Freesurfer

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19 participants
30088 discussions

MNI305 to MNI152 coordinates
by Anita van Loenhoud 12 Nov '13

12 Nov '13

Dear FreeSurfers, I have a question regarding conversion from MNI152 coordinates to MNI305 coordinates. I want to take ROIs from a VBM study and use these exact same ROIs in my vertexwise analysis. So I need to translate the x, y, z coordinates from MNI152 space into MNI305 space. In previous posts, I found a matrix that converts from MNI305 coordinates to MNI152: M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 However, I want to do it the other way around. I tried to calculate the inverse matrix but haven't succeeded. Does anyone have (or know how to create) the matrix/formula I need? It would be very helpful, thanks in advance. Anita

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Re: [Freesurfer] bvecs and bvals don't have the same number of entries
by Anastasia Yendiki 12 Nov '13

12 Nov '13

Thanks. What do these files look like? /export/data/brain1/RSTOM/TLR108/dmri/bvecs /export/data/brain1/RSTOM/TLR108/dmri/bvals These are the ones that the error message in trac-all.log is about, so something probably goes wrong with the conversion from your original files. Also, I recommend very strongly that you use the latest version of tracula (from freesurfer 5.3). It's improved on both speed and performance. On Tue, 12 Nov 2013, Laura Christine Anderson wrote: > Hi Anastasia, I have version 5.1. Attached are bvecs and bvals files with > 3 and 1 columns respectively as well as the trac-all.log file. > > Thanks! > Laura > > Laura C. Anderson, B.A. > Graduate Student > Clinical & Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > > > > > On 11/11/13 9:00 PM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > >> >> Hi Laura - First of all, which version of freesurfer do you have? It >> looks >> to me like you've based your config file on the old example file that >> came >> with version 5.1. >> >> Second, could you please convert your bvecs and bvals files to 3 columns >> and 1 column, respectively, then run trac-all and send the trac-all.log >> file that shows the errors that you get? >> >> Thanks! >> a.y >> >> On Mon, 11 Nov 2013, Laura Christine Anderson wrote: >> >>> Hi Anastasia, I am still struggling with this same error message, >>> despite >>> having rearranged the bval and bvec files in many different >>> configurations >>> (and making sure that each value in these files had the same number of >>> digits, which I am not sure even matters). I am attaching my most recent >>> bval and bvec files as well as the config file to see if you have any >>> advice. >>> >>> Thanks so much for your help! >>> >>> Laura C. Anderson, B.A. >>> Graduate Student >>> Clinical & Developmental Psychology >>> University of Maryland >>> College Park, MD 20742 >>> BPS 0112 >>> >>> >>> >>> >>> On 10/15/13 11:17 AM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>>> >>>> Hi Laura - This means that there is only 1 line in each of the files, >>>> so >>>> the end-of-line characters aren't recognized. I'd make sure that the >>>> file >>>> is saved as plain text. >>>> >>>> a.y >>>> >>>> On Tue, 15 Oct 2013, Laura Christine Anderson wrote: >>>> >>>>> When I run "wc -l" on the bvec and bval files, I get "1" for both. >>>>> Running >>>>> just "wc" gives "1 279 3312" for bvec and "1 93 456" for bval >>>>> >>>>> Laura C. Anderson, B.A. >>>>> Graduate Student >>>>> Clinical & Developmental Psychology >>>>> University of Maryland >>>>> College Park, MD 20742 >>>>> BPS 0112 >>>>> >>>>> >>>>> >>>>> >>>>> On 10/14/13 5:18 PM, "Anastasia Yendiki" >>>>> <ayendiki(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>>> >>>>>> Hi Laura - I don't think the error "bvecs and bvals don't have the >>>>>> same >>>>>> number of entries" should have to do with interspersed zero b-values. >>>>>> When >>>>>> you run "wc -l" on the bvecs and bvals files, what do you get? >>>>>> >>>>>> a.y >>>>>> >>>>>> On Mon, 14 Oct 2013, Laura Christine Anderson wrote: >>>>>> >>>>>>> Hi Anastasia, the bval/bvec files were created on a Mac and not with >>>>>>> excel. I am not seeing the ^M character when I view the files in >>>>>>> unix >>>>>>> with >>>>>>> the more command or in gedit perhaps when I sent you the files, >>>>>>> something >>>>>>> became corrupted? I am wondering if my issue has something to do >>>>>>> with >>>>>>> the >>>>>>> fact that there are 3 sets of 30 rows with a b0 image before each of >>>>>>> the 3 >>>>>>> sets. In the examples I have seen, the b0 images all seem to be at >>>>>>> the >>>>>>> beginning of the bvec and bval files. I am attaching a screenshot of >>>>>>> the >>>>>>> bvec and bval files as I see them in case that is helpful. If you >>>>>>> would >>>>>>> rather me send the actual files again, what is the best way to do >>>>>>> that >>>>>>> without the formatting getting messed up? Before, I was using a free >>>>>>> fileshare program. >>>>>>> >>>>>>> Thank you! >>>>>>> Laura >>>>>>> >>>>>>> Laura C. Anderson, B.A. >>>>>>> Graduate Student >>>>>>> Clinical & Developmental Psychology >>>>>>> University of Maryland >>>>>>> College Park, MD 20742 >>>>>>> BPS 0112 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 10/11/13 2:38 PM, "Anastasia Yendiki" >>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>> wrote: >>>>>>> >>>>>>>> >>>>>>>> Hi Laura - Were these bval/bvec files created on windows or with >>>>>>>> excel >>>>>>>> by >>>>>>>> any chance? When you view them in unix (with the more command for >>>>>>>> example) >>>>>>>> you'll see an "^M" character instead of every end-of-line. Can you >>>>>>>> try >>>>>>>> editing these files in a unix editor to fix that? Let me know if >>>>>>>> this >>>>>>>> solves the problem. >>>>>>>> >>>>>>>> a.y >>>>>>>> >>>>>>>> On Fri, 11 Oct 2013, Laura Christine Anderson wrote: >>>>>>>> >>>>>>>>> Hi Anastasia, >>>>>>>>> Thanks so much for your help! Attached are bvec, bval and >>>>>>>>> trac-all.log >>>>>>>>> files. >>>>>>>>> >>>>>>>>> I have been stuck at one of the preprocessing steps (trac all) for >>>>>>>>> some >>>>>>>>> time and keep getting the >>>>>>>>> error: bvecs and bvals don't have the same number of entries. I >>>>>>>>> saw >>>>>>>>> a >>>>>>>>> couple blogs online about >>>>>>>>> this, but did not see any resolution. I am wondering if it is >>>>>>>>> because >>>>>>>>> the B0 images are >>>>>>>>> interspersed? (see attached bvec file). If you have any insight, I >>>>>>>>> would love some feedback >>>>>>>>> whenever you get the chance. >>>>>>>>> >>>>>>>>> Laura >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 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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qdec visualization problems
by Daniel Wakeman 12 Nov '13

