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Re: [Freesurfer] groupwise surface resampling and registration
by Douglas N Greve 11 Jun '12

11 Jun '12

yes On 06/11/2012 11:09 AM, Sourena Soheilinezhad wrote: > Thanks Douglas > Do I have the correct impression that this command will also perform > the registration process from subject to fsaverage (based on scalar > maps) before resampling the number of vertices? > > On 6/11/12, Douglas N Greve<greve(a)nmr.mgh.harvard.edu> wrote: >> You can do this with mri_surf2surf, something like >> >> mri_surf2surf --srcsubject yoursubject --trgsubject fsaverage --hemi lh >> --sval-xyz white --tval lh.yoursubject.white-in-fsaverage --tval-xyz >> >> The output lh.yoursubject.white-in-fsaverage will have the xyz from the >> native space but the number of vertices will be that of fsaverage. >> >> doug >> >> >> >> On 06/11/2012 09:25 AM, Sourena Soheilinezhad wrote: >>> Greetings, >>> >>> Considering mris_preproc pipeline, I guess that the concatenated >>> output doesn't provide each subject's resamapled and registered >>> "topological" surface in his native space, rather, it encapsulates the >>> interpolated .curv (scalar) data only in a common template space. >>> But, what is the best approach to have subject-wise topological >>> surfaces which all share the same number of vertices and are >>> anatomically registered (i.e. vertex #s are in correspondence), but >>> each surface is still in its native subject space? >>> >>> Thanks in advance, >>> Sourena Soheili >>> >>> >>> >>> _______________________________________________ >>> 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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Creating ROI and only looking at this ROI in analysis
by Kairys, Anson 11 Jun '12

11 Jun '12

Hi everyone, I am attempting to create and ROI and look at cortical thickness only within this region (ignoring results outside this region in hopes of saving some time going through and re-assiging voxels with poor segmentation). Question: How should I create the ROI (typically I would use MARSBAR, but I don't think I quite understand the space relationship between MNI-normal and "FS" space, so what would be the easiest way to make compatiable ROIs and apply them to my group data if I am starting with un-processed T1. Images (recon-all everyone, then quality check only the ROI?) Thanks a lot! Anson ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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groupwise surface resampling and registration
by Sourena Soheilinezhad 11 Jun '12

11 Jun '12

Greetings, Considering mris_preproc pipeline, I guess that the concatenated output doesn't provide each subject's resamapled and registered "topological" surface in his native space, rather, it encapsulates the interpolated .curv (scalar) data only in a common template space. But, what is the best approach to have subject-wise topological surfaces which all share the same number of vertices and are anatomically registered (i.e. vertex #s are in correspondence), but each surface is still in its native subject space? Thanks in advance, Sourena Soheili

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Another silly question
by Shay Ohayon 10 Jun '12

10 Jun '12

Hi All, Another silly question. When one is rendering a flat map or an inflated surface, there are usually two colors (dark gray/light gray) that indicate whether regions originate from sulci or gyri. How are those usually obtained / derived? In other words, how do I determine the color of a surface vertex (i.e., whether it is a gyrus or a sulcus)? Are these derived from some thresholded curvature values? Thanks, -- Shay Tsao Lab Caltech

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Re: [Freesurfer] mri_glmfit allocate memory error
by Douglas Greve 10 Jun '12

