Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Group Analysis
by Ali Radaideh 02 Oct '15

02 Oct '15

Hi, I am running a group analysis (patients versus controls). I am following the tutorial and managed to create the FSGD file with four classes MSMale MSFemale HealthyMale HealthyFemale and one variable: Age So the number of NregressorsDODS is equal to 8 [ MSMale MSFemale HealthyMale HealthyFemale Age_ MSMale Age_ MSFemale Age_ HealthyMale Age_ HealthyFemale ] I have created my own contrast files as follows: lh-female_MS_vs_Healthy .mtx *to * *compare between Female MS and Female Healthy regardless of age*: *[ 0 1 0 -1 0 0 0 0 ]* *lh-female_MS_vs_Healthy_Age.mtx* * * *to * *compare between Female MS and Female Healthy_with age effect*: *[0 0 0 0 0 1 0 -1]* *lh-male_MS_vs_Healthy.mtx * *to * *compare between Male MS and Male Healthy regardless of age*: *[1 0 -1 0 0 0 0 0]* *lh-male_MS_vs_Healthy_Age.mtx to * *compare between Male MS and Male Healthy_with age effect* : *[0 0 0 0 1 0 -1 0 ]* ** ** *lh-MS_vs_Healthy.mtx to compare between MS and Healthy regardless of Age and Gender*: *[ 0.5 0.5 -0.5 -0.5 0 0 0 0 ] * *I ran the glm_fit using the following command line:* *mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir* *Everything went OK except when loading the sig.mgh in freeview using the following command:* *freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=4,5 -viewport 3d1- It complained that the flag annot_outline=1 is not recognized2- after removing this flag from the command line, the overlay only was two colors (green and red) (I have attached a copy of it) * *Then I did * a cluster-wise correction for multiple comparisons by run n ing a simulation * as follows:* *mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp 0.05 --2spaces* *Nothing has changed. in free view the same overlay.* *I opened the "*cache.th40.neg.sig.cluster.summary " file and got the following: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2015/10/02-15:06:07-GMT # cmdline mri_surfcluster --in lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/neg/th40/mc-z.csd --mask lh.disease_Healthy_Age.glmdir/mask.mgh --cwsig lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.mgh --vwsig lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.voxel.mgh --sum lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.summary --ocn lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.mgh --oannot lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white # cwd /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/freesurfer_HU # sysname Linux # hostname ali-XPS-L501X # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/freesurfer_HU # SearchSpace_mm2 65416.6 # SearchSpace_vtx 149955 # Bonferroni 2 # Minimum Threshold 4 # Maximum Threshold infinity # Threshold Sign neg # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 4.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 2.82441 at vertex 65720 # Overall min -3.14816 at vertex 26640 # NClusters 0 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot As you can see, the columns are empty!!! Any ideas please? was there any mistake in my processing? Many thanks for your help. Ali *Ali M. Al-Radaideh. PhD* *Head of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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Re: [Freesurfer] Parcellation stats
by Ali Radaideh 02 Oct '15

