Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

Error: bvecs and bvals don't have the same number of entries (tracula error in step 1.6)
by christian buhl 11 Jan '14

11 Jan '14

Hi I would like to use tracula for analysis of our dataset of DWI-images. Freesurfer reconstructions of the corresponding T1-images have been performed. Our DWI-dicom-images have been aquired using a Philips 1.5T scanner (E_sDW_SSh). I have used MRICRON to extract the bvals and bvecs. (I attach these original b-files, x20080912...) The Trac-all prep step works fine until the tensor fit in step 1.6 where the run stops with: "Error: bvecs and bvals don't have the same number of entries" The Bvals-file has to be flipped in order to run tracula (not getting the "missing 1000 file"-error=. I guess that bvec-file should be in either 3-row or 3-column format. Flipping this file doesn't help. In the .tschrc-file I have set the language to english as proposed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19747.html This didn't help. I attach my log-file for the tracall-prep, the configuration-file and the bvecs.txt and bvals.txt used. In the configuration-file I have set the run list to only the first subject. The files bvals and bvecs from the output/dmri - directory are also attached. They are quite different from the original files? Any input and help will be warmly appreciated. Best regards Christian Christian Buhl Medical Doctor (MD), PhD-student Aarhus University Denmark

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wmparc.mgz and aparc.a2009s+aseg.mgz
by sujith vijayan 11 Jan '14

11 Jan '14

Hi All I am using wmparc.mgz and aparc.a2009s+aseg.mgz to determine the closest grey matter region for electrodes in some human epileptic patients; I have the RAS coordinates of the electrodes. I have a couple of questions: 1) When the electrode (its RAS coordinate) is close to the midline and out of the grey matter it won't give me the closest grey matter label (like wmparc does with the white matter). Is there someway to get this in a principled manner? For example, is there a way to get a file with all the RAS coordinates and the parcellation labels, so I could find the closest neighbor in Matlab? 2) The recons for three subjects were done between 2008 and 2010 using freesurfer. Therefore files like aparc.a2009s+aseg.mgz, wmparc.mgz, lh.aparc.a2009s.annot are missing. Is there a simple way just to recreate these set of files (one command would be great, even if it takes a little bit of time)? Or does the entire recon have to be done again? Thanks, Sujith

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Change in Tracula ability to use bvec / bval file containing zeros for b0 images?
by Salil Soman 10 Jan '14

10 Jan '14

Hi, I have been trying to rerun cases through the new (12/13) tracula code, which I had successfully ran through the pre 12/13 code. While I am still trying to sort out the libnetcdf.so.6 issue on our cluster, I also noticed that cases which I ran using the bvec and bval files including 0's for the b0 files were processed with the old code, but result in a xx:subscript out of range error in the current code. Removing the b0 entries fixed the problem and the remainder of the processing (other than the part requiring libnetcdf.so.6) works. I did notice that the bvecs and bval files in the diffusion tutorial do include the b0 0. Does the current version of tracula require the b0 entries to be removed? If not, any suggestions on what I may be doing incorrectly would be great. Thank you. Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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problem with bvecs file with new (12/13) TRACULA code
by Salil Soman 10 Jan '14

10 Jan '14

Hi, I am re-running GE acquired 3T product DTI data which ran without trouble through the older tracula code. However, now when I run the code, the bvec file that gets generated has an extra 0 placed at the very end, and then trac-all -prep eventually fails because it complains the bvec and bvals files have non-matching number of entries. I do have the dorotbvecs option set to 1 (as I had before). Any suggestions on what I am doing incorrectly would be greatly appreciated. I have attached the bvec and bval files I am providing a input. Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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Pooling data across experiments
by Cesar Echavarria 10 Jan '14

10 Jan '14

Hi freesurfers, I have run 2 separate blocked fMRI experiments ,each on a different pool of subjects, with couple of conditions identical in both experiments. I would like to pool the data for the conditions in common across these 2 experiments/group of subjects. I was wondering if anyone had any insight as to whether this is statistically valid or if there are any complications I should take into consideration when interpreting the pooled data. Thanks in advance for your help Cesar

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QAtools_v1.1 package
by Harms, Michael 10 Jan '14

10 Jan '14

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qdec error
by Cherise R. Chin Fatt 10 Jan '14

10 Jan '14

Hello All: I am hoping someone can help me with qdec. I am running -qcache and running into the following error: ERROR: number of vertices in /Recon/subj1/surf/lh.volume does not match surface (129774,129379) I tried running "recon-all -s subj1 -make all" but still getting the same error. I did manual edits after running the entire reconstruction so I am not sure if this is the problem. Can someone please help me? Thank you, Cherise.