10 Jun '12

What is your command-line and what is the terminal output? Also, please post to the list instead of to me directly. thanks doug On 6/6/12 5:24 AM, lordowen wrote: > Dear Prof. Greve: > > Sorry to reply this very old post, but we encountered the same > problem. We processed our data following the instructions in > PairedAnaylsis page on Wiki. Everything is fine but we can't perform > mri_glmfit using command-line. So we need your advise to seek possible > solutions for this problem. > > We are using FS 5.1 under Mac OS 10.7.4. We have 12GB memory and about > 500GB HD space. > > Thanks you for your kindly help. > > 2011/3/16 Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >> So you re-ran mris_preproc and you still get the error? If so, try running >> >> mris_preproc --debug <Your Options> |& tee mris_preprog.err.log >> >> Send me the mris_preprog.err.log, but don't email it as it will likely >> be huge. Instead drop it to me a the file drop listed at the end of this >> email. >> >> doug >> >> >> Andrew Mendlowitz wrote: >>> The mri_prepoc runs fine still but the glmfit still says can not >>> allocate memory, there is 8gb of ram and very little disk space is >>> used up, there is 876.1 gb still free. >>> >>> On Fri, Mar 11, 2011 at 12:49 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>> >>> If you re-run mris_preproc does the same thing happen? Are you >>> running out of disk space? >>> doug >>> >>> Andrew Mendlowitz wrote: >>> >>> The code for the lh.paired-diff.thickness.mgh file is >>> mris_preproc --target fsaverage --hemi lh \ >>> >>> --meas thickness --out lh.paired-diff.thickness.mgh \ >>> >>> --fsgd pairss.fsgd --paired-diff >>> >>> >>> On Thu, Mar 10, 2011 at 10:13 AM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >>> >>> There appears to be something wrong with the >>> lh.paired-diff.thickness.mgh file. How was it created? >>> doug >>> >>> Andrew Mendlowitz wrote: >>> >>> Hello All, >>> I get the following error while trying to run >>> mri_glmfit. I am >>> running a 2.93 ghz imac with 8gb of ram. I am also running >>> freesurfer version 5.0.0 on Snow >>> Leopard OS version 10.6. >>> >>> >>> /Applications/freesurfer/subjects/qdec$ mri_glmfit >>> --glmdir >>> lh.paired-diff --fsgd paired-diff.fsgd --C mean.mtx --y >>> lh.paired-diff.thickness.mghgdfReadHeader: reading >>> paired-diff.fsgd >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT >>> be done. >>> Continuous Variable Means (all subjects) >>> 0 Age 1.5 >>> Class Means of each Continuous Variable >>> 1 Main 1.5000 >>> INFO: gd2mtx_method is dods >>> >>> $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve >>> Exp $ >>> cwd /Applications/freesurfer/subjects/qdec >>> cmdline mri_glmfit --glmdir lh.paired-diff --fsgd >>> paired-diff.fsgd --C mean.mtx >>> --y lh.paired-diff.thickness.mgh >>> sysname Darwin >>> hostname larry >>> machine i386 >>> user amend >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y >>> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh >>> logyflag 0 >>> usedti 0 >>> FSGD paired-diff.fsgd >>> glmdir lh.paired-diff >>> IllCondOK 0 >>> DoFFx 0 >>> Creating output directory lh.paired-diff >>> Loading y from >>> >>> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh >>> mri_glmfit(79576) malloc: *** mmap(size=2563764224) failed >>> (error code=12) >>> *** error: can't allocate region >>> *** set a breakpoint in malloc_error_break to debug >>> MRIallocIndices: could not allocate 1714511945 elt >>> index array >>> Cannot allocate memory >>> >>> The mri_info for the file is : >>> >>> >>> mghRead(/Applications/freesurfer/subjects/qdec/fsgd_input.mgh, >>> -1): could not >>> open file >>> amend@larry /Applications/freesurfer/subjects/qdec$ >>> mri_info >>> >>> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh >>> Volume information for >>> >>> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh >>> type: MGH >>> dimensions: 1714510945 x 1853057372 x 1634628457 x >>> 1668310833 >>> voxel sizes: 72950800688805540228332034981888.0000, >>> 0.0000, >>> 70387746064971392794503413760.0000 >>> type: UNKNOWN (842347100) >>> fov: inf >>> dof: 1668244335 >>> xstart: -inf, xend: inf >>> ystart: -39.8, yend: 39.8 >>> zstart: >>> -57528904905339976080461439864148066304.0, zend: >>> 57528904905339976080461439864148066304.0 >>> TR: 71446969504754118412748034408448.00 >>> msec, TE: >>> 17862977898376175754203558313984.00 msec, TI: >>> 4464583905807213894543171649536.00 msec, flip angle: >>> 4128358109894647822155776.00 degrees >>> nframes: 1668310833 >>> PhEncDir: UNKNOWN >>> ras xform present >>> xform info: x_r = >>> 19441367164500690594879212879872.0000, y_r = >>> 282670772483715414097920.0000, z_r = >>> 4630517930517356511053742080.0000, c_r = >>> 18179207505345150839094025125888.0000 >>> : x_a = >>> 72953300747400503281465327353856.0000, y_a = >>> 71756401321839400437789128392704.0000, z_a = >>> 4721224652433019196440490016768.0000, c_a = 0.0000 >>> : x_s = 0.0000, y_s = >>> 208210237828607676252160.0000, z_s = >>> 4286666299869639999488.0000, c_s = >>> 4622889417339745644740714954752.0000 >>> >>> talairach xfm : >>> Orientation : AAA >>> Primary Slice Direction: coronal >>> >>> voxel to ras transform: >>> inf 12133604733747200.0000 inf >>> -inf >>> inf 3080133850722982464323584.0000 >>> inf >>> -inf >>> 36752183205510726549504.0000 >>> 8937395835633664.0000 inf -inf >>> 0.0000 0.0000 0.0000 1.0000 >>> >>> voxel-to-ras determinant nan >>> >>> ras to voxel transform: >>> mat = NULL! >>> Invalid argument >>> MatrixFree: NULL mat POINTER! >>> >>> Invalid argument >>> >>> -Andrew >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@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> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 >>> <tel:617-726-7422> >>> <tel:617-726-7422 <tel:617-726-7422>> >>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >>> FileDrop: >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >>> >>> >>> 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 <mailto:greve@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 >>> <tel:617-726-7422> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >> -- >> 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 > >

