Freesurfer August 2012

freesurfer@nmr.mgh.harvard.edu

110 participants
170 discussions

TRACULA -prep error
by Richard Binney 16 Aug '12

16 Aug '12

Hi Anastasia et al., I previously had TRACULA running wonderfully on a test dataset. I was tasked with writing an in-house step-by-step manual for dummies. Since then, a colleague has followed my manual with a new dataset and had problems. After trying to determine whether it was her install or something about her data and failing to find anything, I returned to re-run the subject I had already successfully processed. Nothing has changed in my install (TRAC-all version etc) ODDLY, this re-run is suffering from the same problem as my colleague. We ran trac-all -prep -dmrirc and it exited without any errors. However, there seem to be some files missing from the output: control.dat data.nii.gz nodif_brain_mask.nii.gz Bedpostx will not run due to the *data* file being missing and I'm sure the other missing files will cause problems. What is going on? I knew to look for these files as at some point I found the following list for the \dmri\. I can not re-find a post with this list so I'm sorry if it related to a solution to our current problem. Please help Richard brain_anat_mni.nii.gz dtifit_L2.nii.gz dwi_orig_flip.nii.gz brain_anat.nii.gz dtifit_L3.nii.gz dwi_orig.mghdti.bvals brain_anat_orig.nii.gz dtifit_MD.nii.gz dwi_orig.mghdti.bvecs bvals dtifit_MO.nii.gz dwi_orig.nii.gz bvecs dtifit_S0.nii.gz dwi_snr.txt bvecs.norot dtifit_V1.nii.gz lowb_brain.nii.gz control.dat dtifit_V2.nii.gz lowb.nii.gz data.nii.gz dtifit_V3.nii.gz mni dtifit_FA.nii.gz dwi.ecclog nodif_brain_mask.nii.gz dtifit_L1.nii.gz dwi.nii.gz xfms

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Re: [Freesurfer] TRACULA -prep error
by Richard Binney 16 Aug '12

