> AC30_1319 001 0.4437 >> >> I'm not sure what the problem is with these subjects. Is there another >> way >> I should check the data? Do you have any other suggestions? >> >> Best, >> Omar >> >>> Hi Omar, it is not finding any ventricle voxels. Check the FS >>> segmentation to make sure that the ventricles are labeled and also >>> check >>> the registration to make sure it looks ok. >>> doug >>> >>> >>> On 8/14/13 12:04 PM, O S wrote: >>>> 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) >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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/ > > >

2 4

Different results related to ICV (eTIV) difference between FS 4.5.0 and 5.3.0 - any suggestions?
by Kjetil Nordbø Jørgensen 24 Aug '13

24 Aug '13

Dear FreeSurfer experts! I have a problem which relates to the ICV (eTIV) measure in different versions, and would be thankful for any suggestions: I have previously examined associations between body mass index (BMI) and global cortical measures (e.g. cortical volume) in a sample of patients with severe mental illness using stats from FS 4.5.0. I then found a small but significant positive association between BMI and volume (p<0.05) (corrected for age, gender and diagnosis), which became more highly significant when covarying for ICV (p<0.0001). According to my hypothesis, I interpreted this as a tendency towards larger brains relative to skull size with increasing BMI (it should be noted that although the association was significant, a beta-value of about .1 indicated the effect was small). Now, when I updated the analyses with stats from FS 5.3.0, using the same data set, no significant results emerge: The positive association is now at trend-level (p=0.105), and when covarying for ICV (eTIV) it disappears altogether. I’m struggling to understand this difference. The analyses are fairly similar up to the point where ICV (eTIV) is added as a covariate, but adjusting for ICV changes the results quite a lot. Both cortical volume and ICV correlates highly between the two versions (r = .96 and .94, respectively), but when I calculate cortical volume/ICV-ratios based on stats from each version, the correlation between these is lower (r = .75). I have so far ruled out (I believe) any differences in quality control or editing as a source of the difference. Both versions have used the talairach.xfm transform and not the older talairach_with_skull. The problem could be related to collinearity (correlations between cortical volume and ICV were r=.81 in FS 4.5.0 and r=.74 in FS 5.3.0), but VIF and tolerance statistics does not indicate a problem (and I suppose this would affect results equally much between versions (?)). So, my questions are: - Are there any differences between FS 4.5.0 and FS 5.3.0 in how ICV (eTIV) is calculated? - Is it inappropriate to correct for intracranial volume when examining global cortical volume rather than regional volumes? - Do any of you have suggestions as to how I can figure out what is the ‘true’ result here? Any help is appreciated!

1 0

FW: FW: Contrast and F-test
by Jacobs H (NP) 24 Aug '13

24 Aug '13

Arrghh, again wrong email, sorry.... Thanks. I think I understand the rational behind it. Just to be sure, would this be correct: For each group separately 0 0 0 1 0 0 (group - cognition - education - cognition x education - age - ICV) For the F-test (same order) 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 Heidi ________________________________________ Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Verzonden: donderdag 22 augustus 2013 16:46 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: Contrast and F-test you need to have all 3. If you want to examine the interaction, then you need a new contrast to test the interaction. Set all to 0 except for the interaction term doug On 08/22/2013 10:42 AM, Jacobs H (NP) wrote: > Dear Doug, > Thank you for the information. Sorry for not sending this to the list. > Do you mean that I then have to include the three variables (covariate 1, covariate 2, product of these two) or only the product in the fsgd file? > If I need to include all three of them, can you advise me on the contrasts? > If it is only the product, I think I can use the same contrasts as before, right? > > Thanks > Heidi > ================================================ > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > h.jacobs(a)maastrichtuniversity.nl > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > ================================================ > ________________________________________ > Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Verzonden: donderdag 22 augustus 2013 16:34 > Aan: freesurfer(a)nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] Contrast and F-test > > If you want to test for an interaction between continuous variables, > then you should create a new regressor by multiplying them together then > test that regressor > doug > > > On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: >> Hi all, >> >> I my manuscript, I examined the association between cognition and cortical thickness. I first did this in three groups separately and then ran a F-test. >> One of the reviewers, now wants me to examine the interaction between cognition and education (all continuous). >> >> Would this be the correct contrast for each group separately (last two zeros are for covariates, also continuous) >> >> 0 1 -1 0 0 >> >> Would this be the correct way for the F-test: >> >> 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 >> 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 >> >> Thanks! >> >> Heidi >> >> ================================================ >> Dr. Heidi Jacobs >> Postdoc researcher >> Faculty of Health, Medicine and Life Sciences >> School for Mental Health and Neurosciences >> Division Cognitive Neuropsychiatry and Clinical Neurosciences >> Alzheimer Center Limburg >> h.jacobs(a)maastrichtuniversity.nl >> www.maastrichtuniversity.nl >> www.heidijacobs.nl >> >> Dr. Tanslaan 12, 6229 ET Maastricht >> P.O. Box 616, 6200 MD Maastricht, The Netherlands >> T +31 43 38 84 090 F +31 43 38 84 092 >> ================================================ >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 7

