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30132 discussions

Re: [Freesurfer] aparc stats file; missing 'mean cortical thickness' value
by Douglas N Greve 07 Jan '13

07 Jan '13

I can see that the command line is not set up to create the mean cortical thickness, but I don't know why the arguments for the command are not being set up properly. Did you run mris_anatomical_stats yourself or did you just run recon-all again? If you ran recon-all, can you send me your recon-all script? doug On 01/07/2013 01:25 PM, Deirdre O Shea wrote: > Thanks Doug, > > I have attached two files. You will see in 'aparc.stats' that there is > no mean for cortical thickness and in the aparc.stats2 file there is. > > thanks > Deirdre > > On Mon, Jan 7, 2013 at 12:48 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Can you send the aparc.stats file in question? > doug > On 01/07/2013 11:44 AM, Deirdre O Shea wrote: > > Dear FreeSurfers, > > > > My query relates to the aparc stats file in FreeSurfer. Upon the > > editing and reconstruction of my subjects I have noticed that > the Mean > > Thickness for the cortex was missing, i.e., no value was provided > > despite it being there before I ran another reconstruction. > While this > > has only occurred in a couple of my subjects (out of many) I'm > > wondering what may be the cause and how I may I now go about getting > > this value? > > > > > > Best, > > Deirdre > > > > > > _______________________________________________ > > 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 <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> > 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. > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] 回复: 回复: about ROI to SPSS
by Douglas N Greve 07 Jan '13

07 Jan '13

what was your command line? On 01/05/2013 01:43 AM, xiangbo_2010 wrote: > Dear doug > Using the command to only obtain the size of volume from every > subject, however, I want to obtain the size of surface area from every > subject, what should I do? thanks! > Bo Xiang > > > > > > At 2013-01-05 13:12:18,"Douglas Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > > Drawing the ROI as a label is fine. Just don't transfer the label > to each individual subject. The y.mgh is all the data for all the > subjects in the fsaverage space (where the label is defined). You > can use mri_segstats, something like > > mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1 > > avg.dat will have one column and number of rows equal to the > number of subjects > > doug > > > On 1/4/13 11:20 PM, xiangbo_2010 wrote: >> Dear doug >> I am sorry to disturb you again, I still do not know how to >> direct obtain the label of two significant clusters, is not to >> draw the ROI? thanks! >> Bo Xiang >> >> >> >> >> >> At 2013-01-05 06:49:14,"Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> wrote: >> >yes y.mgh >> >On 01/04/2013 05:13 PM,xiangbo_2010(a)126.com wrote: >> >> Do you mean input the file of y.mgh to mri_glmfit and run? Thanks! >> >> Bo Xiang >> >> 发送自我的HTC One SUJ >> >> >> >> ----- Reply message ----- >> >> 发件人： "Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> >> >> 收件人：<xiangbo_2010(a)126.com> >> >> 抄送： "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> >> >> 主题： [Freesurfer] 回复: about ROI to SPSS >> >> 日期：周六, 1 月 5 日, 2013 年 05:48 >> >> >> >> >> >> >> >> >> >>> That technique can yield inconsistent results when the ROI is small (as >> >>> in your case). You are better off extracting the data directly from the >> >>> input to mri_glmfit. This is created by QDEC and is called y.mgh. This >> >>> will be a file with number of frames equal to the number of subjects. >> >>> >> >>> doug >> >>> >> >>> >> >>> >> >>> >> >>> On 01/04/2013 04:13 PM,xiangbo_2010(a)126.com wrote: >> >>>> I drawing two ROIs in two clusters, and mapping two labels to all subjects, following extract the average surface area of two ROIs from every subject. Anyway, whether have command to direct obtain the label of two clusters, not to drawing the ROIs from these clusters, then there have exactly data to be obtained. Thanks! >> >>>> Ho Xiang >> >>>> >> >>>> 发送自我的HTC One SU >> >>>> >> >>>> ----- Reply message ----- >> >>>> 发件人： "Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> >> >>>> 收件人：<freesurfer(a)nmr.mgh.harvard.edu> >> >>>> 主题： [Freesurfer] about ROI to SPSS >> >>>> 日期：周六, 1 月 5 日, 2013 年 02:42 >> >>>> >> >>>> >> >>>> >> >>>> >> >>>>> Hi Bo, you need to make sure that you have exactly the same design >> >>>>> matrix in SPSS. The design matrix for qdec is Xg.dat in the output >> >>>>> directory. How did you extract the data out of the ROIs? >> >>>>> >> >>>>> doug >> >>>>> >> >>>>> >> >>>>> >> >>>>> On 01/02/2013 11:46 PM, xiangbo_2010 wrote: >> >>>>>> Dear experts >> >>>>>> I has obtained two ROIs (corrected FDR) difference between AA and >> >>>>>> GG regressing out the effect of age and gender using the QDEC with >> >>>>>> attachment, following extract the average surface area of two ROIs to >> >>>>>> analysis using SPSS, in which I used the >> >>>>>> Univariate Analysis of Variance to find the difference between AA and >> >>>>>> GG, gender and age as covariates, but find that there no significant >> >>>>>> in these ROIs, I want to know why there were significant difference in >> >>>>>> QDEC, but no significant difference in SPSS? I hope that have experts >> >>>>>> to help me, thanks! >> >>>>>> Bo Xiang >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> _______________________________________________ >> >>>>>> 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 >> >>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >>>>> >> >>>>> _______________________________________________ >> >>>>> Freesurfer mailing list >> >>>>>Freesurfer(a)nmr.mgh.harvard.edu >> >>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>>> >> >>>>> >> >>>>> The information in this e-mail is intended only for the person to whom it is >> >>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >> >>>>> contains patient information, please contact the Partners Compliance HelpLine at >> >>>>>http://www.partners.org/complianceline . If the e-mail was sent to you in error >> >>>>> but does not contain patient information, please contact the sender and properly >> >>>>> dispose of the e-mail. >> >>>>> >> >>>> >> >>> -- >> >>> Douglas N. Greve, Ph.D. >> >>> MGH-NMR Center >> >>>greve(a)nmr.mgh.harvard.edu >> >>> Phone Number: 617-724-2358 >> >>> Fax: 617-726-7422 >> >>> >> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >>> FileDrop: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 >> >> >> >> >> > >> >-- >> >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 >> >Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> >> > > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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aparc stats file; missing 'mean cortical thickness' value
by Deirdre O Shea 07 Jan '13

