Freesurfer

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Re: [Freesurfer] command to check the regional cortical thicknesses and volumes
by Douglas N Greve 01 Oct '12

01 Oct '12

Hi Yawu, there is a file in the output called subject/stats/lh.aparc.stats (there is an rh.aparc.stats too as well as ?h.aparc.a2009s.stats files). doug ps. Please send emails to the FreeSurfer list instead of directly to me. Thanks! On 10/01/2012 03:36 AM, Liu Yawu wrote: > Hi Douglas, > After run "recon-all -cw256 -s AA -all", how to check the check the regional cortical thicknesses and volumes? > Regards, > Yawu > > -- 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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Re: [Freesurfer] CT Method Comparison
by Douglas N Greve 01 Oct '12

01 Oct '12

hi Gari, looking at this I don't really see a problem. Yes, the t-test is very significant, but I would expect that from a paired t looking across different methods. the size of the effect is very small, about 1.5%. Do you see this as a problem? doug On 09/28/2012 05:14 AM, Garikoitz Lerma-Usabiaga wrote: > Hi Doug, > I think that the differences are significant enough, but just in case > please find attached an excel file with the data and the t-test. > > Some of the ROI-s are small (Triangularis, Operculum, Orbitalis and > then all together in the IFG). I attached images for each of them for > reference. > > > If in any case you assume that there are going to be differences, > which method would you recommend and why? > > Thanks! > Gari > > PS after mri_preproc I didn't smooth the surface as in the qdec > example, ¿should I do that? > > > > > > > On Fri, Sep 28, 2012 at 4:24 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > OK, got it (finally). I would not expect the answers to be > identical, but I would expect them to be "close". How close are > they? If the ROI is very small, there might be appreciable > differences between the two. > > doug > > > > On 9/27/12 6:26 PM, Garikoitz Lerma-Usabiaga wrote: >> Hi, >> You are right, this was one of the methods. The second one is as >> follows (I copy the repeated steps): >> >>> For a given ROI, you have a nifti file (roi.nii) in 2mm space >>> defined on colin27. This ROI volume has a voxel value == 1 if it >>> is in the ROI or 0 if it is out. >>> >>> You have a registration between roi.nii and orig.mgz >>> >>> You run mri_vol2surf on roi.nii to get lh.roi.mgh >> >> I run mris_preproc for every subject to Colin27: mris_preproc >> --out /subject/surf/ROI_toColin27.mgh --target Colin27 --hemi lh >> --meas thickness --s subject >> >> mri_segstats --seg /Colin27/surf/lh.roi.mgh --in >> /subject/surf/ROI_to_Colin127.mgh --sum >> subject/stats/target_lh.ROI.stats >> >> >> Thanks for your help, >> Gari >> >> >> Note: >> You said: You run mri_cor2label (with --surf option) to convert >> lh.roi.mgh into lh.roi.label >> Just in case, this is how I run it: >> >> * mri_cor2label --i /subjects/Colin27/lh.ROI.mgh --surf Colin27 >> lh --id 1 --l /subjects/Colin27/lh.ROI.label >> * mri_label2label --srclabel >> /subjects/Colin27/lh.ROI.label --srcsubject Colin27 >> --trgsubject subject --trglabel lh.ROI_Colin27_to_bert >> --regmethod surface --hemi lh >> >> >> >> >> On 26/09/2012, at 23:56, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >>> Sorry, I'm still a little lost. Let me see if I have it right: >>> >>> For a given ROI, you have a nifti file (roi.nii) in 2mm space >>> defined on colin27. This ROI volume has a voxel value == 1 if it >>> is in the ROI or 0 if it is out. >>> >>> You have a registration between roi.nii and orig.mgz >>> >>> You run mri_vol2surf on roi.nii to get lh.roi.mgh >>> >>> You run mri_cor2label (with --surf option) to convert lh.roi.mgh >>> into lh.roi.label >>> >>> You run mri_label2label on lh.roi.label to map it into an >>> individual subject >>> >>> You run mris_anatomical_stats on the individual lh.roi.label file >>> >>> Does this describe one of your processing streams correctly? If >>> so, what is the other processing stream (given in this kind of >>> detail)? >>> >>> doug >>> >>> >>> >>> On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga wrote: >>>> I have both. In origin, the ROI-s are 2mm volume based .nii >>>> that I convert to