Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Tracula: Segmentation fault
by andrea cristina Lima 02 Oct '15

02 Oct '15

Please could you help me with this? Computing prior on underlying anatomy (non-truncated streamlines only) Segmentation fault Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Oct 2 19:38:55 BRT 2015 Attached is the log Thank you! -- Andrea Cristina de Lima Pardini CV: http://lattes.cnpq.br/0921194840474573

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Re: [Freesurfer] PVE correction tool within the V 6 beta
by m.bahri＠ulg.ac.be 02 Oct '15

02 Oct '15

Dear Greve, Thank you for your answer. Steps 1 and 2 are ok but in step 3 there are some unclear options (e.g. --mgx .01) Could you please explain which method is used for the pve correction and how can I obtain the 4D-pve-corrected images? Is it possible to extract the TACS of all regions? Many thanks for your help, Best, Mohamed ----- Mail original ----- De: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> À: freesurfer(a)nmr.mgh.harvard.edu Envoyé: Lundi 28 Septembre 2015 17:49:49 Objet: Re: [Freesurfer] PVE correction tool within the V 6 beta I'm still putting all the documentation together, but you can start with the instructions below. They are assuming you will use kinetic modeling. If you have a static scan, #1 and #2 are still the same, but #3 changes and #4 and #5 not needed. Let me know and I can give you further instructions. doug 1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical with bbregister (with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1. 3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i tac.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. --km-hb specifies the highbinding region for MRTM2. --km-ref specifies the reference region. --mgx specifies to output a muller-gartner map (not necessary for GTM ROI analysis). 4. For the GTM (ROI) MRTM1 KM analysis, you would then run mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz where time.dat is a text file withe acquisition time of each time point in the tac. 5. For the MRTM2 analysis set k2p = `cat mrtm1/k2prime.dat` mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o mrtm1 --no-est-fwhm --nii.gz If you want to run a voxel-wise analysis, then you can use the mgx volume as input (--y). Probably you'll want to sample this to the surface using mri_vol2surf and the registration file aux/anat2pet.lta, then smooth on the surface On 9/28/15 11:38 AM, Mohamed Ali Bahri wrote: > Dear Expert, > > Are there any explanation (steps to follow) about the use of FreeSurfer > (version 6 beta) to correct for the partial volume effect (PET dynamic > data)? > > Many thanks in advance, > > Best, > > Mohamed > _______________________________________________ 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.

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Re: [Freesurfer] warping surface label to volume space
by Douglas N Greve 02 Oct '15

02 Oct '15

I'm at a loss here. I run the exact same command with the same version. I get the same terminal output, but my output volume looks ok. The only thing I can think of is that there is an old version that output volume that is not getting overwritten. Can you name the output file differently and make sure that it does not exist prior to running the command? On 09/30/2015 04:37 PM, Jacobs H (NP) wrote: > Hi Doug, > > Just as a reminder: I uploaded the data yesterday. > > Best > Heidi > > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Tuesday 29 September 2015 17:01 > To: "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] warping surface label to volume space > > filedrop2 url at the end of this email > > On 9/29/15 10:34 AM, Jacobs H (NP) wrote: >> Sure, where should I upload it to? >> Thanks! >> Heidi >> >> From: Douglas Greve <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Date: Tuesday 29 September 2015 16:28 >> To: "freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>" >> <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] warping surface label to volume space >> >> Can you upload the subject so I can look at it? >> >> On 9/29/15 9:05 AM, Jacobs H (NP) wrote: >>> Hi Doug, >>> >>> The label looks actually ok and the surface as well. I attached the images to this email, Not sure where it went wrong? >>> >>> Best >>> Heidi >>> >>> ________________________________________ >>> Van:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>> Verzonden: maandag 28 september 2015 23:58 >>> Aan:freesurfer@nmr.mgh.harvard.edu >>> Onderwerp: Re: [Freesurfer] warping surface label to volume space >>> >>> Something is definitely going wrong. Can you load the label as well and >>> verify that the label itself looks ok? >>> >>> On 09/28/2015 05:32 PM, Jacobs H (NP) wrote: >>>> Yes, here it is! >>>> Thanks! Heidi >>>> >>>> >>>> >>>> Yes, here it is! >>>> Thanks! Heidi >>>> >>>> >>>> image1.png >>>> >>>> >>>> >>>> ATT00001.txt >>>> >>>> >>>> >>>>> Op 28 sep. 2015 om 17:26 heeft Douglas N Greve<greve(a)nmr.mgh.harvard.edu> het volgende geschreven: >>>>> >>>>> Can you send a picture? >>>>> >>>>>> On 09/28/2015 05:08 PM, Jacobs H (NP) wrote: >>>>>> Dear Doug, >>>>>> >>>>>> By looking at it in Freeview. Anatomically, I would expect that the entorhinal cortex would not be localized so laterally? And some voxels are not in the temporal lobe. >>>>>> >>>>>> Best >>>>>> Heidi >>>>>> >>>>>> ________________________________________ >>>>>> Van:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>>>>> Verzonden: maandag 28 september 2015 23:00 >>>>>> Aan:freesurfer@nmr.mgh.harvard.edu >>>>>> Onderwerp: Re: [Freesurfer] warping surface label to volume space >>>>>> >>>>>> how are you determining that it is not in the right place? When I run >>>>>> this it works. >>>>>> >>>>>>> On 09/28/2015 04:54 PM, Jacobs H (NP) wrote: >>>>>>> Hi, >>>>>>> >>>>>>> Bringing this to the FS list: >>>>>>> I am trying to warp the entorhinal cortex label (ex vivo) to volume >>>>>>> space, so that I can see and use the full ROI. Using the command >>>>>>> stated below doesnâ€™t seem to work, as it is not in the right location >>>>>>> of the subjectâ€™s brain. Any thoughts? >>>>>>> >>>>>>> I used this command: >>>>>>> mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label >>>>>>> --regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o >>>>>>> lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP --hemi l >>>>>>> >>>>>>> This was the output on the terminal: >>>>>>> subject S_3RSPPP --hemi lh >>>>>>> INFO: subject not needed, igorning. >>>>>>> Number of labels: 1 >>>>>>> S_3RSPPP/label/lh.entorhinal_exvivo.label >>>>>>> Annot File: (null) >>>>>>> Template Volume: (null) >>>>>>> Outut Volume: lh.entorhinal_exvivo_vol.mgz >>>>>>> Registration File: (null) >>>>>>> Fill Threshold: 0 >>>>>>> Label Vox Vol: 1 >>>>>>> ProjType: (null) >>>>>>> ProjTypeId: 0 >>>>>>> ProjStart: 0 >>>>>>> ProjStop: 0 >>>>>>> ProjDelta: 0.1 >>>>>>> Subject: S_3RSPPP >>>>>>> Hemi: lh >>>>>>> UseNewASeg2Vol: 0 >>>>>>> DoLabelStatVol 0 >>>>>>> LabelCodeOffset 0 >>>>>>> setenv SUBJECTS_DIR /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS >>>>>>> $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ >>>>>>> INFO: loading >>>>>>> surface /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white >>>>>>> >>>>>>> nvertices = 120130 >>>>>>> Reading thickness >>>>>>> /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.thickness >>>>>>> nlabels = 1 >>>>>>> Loading >>>>>>> /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ribbon.mgz >>>>>>> Loading S_3RSPPP/label/lh.entorhinal_exvivo.label >>>>>>> Mapping >>>>>>> >>>>>>> Any suggestions how I can improve this? >>>>>>> Thanks >>>>>>> Heidi >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.eduhttps://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/filedrop2www.nmr.mgh.harvard.edu/… >>>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>>> contains patient information, please contact the Partners Compliance HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in error >>>>>> but does not contain patient information, please contact the sender and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.eduhttps://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/filedrop2www.nmr.mgh.harvard.edu/… >>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.eduhttps://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/filedrop2www.nmr.mgh.harvard.edu/… >>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.eduhttps://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/