07 Jan '13

Dear FreeSurfers, My query relates to the aparc stats file in FreeSurfer. Upon the editing and reconstruction of my subjects I have noticed that the Mean Thickness for the cortex was missing, i.e., no value was provided despite it being there before I ran another reconstruction. While this has only occurred in a couple of my subjects (out of many) I'm wondering what may be the cause and how I may I now go about getting this value? Best, Deirdre

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Checking cerebellar segmentations
by charles laidi 07 Jan '13

07 Jan '13

Dear freesurfers, I just finished cerebellar segmentation on almost 100 subjects. I have read the usual checking procedure that should be performed on freesurfer website. However I wasn't able to find if there is a specific checking workflow that can be performed when freesurfer is used for 100 / a lot of subjects. For example FSL provides a tool called slicesdir that allows to check segmentation faster. Is there such a feature with freesurfer ? What kind of checking would you recommend for cerebellar segmentation on 100 subjects ? Thank you very much and happy new year ! Charles

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Differences between avg33 and avg32 in dpath folders
by Alessia Sarica 06 Jan '13

06 Jan '13

Dear Freesurfer Experts, i'm here again, maybe for a trivial question, but I didn't find any information about my doubt. I'm doing tractography on 36 patients and I noticed that some of them have dpath folders named "_avg33_mni_flt" and in other patients, they are named "_avg32_mni_flt". Which is the reason for this? Something has gone wrong? Thanks a lot, Alessia. -- Alessia Sarica Ph.D. Student Biomedical and Informatics Engineering, Bioinformatics Laboratory, Department of Surgical and Medical Sciences, University "Magna Græcia" of Catanzaro, Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. Phone: +3909613694193

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Freesurfer 5.2 release date?
by Mehul Sampat 05 Jan '13

05 Jan '13

Hi Folks, I just wanted to inquire about the estimated release date for Freesurfer 5.2 ? Is there a beta version we could try out ? Thanks Mehul

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applying distortion correction output from epi_reg in fsl to freesurfer
by Ted Satterthwaite 04 Jan '13

04 Jan '13

Hi Bruce, Doug, and FreeSurfer Team, We have calculated coregistrations between bold timeseries and T1 images using BBR & distortion correction as implemented in the epi_reg utility in FSL5. We would like to map our functional timeseries to surface space for connectivity analyses (analagous to papers by Yeo & Buckner). Normally, without distortion correction, we would use tkregister tp convert the rigid body coregistration calculated in fsl by flirt(.mat) to a register.dat file, and then use mri_vol2surf to birng the data to surface space. However, with distortion correction, the coregistration between the epi & T1 is represented as a deformation field (_warp.nii.gz). Is there a way for FreeSurfer to read this warp and use the information? We could of course simply do a two-step registration by moving our epi data into T1 space first using FSL and then use FreeSurfer to get it to the surface, but that would involve an extra interpolation. Are the ways to do this in one step using our already-calculated & QA'd deformation fields from FSL? Thanks so much for your time & advice. Best, Ted Satterthwaite