12 Nov '13

Hi, I am having trouble running qdec over an NX session. I downloaded a FreeSurfer installation (5.3.0) to a network drive (/cluster/neuromind/dwakeman/software/freesurfer/). The installation has no trouble running recon-all; however, when I try to run qdec, I get vtk errors (see below): ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x27454520): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /autofs/cluster/neuromind/dwakeman/study/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects ead_01 ead_02 ead_03 ead_04 ead_11 ead_12 ead_13 ead_14 Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /autofs/cluster/neuromind/dwakeman/study/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects ead_01 ead_02 ead_03 ead_04 ead_11 ead_12 ead_13 ead_14 while executing "vtkTemp2 GenerateStatsDataTables" help(a)nmr.mgh.harvard.edu told me that I shouldn't need vglrun (as indicated on the wiki). Is there something I need to do to fix the installation, or do I need vglrun? Thank You, Dan Wakeman

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Getting substantially different Etiv for same patients for consecutive scans
by Salil Soman 11 Nov '13

11 Nov '13

Hi, My understanding of etiv is that it is derived from the registration of a brain to atlas space and not actually derived from the freesurfer segmentation. I have a set of patients imaged at 2 time points that all have different etiv values between the first and second scan that are statistically significant. As there was no change in their skulls between scans, I am having difficulty understanding how this is possible. Can anyone suggest what I may be doing wrong? Best wishes, Salil

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aparcstats2table for multiple labels
by Chung, Yoonho 11 Nov '13

11 Nov '13

Dear fs experts, I have created 5 customized labels that I want to extract mean thickness from each subject. Is there a way to generate a text file for all the labels I made? For example, aparcstats2table --parc option only allows to read one label at a time. I am wondering if there is a way for this function to take all 5 labels I created so that I will have all the measures in one text file. Right now I have to do them independently for each label and manually combine them together into one text file. Thanks! Yoon

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question about atrophy and FS-FAST
by Mario Ortega 11 Nov '13

11 Nov '13

Hello Freesurfer group, I have a general question about the Freesurfer pipeline when applied to fMRI BOLD scans. In general, with heavily atrophied or older individuals, would there be no necessary corrections to make for atrophy due to the non-linear surface inflation transformation that is applied to every individual subject? I ask, as I we have atrophied subjects in our dataset and want to make sure a BOLD signal is comparable between tissues and subjects. Thanks

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aparcstats2table question
by Jonathan Holt 11 Nov '13

11 Nov '13

Hi FS experts, I’m about to run aparcstats2table for a longitudinal study, and I’m wondering seeing as I’ve already written a longitudinal qdec table that includes subject IDs under the fsid column, is it necessary to pass -subjects subj1 subj2 subj3 … etc AND the qdec to aparcstats2table or should I just pass the qdec? I only ask as the tutorial says -subjects is required, but it seems redundant and I wanted to verify. jon