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Re: [Freesurfer] mri_convert doubles file size when changing TR header information
by Douglas Greve 02 Oct '15

02 Oct '15

It is probably changing the data type from short to float. Try adding -odt short --no_scale 1 You can also look at the data type with mri_info --type file.nii On 10/1/15 10:52 AM, Shaun Patel wrote: > I noticed after running slice-time correction with SPM, the resulting Nifti files do not have TR information in the header. This breaks the Freesurfer pipeline. To get around this, I attempted to use the mir_convert function with the “tr” flag to set the TR. However, in doing so, I noticed that the resulting nifti file doubles in size. I used the following command: mri_convert f.nii f.nii -tr 2000, to set the TR to 2s. Any suggestions as to what is happening to the file size and how to prevent it? > > Many Thanks, > > Shaun > > -- > Shaun Patel, Ph.D. > Research Fellow > Department of Neurosurgery > Massachusetts General Hospital > Harvard Medical School > e. shaun.patel(a)me.com > w. http://shaunpatel.com > c. 317.340.7260 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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] dt_recon
by Alshikho, Mohamad J. 02 Oct '15

02 Oct '15

Hi Doug, Thank you very much for your answers! Kindly I have one more question: At the end of DTI analysis using the tool “dt_recon” we will have “ stats” file including the FA value for every segment and parcellate in the brain. Depending on this output can we use the term “ DTI morphometry” to describe the analysis? Thanks Mohamad From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Monday, September 28, 2015 11:26 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dt_recon On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote: Hi Doug and Bruce, After running the command : dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>> I need to generate the final statistics ( FA for every parcellate and segment in aseg and wmparc atlases) using the command “mri_segstats” In order to do so I need to move “fa.nii” to anatomical space using the command: mri_vol2vol –mov fa.nii –lta register.lta –fstarg –o fa.anat.mgh <<< source: Freesurfer wiki>>> My questions are about the file “register.lta” : 1. What is the difference between this file and the file “register.dat” ( which I can see it as an output of the command ” bbregister” in the final analysis using the command “dt_recon”) They hold the same basic registration information just in different formats. We are trying to move to the LTA as it is a much better format for these things. 2. How can I generate the file “ register.lta”? Use lta_convert, something like lta_convert --inreg register.dat --outlta register.lta --src lowb.nii.gz --trg $SUBJECTS_DIR/$subject/mri/orig.mgz 3. Can I feed the file “ register.dat” instead of the file “ register.lta” into the command “mri_vol2vol “ (in order to move the ‘’fa.nii” to anatomical space). If so which flag I should use instead of the flag “--lta” in the command mri_vol2vol? Yes, pass it with --reg flag. Many thanks Mohamad _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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=>*

3 5

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.

3 2

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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