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spatialsmooth-sess with option to set mask file name
by Caspar M. Schwiedrzik 10 Jan '14

10 Jan '14

Hi Doug, do you have a version of spatialsmooth-sess with the option to set mask file name? Thanks, Caspar

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Comparison of surface and euclidean distances
by Jörg Pfannmöller 10 Jan '14

10 Jan '14

Dear FreeSurfer experts, I computed distances on the cortex surface using mris_pmake on a data set acquired at a 3T scanner (using an MPRAGE sequence and protocol recommendations for FreeSurfer). The exact syntax of the distance computation was: mris_pmake --subject SUBJECT_ID --hemi lh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:66245,endVertex:59104 . Subsequently, the euclidean distance was computed using the Talairach coordinates displayed by tksurfer if the startVertex and the stopVertex are selected: distance_euc = sqrt[(startTal_x-stopTal_x)^2+(startTal_y-stopTal_y)^2+(startTal_z-stopTal_z)^2] . As you all know from your Tutorials, the in-surface distance must be larger or equal to the euclidean distance. Surprisingly, in the majority of cases investigated the opposite is computed. Typical distances calculated are in the range of 7 mm. Do you have an explanation for this outcome and a possible solution how it can be corrected? I am using FreeSurfer 5.1 and did not encounter any other problems in data evaluation. Any help us highly appreciated! Sincerely yours pfannmoe

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Re: [Freesurfer] questions about cortical thickness using qdec.
by Douglas N Greve 10 Jan '14

10 Jan '14

Please remember to post to the list. For the 0 0 1 -1 contrast, did any results survive multiple comparisons correction? If so, then at least the voxels in that region cannot be used with DOSS. I'm not sure why the patter was opposite between the two contrasts. I could mean that there is a nonlinear relationship with age. doug On 01/09/2014 03:54 AM, yaya ya wrote: > Dear Greve, > > Thank you very much for your response. I am now a little more clear, > although I still have some further questions. > > According to your suggestion, I just tried to test whether there is a > difference between group age. I included age as a continuous variable > in qdec. After running, I got the results arising from the contrast 0 > 0 1 -1 (which is called does the thickness-age correlation differ > between two groups?). That is, the results revealed the thinner in > some brain areas. But when I checked the results relating to the > comparision of groups (1 -1 0 0 ), the results were the same expect > the opposite pattern. That is, the results became thicker in the same > region. > > Does this imply that there is an age effect? It means I could not use > DOSS to do analysis, right? > > Best, > Lickey > > > On Thu, Jan 9, 2014 at 12:32 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > On 01/08/2014 04:28 PM, yaya ya wrote: > > Dear Freesurfer experts, > > > > I have a question about cortical thickness analysis using > freesurfer. > > Since I don't know how to post my question in freesurfer mailing > > list, that is why I am writing to you to get some help. > Hopefully, my > > email will not cause you any troubles. > Thanks for posting to the list. > > > > My question is : When I compared thickness from two groups (a > patient > > group and a healthy contrl group), that is say I got the thinner > in a > > subdivision of a particular brain region in patients than that in > > controls. But when I added age as a nusiance factors (not in the > > continuous covariate because I want to control for or regress > out the > > age effect) in qdec, the results changed. In the same region, the > > thickness became thicker in the patients than that in the > controls. I > > have no idea what happened. Which of them do I need to trust? > The age > > between two groups has been matched. > It depends on several things. It might be that there is an interaction > between group and age. Try testing for a difference between the age > slopes of the two groups. If there is no difference, then re-run using > DOSS (DOSS was removed from QDEC so you'll have to create an FSGD file > and use mri_glmfit). > > > > In addition, when I do FDR correction on the results, the min in the > > threshold jumped to more than 5 , making all the clusters > disappear. I > > think this correction is too high, unabling the genious effects to > > show up. How to deal with it? > Try using a cluster correction instead of FDR. > doug > > > > > By the way, our lab's IT staffs install the lastest released > > freesurfer. But when I use the qdec, I could not find the option of > > DODS and DOSS, as discussed in the mailing list. I am wondering > if it > > has been deleted in this new version. > > > > I really appreciate your help in advance. > > > > Best, > > Lickey > > > > > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer January 2014