16 Aug '12

voila....thanks for your help On Thu, Aug 16, 2012 at 2:09 PM, Anastasia Yendiki < ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Can you send me trac-all.log? > > > On Thu, 16 Aug 2012, Richard Binney wrote: > > So looking back at my previous successful attempts, it appears that both >> data.nii.gz and nodif_brain_mask.nii.gz should be symbolic links (to dwi >> and >> lowb_, presumably). that correct? >> >> So for some reason these symbolic links were not created. I wasn't >> over-writing. It was a fresh run on a previously non-existent directory >> (the >> trac-all script automatically creates a new subject-specific directory in >> my >> TRACULA_output directory [specified in dmrirc]). >> >> The control.dat file is an oddity. It appears to be a control points file >> from the RECON output and has a modification date 2 days after the -prep >> was >> run and on the day (but a few hours before) I ran bedpost (wierdly it has >> a >> write date of 1969). I have no idea what has happened here. May have been >> a >> random copying/saving error I made at some point (???? :s) >> >> Forgetting control.dat, what do you think could be happening here? >> >> Many thanks for your help. >> >> Richard >> >> On Thu, Aug 16, 2012 at 1:24 PM, Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >> Hi Richard - In the listing you sent below I do see the a >> nodif_brain_mask.nii.gz and a control.dat, although I have no >> idea what control.dat is. As for data.nii.gz, it should be >> created as a symbolic link to dwi.nii.gz, since bedpostx indeed >> expects it to be called "data". I have not seen this problem >> before, but does it occur only when you rerun and overwrite >> things in the same directory, or also when you start a fresh run >> on a previously non-existent directory? >> >> a.y >> >> On Thu, 16 Aug 2012, Richard Binney wrote: >> >> Hi Anastasia et al., >> >> I previously had TRACULA running wonderfully on a >> test dataset. I was tasked >> with writing an in-house step-by-step manual for >> dummies. Since then, a >> colleague has followed my manual with a new dataset >> and had problems. After >> trying to determine whether it was her install or >> something about her data >> and failing to find anything, I returned to re-run >> the subject I had already >> successfully processed. Nothing has changed in my >> install (TRAC-all version >> etc) ODDLY, this re-run is suffering from the same >> problem as my colleague. >> >> We ran trac-all -prep -dmrirc and it exited without >> any errors. However, >> there seem to be some files missing from the output: >> >> control.dat >> >> data.nii.gz >> >> nodif_brain_mask.nii.gz >> >> >> >> Bedpostx will not run due to the data file being >> missing and I'm sure the >> other missing files will cause problems. >> >> What is going on? >> >> I knew to look for these files as at some point I >> found the following list >> for the \dmri\. I can not re-find a post with this >> list so I'm sorry if it >> related to a solution to our current problem. >> >> Please help >> >> Richard >> >> brain_anat_mni.nii.gz >> >> dtifit_L2.nii.gz dwi_orig_flip.nii.gz >> >> brain_anat.nii.gz >> >> dtifit_L3.nii.gz >> >> dwi_orig.mghdti.bvals >> >> brain_anat_orig.nii.gz dtifit_MD.nii.gz >> >> dwi_orig.mghdti.bvecs >> >> bvals >> >> dtifit_MO.nii.gz dwi_orig.nii.gz >> >> bvecs >> >> dtifit_S0.nii.gz dwi_snr.txt >> >> bvecs.norot >> >> dtifit_V1.nii.gz lowb_brain.nii.gz >> >> control.dat >> >> dtifit_V2.nii.gz >> >> lowb.nii.gz >> >> data.nii.gz >> >> dtifit_V3.nii.gz >> >> mni >> >> dtifit_FA.nii.gz >> >> dwi.ecclog >> >> nodif_brain_mask.nii.gz >> >> dtifit_L1.nii.gz >> >> dwi.nii.gz >> >> xfms >> >> >> >> >> >> >> 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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Error - QDEC
by rajeev krishnadas 16 Aug '12

16 Aug '12

Hi Please help.. I am getting this error message on QDEC when trying to generate stats table. *asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects a01 a02 a03 a04 a05 a06 a07 a08 a09 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 p01 p03 p04 p05 p07 p08 p09 p10 p11 p12 p13 p14 p15 p16 p17 p18 p19 p20 p21* *SUBJECTS_DIR : /usr/local/freesurfer/subjects* *Parsing the .stats files* *ERROR: The stats file /usr/local/freesurfer/subjects/a01/stats/aseg.stats is not found or is too small to be a valid statsfile* *Use --skip flag to automatically skip bad stats files* *ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230* *vtkKWQdecApp (0x2852ad20): * * Script: * *vtkTemp2 GenerateStatsDataTables* * Returned Error on line 1: * *Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects a01 a02 a03 a04 a05 a06 a07 a08 a09 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 p01 p03 p04 p05 p07 p08 p09 p10 p11 p12 p13 p14 p15 p16 p17 p18 p19 p20 p21* * * *Stack trace: * *Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects a01 a02 a03 a04 a05 a06 a07 a08 a09 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 p01 p03 p04 p05 p07 p08 p09 p10 p11 p12 p13 p14 p15 p16 p17 p18 p19 p20 p21* * * * while executing* *"vtkTemp2 GenerateStatsDataTables"* However, the aseg.stats file is in place for a01. I have run these before, but recently i ran a hippo-subfields on a01. I wonder if that has anything to do with this!! I wonder if there is a work around. Cheerio -- Dr Rajeev Krishnadas MBBS, MD, DipNB, MRCpsych Clinical Lecturer Sackler Institute of Psychobiological Research Southern General Hospital, Glasgow G51 4TF *http://tinyurl.com/67ah4vk* *http://tinyurl.com/cwec6mf*

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Re: [Freesurfer] Whole brain vertex values?
by Douglas N Greve 15 Aug '12