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How to report aseg.state values
by Efrat Kliper 10 Jun '12

10 Jun '12

Dear FreeSurfer expert, If I want to report on hippocampal volume in an article, should I report the value as stated in the aseg.state table or should I normalize the value to the eTICV ( i.e aseg value/eTICV )? Thanks in advance Efrat

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averaging sessions with different TRs
by SHAHIN NASR 09 Jun '12

09 Jun '12

Hi, I was wondering if I can average two scan sessions with different TRs or not. Number of conditions and all other factors are exactly the same between the two sessions. regards

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Re: [Freesurfer] Creating a label from an .mgh file
by Ilia 08 Jun '12

08 Jun '12

Thanks for the reply. Couple of follow up questions. (1) Which "ID" should be used when creating the mask? The "mc-z.abs.th23.sig.cluster.mgh" file contains clusters labeled based on z values (i.e., non-integers such as -3.698970, +2.130768, etc). Is it possible to divide the *.mgh file by itself to produce a file with 1's where clusters exist? That approach would work in FSL, but I am not quite sure what tools exist in FS or how to use them. (2) How would one visualize the resulting label file in tksurfer? Using "File-->Label-->Load Label" results in yellow specks showing up on the brain surface, but the spatial locations aren't correct (they don't correspond to where clusters exist on the original volume). Any help would be appreciated. > Message: 13 > Date: Wed, 06 Jun 2012 18:04:56 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Creating a label from an .mgh file > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <4FCFD408.6050402(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > you can use mri_cor2label, eg, for cluster #2, something like > > mri_cor2label --id 2 --i cluster.mgh --o cluster2.label > > doug > > On 6/6/12 4:22 PM, Ilia wrote: > >> Hello, >> >> How would one create a label (to be used as an input for >> "mris_anatomical_stats") based on a a statistical map generated by qdec >> (for example, the result of a Monte Carlo simulation such as >> "mc-z.abs.th23.sig.cluster.mgh"). >> >> The goal is to obtain average cortical thickness for regions where qdec >> detected significance. >> >> Thank you!! >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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Using an ROI and not correcting/"fixing" the rest of the image
by Kairys, Anson 08 Jun '12

08 Jun '12

Hi, I am planning on looking at a specific region of interest, and I am wondering it is possible to only "quality check" this region and leave the rest of the brain as is. Meaning, can I save the time of going through every slice and re-assigning voxels for the entire brain and just focus on making sure the estimation of WM etc. is correct in my ROI? Thanks a lot for any help you can provide. Best wishes Anson ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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/path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
by Xiangzhen Kong 08 Jun '12

08 Jun '12

Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv -f /xxx/dmri/dwi_orig_flip.mghdti.bvecs /xxxx/dmri/bvecs mv: cannot stat `/xxx/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz' and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM data? My data is from a siemens scanner. Thanks! Xiangzhen 2012-02-03 Xiangzhen Kong

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