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Re: [Freesurfer] bvecs and bvals don't have the same number of entries
by Anastasia Yendiki 11 Nov '13

11 Nov '13

Hi Laura - First of all, which version of freesurfer do you have? It looks to me like you've based your config file on the old example file that came with version 5.1. Second, could you please convert your bvecs and bvals files to 3 columns and 1 column, respectively, then run trac-all and send the trac-all.log file that shows the errors that you get? Thanks! a.y On Mon, 11 Nov 2013, Laura Christine Anderson wrote: > Hi Anastasia, I am still struggling with this same error message, despite > having rearranged the bval and bvec files in many different configurations > (and making sure that each value in these files had the same number of > digits, which I am not sure even matters). I am attaching my most recent > bval and bvec files as well as the config file to see if you have any > advice. > > Thanks so much for your help! > > Laura C. Anderson, B.A. > Graduate Student > Clinical & Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > > > > > On 10/15/13 11:17 AM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > >> >> Hi Laura - This means that there is only 1 line in each of the files, so >> the end-of-line characters aren't recognized. I'd make sure that the file >> is saved as plain text. >> >> a.y >> >> On Tue, 15 Oct 2013, Laura Christine Anderson wrote: >> >>> When I run "wc -l" on the bvec and bval files, I get "1" for both. >>> Running >>> just "wc" gives "1 279 3312" for bvec and "1 93 456" for bval >>> >>> Laura C. Anderson, B.A. >>> Graduate Student >>> Clinical & Developmental Psychology >>> University of Maryland >>> College Park, MD 20742 >>> BPS 0112 >>> >>> >>> >>> >>> On 10/14/13 5:18 PM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>>> >>>> Hi Laura - I don't think the error "bvecs and bvals don't have the same >>>> number of entries" should have to do with interspersed zero b-values. >>>> When >>>> you run "wc -l" on the bvecs and bvals files, what do you get? >>>> >>>> a.y >>>> >>>> On Mon, 14 Oct 2013, Laura Christine Anderson wrote: >>>> >>>>> Hi Anastasia, the bval/bvec files were created on a Mac and not with >>>>> excel. I am not seeing the ^M character when I view the files in unix >>>>> with >>>>> the more command or in gedit perhaps when I sent you the files, >>>>> something >>>>> became corrupted? I am wondering if my issue has something to do with >>>>> the >>>>> fact that there are 3 sets of 30 rows with a b0 image before each of >>>>> the 3 >>>>> sets. In the examples I have seen, the b0 images all seem to be at the >>>>> beginning of the bvec and bval files. I am attaching a screenshot of >>>>> the >>>>> bvec and bval files as I see them in case that is helpful. If you >>>>> would >>>>> rather me send the actual files again, what is the best way to do that >>>>> without the formatting getting messed up? Before, I was using a free >>>>> fileshare program. >>>>> >>>>> Thank you! >>>>> Laura >>>>> >>>>> Laura C. Anderson, B.A. >>>>> Graduate Student >>>>> Clinical & Developmental Psychology >>>>> University of Maryland >>>>> College Park, MD 20742 >>>>> BPS 0112 >>>>> >>>>> >>>>> >>>>> >>>>> On 10/11/13 2:38 PM, "Anastasia Yendiki" >>>>> <ayendiki(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>>> >>>>>> Hi Laura - Were these bval/bvec files created on windows or with >>>>>> excel >>>>>> by >>>>>> any chance? When you view them in unix (with the more command for >>>>>> example) >>>>>> you'll see an "^M" character instead of every end-of-line. Can you >>>>>> try >>>>>> editing these files in a unix editor to fix that? Let me know if this >>>>>> solves the problem. >>>>>> >>>>>> a.y >>>>>> >>>>>> On Fri, 11 Oct 2013, Laura Christine Anderson wrote: >>>>>> >>>>>>> Hi Anastasia, >>>>>>> Thanks so much for your help! Attached are bvec, bval and >>>>>>> trac-all.log >>>>>>> files. >>>>>>> >>>>>>> I have been stuck at one of the preprocessing steps (trac all) for >>>>>>> some >>>>>>> time and keep getting the >>>>>>> error: bvecs and bvals don't have the same number of entries. I saw >>>>>>> a >>>>>>> couple blogs online about >>>>>>> this, but did not see any resolution. I am wondering if it is >>>>>>> because >>>>>>> the B0 images are >>>>>>> interspersed? (see attached bvec file). If you have any insight, I >>>>>>> would love some feedback >>>>>>> whenever you get the chance. >>>>>>> >>>>>>> Laura >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> 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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Files uploaded
by pietro de rossi 11 Nov '13

11 Nov '13

HI, I succesfully uploaded the files. Thanks in advance for your help! Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com<http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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recon all error
by Boric, Katica A. 11 Nov '13

11 Nov '13

Greetings Freesurfers! recon-all -s XXX_SurferOutput exited with ERRORS These are the errors in the log: Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 I would really appreciate any advice! Thank you very much, Katica

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