FS .mgh with register.dat I obtained with >>>> bbregister. >>>> -- In the case of label2label method I create the surface >>>> version with mri_vol2surf (and the correspondence is perfect), >>>> and then use mri_label2label in order to get the CT averages. >>>> -- In the case of surf2surf, I use the volume based .mgh with >>>> mri_preproc (mri_surf2surf) >>>> >>>> thanks! >>>> Gari >>>> >>>> On Tue, Sep 25, 2012 at 5:57 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>>> >>>> So you have ROIs in Colin27 space and you want to map them into >>>> your CT space and compute average CT intensities over them? Are >>>> the ROIs volume-based or surface-based? >>>> doug >>>> >>>> >>>> On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote: >>>> >>>> Hi Doug, >>>> many thanks for your answer, I try to detail it more: >>>> >>>> 1.- bbregister is registering two Colin27 brains. First >>>> one is >>>> a 2mm found in spm/canonical/single_subject_T1.nii, and >>>> second >>>> one is the FS_spm_Canonical found in SurfRend >>>> distribution. It >>>> was in .COR format and I run recon-all to have a modern >>>> version of it. As they are almost the same brain the >>>> registration matrix is quite simple and the registration was >>>> perfect. This way I had exactly the same ROI-s for Colin27 in >>>> SPM and in FS (it did not work that well for fsaverage, >>>> that's >>>> why I took this approach). >>>> >>>> 2.- In any case, I have several ROI-s in Colin27 space in FS, >>>> and then when I try to obtain average CT values from my >>>> subjects I use these 2 different approaches: label2label and >>>> surf2surf. >>>> mri_anatomical_stats is run on the labels created by >>>> mri_label2label. >>>> >>>> >>>> If you think it will be of help I can send the detailed >>>> command line calls, >>>> thanks! >>>> Gari >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Sat, Sep 22, 2012 at 12:47 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 >>>> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >>>> >>>> Hi Gari, I'll need more information. I can't tell >>>> what you >>>> are doing. >>>> Eg, what is being registered with BBR? what is >>>> mris_anatomical_stats run >>>> on? Where does Colin27 come into it and why? >>>> doug >>>> >>>> On 09/19/2012 06:15 PM, Garikoitz Lerma-Usabiaga >>>> (Gari) wrote: >>>>> Dear Freesurfers, >>>>> We've been comparing 2 different methods to obtain CT averages >>>> for 4 Volume ROI-s (volume ROI-s were in Colin27 space). >>>>> We've used the 40 buckner subjects for the comparisons. >>>>> >>>>> METHOD L2L: bbregister>> mri_vol2surf (mgh)>> >>>> mri_binarize (mgh)>> mri_cor2label (label)>> >>>> mri_label2label>> >>>> mris_anatomical_stats >>>>> METHOD S2S: bbregister>> mri_vol2surf>> mri_preproc >>>> (mri_surf2surf)>> mri_segstats >>>>> >>>>> >>>>> After performing t-test-s over the results, we can observe that >>>> the results are in many cases different. >>>>> >>>>> -- Is there a way to choose the "best" method? Which one should >>>> we use for our work and why? >>>>> >>>>> Many thanks again for your help, >>>>> Gari >>>>> >>>>> PD We've tabulated a third method as well: >>>>> METHOD SurfRend: Surfrend (.w)>> mri_surf2surf(.mgh)>> >>>> mri_binarize(.mgh)>> mri_cor2label (.label)>> >>>> mris_anatomical_stats >>>>> _______________________________________________ >>>>> 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 >>>> <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 >>>> <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> >>>> <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> >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> >>>> _______________________________________________ >>>> 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 >>>> <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 <mailto:greve@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> >>>> <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> >>>> >>>> >>> >>> -- >>> 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: 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

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long_mris_slopes command: temporal average calculation
by Shannon Kogachi 01 Oct '12

01 Oct '12

Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K.