02 Oct '15

Can we get any stats from this type of parcellation? I only can see two annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay. Thanks, Ali On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > that will generate a parcellation on the individual subject surface of > Thomas Yeo's 17-network clustering. It won't do anything with the thickness > though. What are you trying to do? > > On Tue, 29 Sep 2015, Ali Radaideh wrote: > > mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh >> >> --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot >> --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot >> >> scz10 is my subject name >> >> On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu >> > >> wrote: >> what is your surf2surf command? >> >> On 9/28/15 5:11 PM, Ali Radaideh wrote: >> Dear Douglas, >> >> Thanks for your email. I meant to say that after running the >> recon-all, i ran the sur2surf command to get the cortical >> parcellation using Thomas Yeo Atlas. >> >> I thought that the extracted cortical thickness after running >> the surf2surf command will be different from the one extracted >> before running the command. But, Bruce kindly replied to my >> email saying that it is the same if it is calculated on >> vertex-wise basis. >> >> Thanks, >> Ali >> >> On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu> wrote: >> I can't understand what you are asking. Can you >> elaborate? >> >> On 09/28/2015 01:51 PM, Ali Radaideh wrote: >> > Thanks alot Douglas, >> > >> > Yes it is there but after checking it many time I >> found it corrupted >> > for some subjects due to copying them many times >> between machines. >> > >> > But May I ask you some thing related. I have just >> posted a question >> > regarding getting the cortical thickness after >> running the surf2surf >> > command (17 networks cortical parcellation). Now I >> found the stats >> > file not updated after running this command only >> the annotation files >> > in label folder. >> [rh.Yeo2011_17Networks_N1000.annot]. We thought that >> > using Yeo Atlas will give slightly different >> cortical thickness, are >> > we correct? >> > >> > Thanks, >> > Ali >> > >> > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve >> > <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> > >> > does that file exist? >> > >> > On 09/28/2015 01:05 PM, Ali Radaideh wrote: >> > > Dear FreeSurfer experts, >> > > After finishing the recon-all, I am trying >> to extract the cortical >> > > thickness for each subject and group them >> into one table but >> > > unfortunately i keep getting the following >> error: >> > > >> > > rh.aparc.DKTatlas40.stats is not found or is >> too small to be a >> > valid >> > > statsfile >> > > Use --skip flag to automatically skip bad >> stats files >> > > >> > > i tried to change the stats file (e.g I used >> aparc.a2009s) but I got >> > > the same error. >> > > >> > > I tried each brain alone and also got the >> same error. >> > > >> > > Any ideas please >> > > Thanks, >> > > Ali >> > > >> > > -- >> > > /Ali M. Al-Radaideh. PhD >> > > Head of Department of Medical Imaging >> > > Vice Dean of the Faculty of Allied Health >> Sciences >> > > The Hashemite University, >> > > Zarqa, Jordan >> > > W.phone +962 5 3903333 ext.5422, 5355, 5364 >> > > Email: ali.radaideh(a)hu.edu.jo >> <mailto:ali.radaideh@hu.edu.jo> >> > <mailto:ali.radaideh@hu.edu.jo >> <mailto:ali.radaideh@hu.edu.jo>> >> > > / >> > > /webpage: >> http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ >> > > >> > > >> > > >> > > >> _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:Freesurfer@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 >> <mailto:greve@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 >> > Fax: 617-726-7422 >> > >> > Bugs: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: >> https://gate.nmr.mgh.harvard.edu/filedrop2 >> > >> 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(a)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. >> > >> > >> > >> > >> > -- >> > /Ali M. Al-Radaideh. PhD >> > Head of Department of Medical Imaging >> > Vice Dean of the Faculty of Allied Health Sciences >> > The Hashemite University, >> > Zarqa, Jordan >> > W.phone +962 5 3903333 ext.5422, 5355, 5364 >> > Email: ali.radaideh(a)hu.edu.jo >> <mailto:ali.radaideh@hu.edu.jo> >> > / >> > /webpage: >> http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ >> > >> > >> > >> > _______________________________________________ >> > 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 >> >> >> >> >> -- >> Ali M. Al-Radaideh. PhD >> Head of Department of Medical Imaging >> Vice Dean of the Faculty of Allied Health Sciences >> The Hashemite University, >> Zarqa, Jordan >> W.phone +962 5 3903333 ext.5422, 5355, 5364 >> Email: ali.radaideh(a)hu.edu.jo >> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= >> >> >> >> _______________________________________________ >> 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 >> >> >> 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. >> >> >> >> >> -- >> Ali M. Al-Radaideh. PhD >> Head of Department of Medical Imaging >> Vice Dean of the Faculty of Allied Health Sciences >> The Hashemite University, >> Zarqa, Jordan >> W.phone +962 5 3903333 ext.5422, 5355, 5364 >> Email: ali.radaideh(a)hu.edu.jo >> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= >> >> >> > _______________________________________________ > 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. > > -- *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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FreeSurfer Ubuntu Server
by Bruno LAD 02 Oct '15

02 Oct '15

Hi, could you help me please, because a couldn't find the answer for my question in the wiki. Can FreeSurfer be installed on ubuntu server 12.04? How can I do it, if it's possible? Thank you. -- Best Regards Bruno Bragança Mendes Laboratório de Alto Desempenho LAD/PUCRS Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120 +55 51 33538001

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White Matter Edits vs. Control Points, & third party software
by Julio Alberto González Torre 02 Oct '15

02 Oct '15

I have some questions about how to manually correct the white matter regions . It's the same manually edit the volume "brainmask.mgz" and use control points? Would I get the same result? My intention is not to use control points, but directly replace the voxels that have not been classified as white matter with the value 110. Is it right to do this? My second question is: Is it possible to edit the volumes with a third party program? My intention here is to turn the volume "brainmask.mgz" to " brainmask.nii" using "mri_convert" command. Then edit the values of the voxels manually with a third party software or painting tool, and finally, turn the volume back to "brainmask.mgz", replace the file in their respective directory, and finally execute "-autorecon2- wm". Is it right to do this? Or this may compromise my data? Thanks in advance, Alberto.

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Statistical tests on Tracula's path spline
by Yuwen Hung 02 Oct '15