15 Aug '12

Hi Molly, you can use the y.mgh file that is created by qdec. This is a stack of all of your subjects in the standard surface space. You can convert to nifti if that is more convenient. BTW, the stats table just gives you the stats for each ROI. If this is something you want, then use aparcstats2table and/or asegstats2table. doug On 08/15/2012 04:55 PM, Molly DuBray wrote: > thanks for the prompt reply- > > i'd like to export raw thickness values for each vertex for a number of subjects. > (i.e. as if the parcellation were 200,000 rois) > > in order to concatenate this for all subjects, i envisioned using qdec's 'generate stats table' function. > > my understanding is that freesurfer does not store an image file of thickness values, but instead computes these on the fly within qdec... > > the main reason we are trying to do this is because i am trying to run longitudinal study with multiple timepoints, and am having all kinds of trouble. i decided to run the stats models in another package (outside of qdec) with the hope of reimporting the analyzed data. > > thanks again. > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Wednesday, August 15, 2012 2:41 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Whole brain vertex values? > > Hi Molly, I don't understand what you are asking. Can you elaborate? > doug > > On 08/15/2012 04:10 PM, Molly DuBray wrote: >> Hello, >> >> Is there a way to export cortical thickness values for each vertex >> across the entire cortex? Can this be done using Qdec to generate a >> larger stats table for a group of participants? >> >> Thank you, >> Molly >> >> ---- >> Molly DuBray Prigge, PhD >> Research Associate >> Department of Psychiatry >> University of Utah >> >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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error with Hippocampal Subfields
by Einav Sudai 15 Aug '12

15 Aug '12

Hi all, I'm running freesurfer ver 5.1 and I'm receiving an error with the command recon-all -s (subjid) -hippo-subfields. The log file terminates with the following information: Hippocampal Subfields processing Wed Aug 15 13:59:42 EDT 2012 mkdir -p /autofs/space/shimshon_002/users/eiran/subjects/02_bay6/ tmp/subfieldResults kvlSegmentHippocampalSubfields.sh 02_bay6 left /autofs/space/shimshon_002/users/eiran/subjects /autofs/space/shimshon_002/users/eiran/subjects/02_bay6/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh 02_bay6 right /autofs/space/shimshon_002/users/eiran/subjects /autofs/space/shimshon_002/users/eiran/subjects/02_bay6/tmp/subfieldResults Linux shimshon 2.6.18-308.4.1.el5 #1 SMP Tue Apr 17 17:08:00 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 02_bay6 exited with ERRORS at Wed Aug 15 16:59:04 EDT 2012 Does anyone know how I can find out the specific problem causing the error? Thank you! Einav

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Whole brain vertex values?
by Molly DuBray 15 Aug '12

15 Aug '12

Hello, Is there a way to export cortical thickness values for each vertex across the entire cortex? Can this be done using Qdec to generate a larger stats table for a group of participants? Thank you, Molly ---- Molly DuBray Prigge, PhD Research Associate Department of Psychiatry University of Utah

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Converting data from fsaverage to SPM
by Eduardo Europa 15 Aug '12

15 Aug '12

Hello, I have two questions: First: I made left hemisphere anatomical ROIs using the freesurfer cortical parcellation atlas and fsaverage's data. However, when I convert these ROIs from .mgz to an SPM-compatible format (.img), the LH ROIs show up on the right. Any idea on how to resolve this problem? The ROIs I need are customized (i.e., I needed to merge some of the areas, and did so via relabeling), but for simpler purposes let's just say I used lh.BA44.label for now. Here are the commands I used: cd $FREESURFER_HOME/subjects/fsaverage mri_label2vol --label label/lh.BA44.label --temp mri/T1.mgz --identity --o lh.BA44.mgz mri_convert lh.BA44.mgz lh.BA44.img Second: I would like to normalize these anatomical ROIs to MNI space in SPM. To do this I was thinking about taking fsaverage's anatomical file, converting it to an SPM-compatible format, estimate the normalization parameters from fsaverage's anatomical to SPM's T1 template, and then writing those parameters to the anatomical ROIs. Therefore am I correct in converting fsaverage's T1.mgz to .img since I am specifying that as the template in the mri_label2vol above? Thanks! -- Eduardo Europa Ph.D. Student, Aphasia and Neurolinguistics Research Laboratory President, Queer Pride Graduate Student Association Co-Chair, Graduate Leadership Council Member, LGBTQA Campus Advisory Network Northwestern University Department of Communication Sciences and Disorders Frances Searle Building 2240 Campus Drive Evanston, IL 60208-3570 europa(a)u.northwestern.edu