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cluster to annotations
by jm 01 Oct '12

01 Oct '12

Dear FS: We compared two groups using cluster-wise Montecarlo simulation. Clusters obtained are extended for more than one region of aparc.2009 atlas. How to identify automatically those regions in each cluster?May I get a file with list of aparc.2009 regions and corresponding clusters? best regards

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amira
by Colin Reveley 29 Sep '12

29 Sep '12

It's slightly off topic, but begging your leave: If there is anyone out there who is experienced in amira, and might be willing to offer a little email help for a very tricky segmentation, I'd be very grateful. The segmentation is for use with freesurfer, at least, so it's not a total outrage to ask I hope. best, Colin Reveley, Sussex

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Cerebellar volume correction
by Rachel Steinhorn 29 Sep '12

29 Sep '12

We'd like to obtain total cerebellar volumes. There are errors within the cerebellar segmentation as revealed in the aseg.mgz file. Is there a method to manually edit the cerebellar segmentation? Thank You, Rachel Steinhorn

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Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries
by Anastasia Yendiki 28 Sep '12

28 Sep '12

There are 10 empty lines at the end of your Tbvecs.txt file. Can you try removing those and reruning? Hope this helps, a.y On Fri, 28 Sep 2012, Loi wrote: > Hello again, > > Here is the configuration file and some variations of the bvec and > bval files I have tried using. > > Also, I have noticed that the first time I run trac-all (without > specifying the bvecs and bvals), the bval file generated seems to list > the values twice. ie: > > 0 > 0 > 7 > 7 > 7 > 7 > 0 > 0 > 7 > 7 > 7 > 7 > > I hope this make sense. Thank you, > > Joy-Loi > > > On 9/27/12, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >> Thanks, no problem. I'd like to see the actual files on one of our >> machines just to make sure. >> >> On Thu, 27 Sep 2012, Loi wrote: >> >>> Hello Anastasia, >>> >>> I am in Norway and home from work for the evening, but will send you >>> the files first thing tomorrow morning. >>> Meanwhile, here is a copy of the contents in the files (as included in >>> my original e-mail). >>> Thank you for your help! >>> >>> ********************* >>> My configuration file: >>> >>> >>> setenv SUBJECTS_DIR >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons >>> >>> set dtroot = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >>> >>> set subjlist = id101 >>> set runlist = 1 >>> >>> set dcmroot = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >>> set dcmlist = id101/orig/1.dcm >>> >>> set bvalfile = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt >>> >>> set bvecfile = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt >>> >>> set nb0 = 10 >>> >>> set doeddy = 1 >>> set dorotbvecs = 1 >>> set thrbet = 0.3 >>> set doregflt = 1 >>> set doregbbr = 0 >>> set doregmni = 1 >>> set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz >>> >>> #set trainfile = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt >>> >>> set pathlist = (lh.cst_AS rh.cst_AS \ >>> lh.ilf_AS rh.ilf_AS \ >>> lh.unc_AS rh.unc_AS \ >>> fmajor_PP fminor_PP \ >>> lh.atr_PP rh.atr_PP \ >>> lh.cab_PP rh.cab_PP \ >>> lh.ccg_PP rh.ccg_PP \ >>> lh.slfp_PP rh.slfp_PP \ >>> lh.slft_PP rh.slft_PP) >>> >>> >>> set ncpts = 5 >>> >>> set usetrunc = 1 >>> >>> >>> >>> >>> >>> ********************* >>> My