02 Oct '15

Hi, Thanks for the great FreeSurfer Course this past week. After running through Tracula and extracted the path stats (by voxel) across all subjects, can I apply mri_glmfit to test the group differences using the generated txt file that has all subject's diffusion meassure (e.g., FA) along particular spline voxels (the pathstats.byvoxel.txt, for example)? Thanks! ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: 01 October 2015 12:00 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 140, Issue 3 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. WM segmentation error longitudinal stream (Adam, Ruth) 2. Test incoming emails - (pablo najt) 3. Re: dt_recon (Alshikho, Mohamad J.) 4. mri_convert doubles file size when changing TR header information (Shaun Patel) 5. Re: PVE correction tool within the V 6 beta (m.bahri(a)ulg.ac.be) 6. Re: Error Messages for Accessing Bin (Bruce Fischl) 7. Re: Calculate the cortical thickness in patients with brain tumor (Bruce Fischl) 8. Re: Calculating local gyrification using CIVET's surface file ('.obj') (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Thu, 1 Oct 2015 14:35:30 +0200 From: "Adam, Ruth" <Ruth.Adam(a)med.uni-muenchen.de> Subject: [Freesurfer] WM segmentation error longitudinal stream To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <AF867463-A1D8-432B-A4F3-83396DB900B1(a)med.uni-muenchen.de> Content-Type: text/plain; charset="us-ascii" Hi all, We have run longitudinal analysis on two time points. The resulting longitudinal WM surface for both time points excludes large parts of the cortex. The cross sectional surfaces and the wm.mgz are correct. The base wm.mgz also seems to be fine, however, the base white and pial surfaces do not follow the wm volume properly. We have rerun the longitudinal anlaysis (recon-all -long) according to the cheat sheet: 1. marking the base wm.mgz border with 255 voxel value (instead of 110) 2. adding control points to the base wm.mgz but it did not change the original result. Any idea how this can be fixed? Thank you very much in advance! Best, ruthi ------------------------------ Message: 2 Date: Thu, 1 Oct 2015 13:27:37 +0000 From: pablo najt <pablonajt(a)hotmail.com> Subject: [Freesurfer] Test incoming emails - To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BLU181-W20EA2FE3E891F70E4CF592AE4C0(a)phx.gbl> Content-Type: text/plain; charset="iso-8859-1" I am sending this message as a test since my income emails from FS stopped working on the 29 of September.Regards

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Cannot change min threshold in Configure Overlay Display TKSurfer
by Oana Georgiana Rus 02 Oct '15

02 Oct '15

Dear developers/users? When I load a *mgh.sig* file in *TkSurfer* and I go on *Configure Overlay Display* and want to change the *min Threshold on 1.3* or wathever number I can't edit or do that? did somebody encounter the same problem? How can you solve it? Thank You. -- Oana Georgiana Rus PhD Student Neuroimaging Center TUM-NIC Klinikum rechts der Isar Technische Universität München Einsteinstr.1 81675 München Raum 5.8 Tel. 089 4140 7971

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Hippocampus visualisation
by Erik O'Hanlon 02 Oct '15

02 Oct '15

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Post-doctoral Positions in Affective Neuroscience at McLean Hospital/Harvard Medical School
by Poornima Kumar 01 Oct '15

01 Oct '15

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Re: [Freesurfer] Registering set of extracted hippocampus
by Chester Dolph 01 Oct '15

01 Oct '15

Hello, Rewording to clarify in case the wording was confusing. What I would like to do is to use each registered ROI for intensity based analysis. I am confused how to use Freesurfer to register and align about three axis. I understand there is variability with positioning the head within the scanner of MRI. I am guessing one solution might be to align each ROI centroid to the same location. This seems to be a trivial concept, but I was hoping there was a simple way of doing this using Freesurfer tools. I appreciate your time and help. Thanks, Chester > On Sep 11, 2015, at 5:31 PM, CHESTER DOLPH <cdolp001(a)odu.edu> wrote: > > Dear experts, > > I look like to register a set of extracted hippocampus to a common atlas. Here is my workflow: > > I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the axial axis. > > I have been looking at the registration tools at: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration> > > Would someone please make a recommendation of a freesurfer tool well suited to registering a set of extracted left or right hippocampus to a common atlas? Also is there a flag to indicate the region, for instance from the look up table: $FREESURFER_HOME/FreeSurferColorLUT.txt > > Thanks, > Chester

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Re: [Freesurfer] Error Messages for Accessing Bin
by Bruce Fischl 01 Oct '15

01 Oct '15

can you try chmod a+x on one of them and see if it can then be executed? e.g.: chmod a+x /home/tle7/freesurfer/bin/mri_convert /home/tle7/freesurfer/bin/mri_convert and see if you get an error. If not, you probably downloaded the wrong hardware version cheers Bruce On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote: > > Hello, > When I run the command "sFSstart" on version 5.0.0, I am receiving the > messages below. Would you please explain to me what the problem is? It > seems like there is trouble accessing the bin. > Thank you > > -------- freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /home/tle7/freesurfer > FSFAST_HOME /home/tle7/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /home/tle7/freesurfer/subjects > MNI_DIR /home/tle7/freesurfer/mni > tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2 > studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter > H 0 > checking sid number 00152-DT2 > 1 > 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm > Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects > Actual FREESURFER_HOME /home/tle7/freesurfer > Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP > Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_robust_register: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_robust_template: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_and: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_or: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_fuse_segmentations: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_segstats: Exec format error. Binary file > not executable. > -cw256 option is now persistent (remove with -clean-cw256) > /home/tle7/freesurfer/subjects/00152-DT2_v5 > > mri_convert/home/tle7/freesurfer/subjects/practicemotherdaughter/rawdata/00152-DT2/MR. > 1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm > /home/tle7/freesurfer/subjects/00152-DT2_v5/mri/orig/001.mgz > > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP > Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 00152-DT2_v5 exited with ERRORS at Mon Sep 28 10:43:57 > PDT 2015 > > tle7@sni-vcs-gotlib:~$ > > > >

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