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T-value intensity overlayed onto 2009 Destrieux Parcellations
by David Vazquez 15 Aug '12

15 Aug '12

Hi, We would like to visually display some t-values onto a brain using the 2009 Destrieux freesurfer parcellations. We have our own t-values for each parcellation. We would like to display a color-coded spm map for all parcellations, and would like each parcellation to represent the same intensity, instead of voxel by voxel, as was done by Watkins et al. (2001). Has anyone done this? Or have a clue where to find the relevant options? Thank you, David Vazquez Watkins, K.E., Paus, T., Lerch, J.P., Zijdenbos, A., Collins, D.L., Neelin, P., Taylor, J., Worsley., K.J., and Evans, A.C. (2001). Stuctural Asymmetries in the human brain: A voxel-pased Statistical Analysis of 142 MRI scans. *Cerebral Cortex, 11*(9), 868-877.

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Re: [Freesurfer] sulcal depth/cortical folding
by Douglas N Greve 14 Aug '12

14 Aug '12

Hi Hugh, you can run mris_anatomical_stats passing it the sulc file as input. This will give you averages within aparc. I'm not sure what you mean by "measuring cortical folding". What measure would you accept? There's the sulcal depth and then there's curvature (?h.curv). There are two types of "normalization". One is intensity normalization which is a preprocessing step before the segmentation. "Normalization" is also refers to intersubject registration. Probably you mean the latter. doug On 08/13/2012 09:56 PM, Hugh Pemberton wrote: > Hi Doug, > > Thanks so much for getting back to my original question (have included > below) and apologies if my question seems trivial but I'm a bit of a > novice with freesurfer.. I've found the ?h.sulc file but how do I go > about extracting the sulcal depth measurements? Is there a command > like aparcsstats2table? > > Also, is there a way of measuring cortical folding with freesurfer? > And I've read about the noramlization step but am still not completely > clear on it, is this part of the segmentation of white/gray surface > and pial surface? > > Thanks so much for your help, > Best, > Hugh > > Message: 5 > Date: Sun, 12 Aug 2012 22:25:02 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] (no subject) > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <5028657E.8070908(a)nmr.mgh.harvard.edu > <mailto:5028657E.8070908@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="iso-8859-1" > > The values are in the ?h.sulc file > doug > > On 8/12/12 10:12 PM, Hugh Pemberton wrote: > > Hi, > > > > How can I get sulcal depth measurements from Freesurfer? > > > > Cheers, > > Hugh > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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aparc2aseg
by Herting, Megan 14 Aug '12

14 Aug '12

Hello, I am new to FreeSurfer and had a quick question about the calculation of cortical volumes using the aparc2aseg. In the aseg images, "cortical volume" is sometimes assigned to extra dura at the superior midline of the brain. My understanding is that this dura will not impact my final gray matter cortical volumes output by aparc2aseg as the cortical ribbon masks are used by default to only calculate volume for voxels that fall with in these masks (lh.ribbon.mgz and rh.ribbon.mgz). Is this correct? (I.e. Should I be manually removing the aseg areas of dura labeled as "cortical" if they fall outside the pial surface/cortical ribbon, or will using aparc2aseg take care of this for me? I want to verify that assuming the latter is indeed correct!) Thanks for your help! Megan --------------------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of this original message. ---------------------------------------------------------------------

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Freesurfer August 2012