bvals: >>> >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> >>> ********************* >>> My bvecs: >>> >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> -0.9998760 0.0011040 0.0157340 >>> -0.7705615 0.6320276 0.0823114 >>> -0.2461791 0.0273479 0.9688392 >>> -0.7953558 0.1076421 0.5965091 >>> 0.4620816 -0.8755928 0.1407778 >>> 0.2261090 -0.8553081 -0.4661796 >>> 0.2601186 0.4095102 -0.8744363 >>> -0.7969547 -0.5877791 0.1392076 >>> -0.5028073 -0.5104712 0.6975709 >>> -0.3073035 0.1334521 -0.9422074 >>> 0.7957742 0.1950272 -0.5733304 >>> 0.8041493 0.5924478 -0.0484727 >>> -0.1867079 -0.9528833 0.2390659 >>> 0.3898569 -0.1063898 0.9147088 >>> 0.1341999 -0.6614532 0.7378819 >>> 0.3382555 0.8823941 0.3270553 >>> -0.7688307 -0.3139264 -0.5570900 >>> -0.4086013 0.6653325 0.6248017 >>> -0.2933309 0.7581020 -0.5824408 >>> 0.7689370 -0.4282441 0.4747016 >>> 0.1800972 0.5296402 0.8288835 >>> 0.7680658 0.3158178 0.5570763 >>> -0.2214999 0.9744585 0.0370050 >>> -0.4175692 -0.8418782 -0.3418731 >>> -0.1784475 -0.4817282 -0.8579599 >>> 0.3361637 0.8554551 -0.3939400 >>> 0.7858656 -0.5091907 -0.3509137 >>> 0.4194232 -0.2589429 -0.8700761 >>> -0.7760561 0.3511497 -0.5238622 >>> 0.9987836 -0.0413076 0.0269219 >>> >>> >>> >>> >>> >>> >>> On Thu, Sep 27, 2012 at 8:14 PM, Anastasia Yendiki >>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> Can you please send the original bvals and bvecs files (the ones that >>>> you >>>> specify in the configuration file), and the configuration file itself? >>>> Thanks! >>>> >>>> a.y >>>> >>>> >>>> On Thu, 27 Sep 2012, Loi wrote: >>>> >>>>> Hello, >>>>> >>>>> I generate the files in Linux (using gedit) and they look normal (I >>>>> have compared them to the files in the tutorial). >>>>> >>>>> So far I have tried ending both with and without .txt, transposing the >>>>> files, changing to equal number of decimals and adding 'setenv LC_ALL >>>>> en_US' to the .tchsrc file. >>>>> >>>>> The inputs I am using are dicoms, and even though I specify a path to >>>>> the b-value files and gradient tables I make (I originally didn't >>>>> specify these, and got the same error message), new bvecs and bvals >>>>> are generated in the trac-all -prep process, leading to the error. >>>>> >>>>> Thank you, >>>>> Joy-Loi >>>>> >>>>> >>>>> >>>>> >>>>> On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki >>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> >>>>>> Hi Joy - How were your bvecs and bvals files generated? In the past >>>>>> some >>>>>> people have had problems with files exported from Excel b/c it >>>>>> generates >>>>>> text files with Windows-specific end-of-line characters that cannot be >>>>>> read >>>>>> properly on Linux. Do the files look normal when you run "more" on >>>>>> them >>>>>> on >>>>>> the system where you ran trac-all? >>>>>> >>>>>> a.y >>>>>> >>>>>> >>>>>> On Wed, 26 Sep 2012, Loi wrote: >>>>>> >>>>>>> Dear FreeSurfers, >>>>>>> >>>>>>> I am trying to run trac-all -prep on a single subject, and get the >>>>>>> following error: >>>>>>> >>>>>>> dtifit -k >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz >>>>>>> -m >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz >>>>>>> -r >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs >>>>>>> -b >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals >>>>>>> -o >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit >>>>>>> Error: bvecs and bvals don't have the same number of entries >>>>>>> >>>>>>> I have searched the message thread, and cannot seem to find a >>>>>>> solution >>>>>>> applicable to my situation: it seems that the trac-all process >>>>>>> generates transposed bvec and bval files. >>>>>>> Therefore, I tried transposing these manually and specifying the >>>>>>> location to these files (as explained in the tutorial: >>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) but >>>>>>> attempting to run trac-all again still leads to the same result: new >>>>>>> bval and bvec files are generated, and I receive the same error >>>>>>> message. >>>>>>> >>>>>>> Does anyone know how I can solve this problem? >>>>>>> >>>>>>> Thank you, >>>>>>> Joy-Loi >>>>>>> >>>>>>> >>>>>>> ********************* >>>>>>> My configuration file: >>>>>>> >>>>>>> >>>>>>> setenv SUBJECTS_DIR >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons >>>>>>> >>>>>>> set dtroot = >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >>>>>>> >>>>>>> set subjlist = id101 >>>>>>> set runlist = 1 >>>>>>> >>>>>>> set dcmroot = >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >>>>>>> set dcmlist = id101/orig/1.dcm >>>>>>> >>>>>>> set bvalfile = >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt >>>>>>> >>>>>>> set bvecfile = >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt >>>>>>> >>>>>>> set nb0 = 10 >>>>>>> >>>>>>> set doeddy = 1 >>>>>>> set dorotbvecs = 1 >>>>>>> set thrbet = 0.3 >>>>>>> set doregflt = 1 >>>>>>> set doregbbr = 0 >>>>>>> set doregmni = 1 >>>>>>> set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz >>>>>>> >>>>>>> #set trainfile = >>>>>>> >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt >>>>>>> >>>>>>> set pathlist = (lh.cst_AS rh.cst_AS \ >>>>>>> lh.ilf_AS rh.ilf_AS \ >>>>>>> lh.unc_AS rh.unc_AS \ >>>>>>> fmajor_PP fminor_PP \ >>>>>>> lh.atr_PP rh.atr_PP \ >>>>>>> lh.cab_PP rh.cab_PP \ >>>>>>> lh.ccg_PP rh.ccg_PP \ >>>>>>> lh.slfp_PP rh.slfp_PP \ >>>>>>> lh.slft_PP rh.slft_PP) >>>>>>> >>>>>>> >>>>>>> set ncpts = 5 >>>>>>> >>>>>>> set usetrunc = 1 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ********************* >>>>>>> My bvals: >>>>>>> >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> >>>>>>> ********************* >>>>>>> My bvecs: >>>>>>> >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> -0.9998760 0.0011040 0.0157340 >>>>>>> -0.7705615 0.6320276 0.0823114 >>>>>>> -0.2461791 0.0273479 0.9688392 >>>>>>> -0.7953558 0.1076421 0.5965091 >>>>>>> 0.4620816 -0.8755928 0.1407778 >>>>>>> 0.2261090 -0.8553081 -0.4661796 >>>>>>> 0.2601186 0.4095102 -0.8744363 >>>>>>> -0.7969547 -0.5877791 0.1392076 >>>>>>> -0.5028073 -0.5104712 0.6975709 >>>>>>> -0.3073035 0.1334521 -0.9422074 >>>>>>> 0.7957742 0.1950272 -0.5733304 >>>>>>> 0.8041493 0.5924478 -0.0484727 >>>>>>> -0.1867079 -0.9528833 0.2390659 >>>>>>> 0.3898569 -0.1063898 0.9147088 >>>>>>> 0.1341999 -0.6614532 0.7378819 >>>>>>> 0.3382555 0.8823941 0.3270553 >>>>>>> -0.7688307 -0.3139264 -0.5570900 >>>>>>> -0.4086013 0.6653325 0.6248017 >>>>>>> -0.2933309 0.7581020 -0.5824408 >>>>>>> 0.7689370 -0.4282441 0.4747016 >>>>>>> 0.1800972 0.5296402 0.8288835 >>>>>>> 0.7680658 0.3158178 0.5570763 >>>>>>> -0.2214999 0.9744585 0.0370050 >>>>>>> -0.4175692 -0.8418782 -0.3418731 >>>>>>> -0.1784475 -0.4817282 -0.8579599 >>>>>>> 0.3361637 0.8554551 -0.3939400 >>>>>>> 0.7858656 -0.5091907 -0.3509137 >>>>>>> 0.4194232 -0.2589429 -0.8700761 >>>>>>> -0.7760561 0.3511497 -0.5238622 >>>>>>> 0.9987836 -0.0413076 0.0269219 >>>>>>> _______________________________________________ >>>>>>> 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. >>>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >>> >> >