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bbregister error: no regisster.dat file
by Shukla,Priyank 04 Jan '13

04 Jan '13

Hi, My bbregistration finished with the warnning" --------------------------------------------------------------------------------------------- WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 -------------------------------------------------------------------------------------------- and does not create subj_RS_register.dat file... I thought, it is only warning so it should create the files. Here is the command, I run to do bbregistration, where ${sub} is substituted by subject number: -------------------------------------- bbregister --s ${sub}_FS --mov $main_path/$sub/${sub}.RS.mgz --reg ${sub}_RS_register.dat --init-fsl --bold --frame $framenum --nearest --o ${sub}.RS.template.mgz ------------------------------------------------------------------------- Thanks Priyank

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FW: FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
by Jeff Eriksen 04 Jan '13

04 Jan '13

FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu>> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Can you cc the list so others can answer? Freeview can rotate.... On Jan 3, 2013, at 8:06 PM, Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu>> wrote: Bruce, This is what I get when I try to use tksurfer to open the scalp surface created with mkseghead: ********************************************************************************************* kje-macbook:mri jefferiksen$ tksurfer AIRC0001 lh seghead subject is AIRC0001 hemi is lh surface is seghead surfer: current subjects dir: /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri Reading image info (/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001) Reading /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/orig.mgz surfer: Reading header info from /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/orig.mgz ltMNIreadEx: could not open file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/transforms/talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=219128, faces=442484 MRISreadVertexPosition(/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig): could not open file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig No such file or directory surfer: single buffered window surfer: tkoInitWindow(AIRC0001) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... mrisReadTriangleFile(/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.white): surface doesn't match /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.seghead mrisReadTriangleFile failed. *********************************************************************************************** The surface displays, but when I click on a point it puts all 0.0s in the Vertex RAS fields. I presume this is because I have not specified a volume or transform. I am confused by the example given below which uses orig.mgz. I tried to substitute T1.mgz, but it still tries to use orig.mgz above. *********************************************************************************************** 1. I have a point on the surface and want to compute the CRS for voxel in the orig.mgz that corresponds to this point: VoxCRS = inv(Torig)*[tkrR tkrA tkrS 1]' where [tkrR tkrA tkrS] is the "Vertex RAS" as seen in the tksurfer Tools window (also output of mris_convert). Torig is the Vox2tkrRAS matrix obtained from "mri_info --vox2ras-tkr orig.mgz" (note: this is the same for all orig volumes). Test: click on a point in tksurfer. Use "Vertex RAS" to compute Vox2CRS. Round Vox2CRS to the nearest integer. Hit Save Point in tksurfer. In tkmedit, Goto Saved Point. Compare VoxCRS to "Volume Index". Note: you may need to use the "Volume RAS" from tkmedit in the computation above to get an exact match ************************************************************************************************ I tried mri_info --vox2ras-tkr T1.mgz and got a matrix, which I could use in Matlab to transform, but not without knowing the vertex RAS coordinates. Have I confused you enough? From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Date: Wednesday, January 2, 2013 7:08 PM To: Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu>> Cc: "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] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Hi Jeff The coordinate conversions are documented on our wiki. Or you could do the marking in tkmedit or freeview which will show you voxel and surface RAS coords. There might also be an option to view them in tksurfer too, I can't remember (view->information or something like that) Cheers Bruce On Jan 2, 2013, at 7:43 PM, Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu>> wrote: HI, I created a scalp surface mesh with mkheadsurf. I need to mark or select some scalp surface points and obtain their MRI coordinates. That is, if my MRI is 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The tksurfer display shows several types of floating point coordinates, but they assume an origin in the center of the head somewhere. If I knew the MRI coordinates of this origin I could calculate the original MRI. Thanks, -Jeff _______________________________________________ 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.

2 1

motion correction
by O'Shea,Andrew 04 Jan '13

04 Jan '13

Hello, Our data set has two T1 weighted scans for some subjects but only one for others. Would you recommend running all subjects with no motion correction (1 scan input)? Also can files be mixed in the analysis that have had motion correction with those who have not? Thanks! -Andrew

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