Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

/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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label shape with mris_divide_parcellation
by Linda Douw 21 May '12

21 May '12

Hi all, I would like to make a fine-grained surface parcellation from aparc - let's say 500 labels, and I would like the labels to be more or less isometric. When subdividing the parcellation with mris_divide_parcellation, the labels become very stretched instead of isometric. Is there a way to get a different result? Thanks! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

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Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> 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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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trac-all -path error
by Chris Watson 07 May '12

07 May '12

Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error: Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 Word too long. ------------------------------------------------------------------------ Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 and FSL 4.1.9. Here's what's in the dmri.bedpostX directory: [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms

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Vertex wise analysis and area/pial area/volume interpretation
by Mahinda Yogarajah 03 May '12

03 May '12

Dear Experts, I had 2 questions with regard to vertex wise analysis using qdec. 1) How should one interpret the dependent variables area/pial area and volume when comparing 2 groups with qdec and a vertex wise (as opposed to ROI based) analysis - or are they uninterpretable in this context ? I read briefly about areal as an alternative measure - could someone explain the difference, and how thickness, volume and area related to one another ? 2) When running monte-carlo cluster wise multiple correction in qdec - if one finds a significant cluster is it ok to view them within qdec by highlighting the "mc-z ... " file in the analysis result box, and then changing the minimum threshold to whatever value one selected for the monte carlo simulation ? The reason I ask is that the text ouput given by the monte carlo cluster analysis gives different coorinates in the cluster table to that output given when one clicks on the "find clusters and go to max" button ... Thanks. Mahinda

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Comparing Cortical Thickness
by Jeff Sadino 03 May '12

03 May '12

Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline? I ran make_average_subject on each group. To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino

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OBJ conversion
by Darshan P 03 May '12

03 May '12

Hello all, I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this . Regards Darshan

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Re: [Freesurfer] bbregister for fmri FEAT data
by Erlend Hodneland 30 Apr '12