2 2

Convert QDEC Talaraich coordinates to MNI152
by Vy Dinh 28 Sep '12

28 Sep '12

Dear Freesurfer Experts, I would like to create ROIs for the MNI152 template using coordinates obtained from our QDEC Monte Carlo Simulations results. However, the QDEC results only list the Talairach Coordinates. Is there a program that I can use to convert these tal coordinates to MNI152? Thanks, Vy

2 1

Re: [Freesurfer] TRACULA Question
by Anastasia Yendiki 28 Sep '12

28 Sep '12

Hi Gabor - The info that tracula uses is which aparc+aseg labels each pathway neighbors at each point along its trajectory. It learns this information from the 33 subjects in the atlas, where the pathways were labeled manually, and then applies that knowledge to reconstruct the pathways in your subject. As long as the aparc+aseg of your subject is consistent with the ones in the atlas, you're fine. But if you think that the version you used to generate your aparc+aseg, and the latest version, that the aparc+aseg's in the atlas were generated with, have significant differences, this *may* be a problem. The extent of the problem will depend on how often the problematic label occurs next to one of the 18 pathways that tracula reconstructs and how different the label is b/w the versions. A small diference will probably not affect tracula at all. Your aparc+aseg's were generated with freesurfer 4.5, and there was no tracula atlas generated with that version of aparc+aseg's. Hope this helps, a.y On Fri, 28 Sep 2012, Gabor Perlaki wrote: > Dear Anastasia, > > Thanks a lot your answer. My fear is that the pars triangular > segmentation also seems bad, because it is right lateralized in most > of our analyzed data. Here is the post about this issue: > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024541.html > > Is it also OK with Tracula? > > Thank you in advance, > Gabor > > 2012/9/27 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Gabor - Tracula doesn't use the BA labels, only the labels in the >> aparc+aseg. I hope this answers your question. >> >> a.y >> >> >> On Sun, 16 Sep 2012, Gabor Perlaki wrote: >> >>> Dear Anastasia, >>> >>> Earlier I was posted an issue about BA44/pars triangular: >>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html >>> >>> Because TRACULA also uses the cortical parcellation it may be >>> important to handle this issue somehow. Is it handled in TRACULA >>> analysis? Does it affect the result of WM-volumes? >>> >>> Thank you for your answer, >>> Gabor >>> _______________________________________________ >>> 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. >> > > >

1 0

Re: [Freesurfer] Fmri_glmfit-sim with pre-cached fails
by Ed Gronenschild 28 Sep '12

28 Sep '12

Hi Doug, For mri_glmfit I used a cortical thickness smoothed with a FWHM of 20, resulting from using the -qcache option in recon-all. Ed On 27 Sep 2012, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 16 > Date: Thu, 27 Sep 2012 11:29:06 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <506470C2.5060906(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking > that no one would ever go above it, or maybe should never go above > it. I > can create tables at higher smoothing levels, but 34mm is a lot of > smoothing. How much did you apply to the data? > doug > > On 09/27/2012 05:48 AM, Ed Gronenschild wrote: >> Hi, >> >> I want to apply a cluster correction with mri_glmfit-sim with >> the --cache option: >> >> mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs >> >> It fails with the error message that it can't find the file: >> >> FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc- >> z.csd >> >> (FSDir is the directory where FreeSurfer is located, >> version 5.0.0, Mac OSX10.5) >> >> Looking at the content of the ....fsaverage/lh/cortex directory >> than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 >> are present. >> >> In the log file from mri_glmfit I can read that the residualFWHM >> is 34.005014. Since this FWHM is automatically derived by >> mri_glmfit, does it mean that I can never use the --cache option >> in this case? >> >> Cheers, >> Ed

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