Make an average activation map of 2 scans
by Alexandra Tanner 23 Aug '13

23 Aug '13

Hi Freesurfers, Does anyone know how to make an average activation map of two subjects without running a group analysis? I have 15 subjects that each have a pre and a post scan (30 scans total) and we would like to combine the pre and post bold runs for each subject to generate an averaged AllvFix activation map for each pair (so I would end up with 1 activation map per subject pair of the pre and post bold runs averaged together -- 15 maps total). Originally I tried treating each of my subject pairs as a group and ran isxconcat-sess and mri_glmfit on each pair (N=2), but because my N was so small the osgm map looked very strange and wispy. Because I'm trying to combine a pre and post scan for the same subject, is it possible to register the post subject's bold scans to the pre subject (or vice versa) so that we can treat all the bold runs as one subject and run selxavg3-sess referencing the pre and post bold runs in the runlist file? Any clarification or suggestions would be greatly appreciated! Thanks, Alex

3 2

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
by Douglas N Greve 23 Aug '13

23 Aug '13

They should be fine. BTW, you can run recon-all -s subject -make all and it will only run the parts that need to be run doug On 08/20/2013 12:13 PM, Pedro Rosa wrote: > Hi, > I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. > Thanks, > Pedro Rosa. > > On 20 Aug 2013, at 10:28 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > >> Hi Pedro, see the release notes for the issue >> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >> doug >> >> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>> Hi experts, >>> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >>> >>> >>> Any help is appreciated. >>> Regards, >>> Pedro Rosa. >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)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(a)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. >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

3 13

Otto: unsupported slice timing pattern 5
by Otto Muzik 23 Aug '13

23 Aug '13

Hi, I am trying to convert a SIEMENS T1-weighted volume to the mgz format (via mri_convert) but I am getting constantly the error message unsupported slice timing pattern 5 in file .... I saw in the archives that a lot of people had problems with this but could not find any solutions posted - what am I missing? Many thanks Otto

3 2

entorhinal ex vivo > stats 2 table?
by Keller, Simon 23 Aug '13

23 Aug '13

Dear all, Sorry if this has been covered previously (I've not been able to find a solution in the archives). Is there a script that automatically puts your sample of entorhinal ex vivo labels into a table for each value (volume, thickness etc), something like asegstats2table or aparcstats2table? mris_anatomical_stats obviously gets the values out for individuals - but with a sample at n>200 I'd obviously rather batch this. Thanks in advance, Simon.

2 1

TBSS doubts
by Anupa AV 23 Aug '13

23 Aug '13

Dear All, I was trying to do TBSS analysis. But I encountered with some problems.I attached a ppt which shows raw DWI, FA map generated using FDT FSL toolbox and the TBSS results. If you see the FA and TBSS results,..some brain areas got removed. I'm wondering where I made the mistake?? Can you please help me out?? Thanks in advance.!!

2 1

Problem with mris_ca_label (seg fault)
by Demian Wassermann 22 Aug '13

22 Aug '13

Dear Support line of free surfer, I have a problem when I try to apply a new atlas to the surfaces. Even with the standard free surfer atlases it segfaults Environment: FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 RedHat release: Fedora release 18 (Spherical Cow) Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64 Command: $FREESURFER_HOME/bin/mris_ca_label -t $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs lh.test.annot Output: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ reading atlas from /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Segmentation fault (core dumped) Am I doing something wrong? How can I diagnose and fix this? Thanks D -- Demian Wassermann, PhD demian(a)bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/

2 5

gradient table question for Tracula
by Salil Soman 22 Aug '13

22 Aug '13

Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang: "To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components." (from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visualizati… ). Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

3 2

← Newer
1
...
4
5
6
7
8
9
10
...
27
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2013