30 Apr '12

Hi again Yes, test.nii is the functional data registered to the anatomy. The following files have now been uploaded to your filedrop and can be downloaded by the email account "greve(a)nmr.mgh.harvard.edu" 1. vol0001.nii.gz : functional input 2. orig.mgz : anatomical target 3. register-test.dat : Output Freesurfer registration file 4. test.nii : Output functional data registered to anatomy Thank you for helping us, Erlend And the functional is test.nii.gz? If so, can you upload vol0001.nii.gz, register-test.dat, test.nii.gz, and orig.mgz to our file drop? doug On 04/25/2012 07:49 AM, Erlend Hodneland wrote: > Both the fmri data registered to orig is mismatched, and also the original > raw fmri data are mismatched with orig, > see the link here showing our raw data (fmri, orig and 152MNI) shown in > fslview > > http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a > > > It is orig.nii converted from orig.mgz that we show yes. > > Erlend > > > What images are mismatched? Specifically, which anatomical image are you > loading into fslview? > If you have not loaded the orig.mgz (converted to nii), then there will be be > a > mismatch. > doug > > > > On 04/24/2012 04:29 AM, Erlend Hodneland wrote: > > Hi again, > > > > We are trying to do the same as was done in Trachtenberg et al 2012 > > (Neurobiology of Aging), ie opt.the commonly used FLIRT+FNIRT registration > > in > > FEAT with BBreg: > > > > "For group analysis, functional data were registered, via the high > > resolution > > anatomical image, to the Montreal Neurological Institute (MNI) standard > > brain. Functional data were aligned to the anatomical image initially using > > FMRIB's Linear Image Registration Tool, (FLIRT) ([Jenkinson and Smith, > > 2001] > > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib27> > > and[Jenkinson et al., 2002] > > > > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib28>), > > then optimized using the Boundary-Based Registration (BBR) approach (Greve > > and Fischl, 2009 > > > > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib21>). > > Registration from anatomical to standard space was carried out using > > FMRIB’s > > Non-Linear Image Registration Tool (FNIRT)." > > > > > > That is, flirt from fmri --> brain, then initializing bbregister fmri --> > > brain by the previous flirt registration, then flirt and fnirt from brain > > --> > > standard space and finally fmri --> standard space and putting all these > > transformations together. > > > > > > However, our images are orientad as follows from top -> bottom (fmri, > > orig, > > 152MNI): > > > > http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a > > > > As shown in the previous communication, when we directly apply the images > > to > > the registration the results are oriented incorrectly, as the input images. > > > > Can you recommend a specific solution to overcome the orientation mismatch > > in > > these images which is compatible with the registration tasks? > > > > > > Thank you for your patience and help! > > > > > > All best > > > > E.H. > > > > > > Hi Erlend, while the images in the tkregister2 pics are oriented > > correctly the registration is way off. What images are you loading into > > fslview? You'll need to convert the orig.mgz into nii and load that to > > check the registration. > > doug > > > > On 04/22/2012 04:16 AM, Erlend Hodneland wrote: > > > Hi again, > > > > > > the registration looks fine in tkregister2, but is apparently wrong in > > > fslview (and also mricron). See the attached files (as link from > > > http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing > > > screenshots of fslview and tkregister2. How can this be explained, and > > > how can we visualize the correct orientation in fslview? > > > What does this misalignment influence any further processing with > > > fnirt and concatenation of the affine transformation fields? > > > > > > This is our command we run for bbregister: > > > > > > bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat > > > --init-fsl --t2 --o test.nii.gz > > > > > > where vol0001 is the first volume in the fmri sequence and is flipped > > > to align with LAS (as the highres). > > > > > > Thank you for your kind help, > > > > > > Erlend Hodneland > > > > > > ean that it is in the wrong orientation? It should be in > > > the same orientation as the anatomical. How does the reg look in > > > tkregister2? Note that fslview can display volumes in odd orientations > > > even when the orientation is correct. > > > doug > > > > > > On 04/13/2012 03:31 AM, Erlend Hodneland wrote: > > > > Hi, > > > > > > > > we are trying to register fmri FEAT data (example_func.nii) to the > > > > anatomical scan (processed in Freesurfer) using bbregister to > > opt. > > > > the affine registration before running FNIRT. > > > > > > > > However, the orientation of the registered image is flipped > > around and > > > > is incorrect after applying bbregister. > > > > > > > > We have tried: > > > > > > > > 1) bbregister --s subj_501 --mov example_func.nii.gz --reg > > > > register.dat --init-header --bold --o example_func2highres-fs.nii > > > > 2) bbregister --s subj_501 --mov example_func.nii.gz --reg > > > > register.dat --init-fsl --bold --o example_func2highres-fs.nii > > > > 3) bbregister --s subj_501 --o example_func2highres-fs.nii > > --feat > > > > "myfeatdirectory" > > > > 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat > > > > (this one looks correct) > > > > followed by > > > > bbregister --s subj_501 --mov example_func.nii.gz --reg > > register.dat > > > > --init-reg tkreg.dat --bold --o example_func2highres-fs.nii > > > > > > > > 5) reorienting to match the highres: > > > > > > > > fslorient -swaporient example_func > > > > fslswapdim example_func x -y z example_func_swap (correct > > > > orientation) > > > > > > > > followed by > > > > bbregister --s subj_501 --mov example_func_swap.nii.gz --reg > > > > register.dat --init-fsl --bold --o > > example_func_swap2highres-fs.nii > > > > > > > > with the output being flipped in wrong orientation for all > > options. > > > > > > > > We would greatly appreciate if you have any suggestions for how to > > > > overcome this problem! > > > > > > > > Cheers/Sincerly/All best > > > > > > > > Erlend Hodneland

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niiRead(): unsuported datatype 64
by Clark Fisher 30 Apr '12

30 Apr '12

Hi all, I'm trying to use Freesurfer to work with a parameter map saved as a nifti volume by another package (mrVista). However, whenever I try to open it using a Freesurfer tool (tkmedit, mri_info, freeview, etc.) I get the following error : niiRead(): unsuported datatype 64 (with scl_slope = 0) in /...path to file.../ParMap.nii.gz Is it obvious what's going on? Is there anything I can do to the file or my Freesurfer configuration to work with this volume? Thanks, Clark

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Unknown areas
by Steven Korycinski 30 Apr '12

30 Apr '12

Hi all, When using TkMedit to view aparc+aseg.mgz for the subjects of my research study I've noticed that in each of their images there exists at least some portion of the cortex labeled as"unknown" in the temporal lobe of the brain. As an example, in the image I've attached to this email there's a particularly large area labeled as "ctx-rh-unknown" in the right temporal lobe (left side of the image). Can anyone explain why such a large area labeled as "unknown" might exist in this image, and why similar smaller areas like this exist in all of my other subjects as well? Thanks, -Steve

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Freesurfer April 2012