Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

RAS to Talairach
by sujith vijayan 19 Aug '13

19 Aug '13

I am looking at intracranial electrode recordings from some epileptic patients. The locations of the electrodes have been determined using a preoperative MRI and a postoperative CT scan. The locations are in RAS coordinates. Is there some sort of function that will allow me to translate the RAS coordinates to Talairach coordiantes? Or some sort of function that will output an anatomical label for each of the RAS coordinates? Please let me know what I need in addition to the RAS coordinates as a .mat file. For example, do I need to install FreeSurfer? What additional files do I need? My preference would be to do this all in Matlab. Sincerely, Sujith

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[Tracula] error running trac-all –path –c Configuration_file.txt
by Francesco Siciliano 19 Aug '13

19 Aug '13

Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory?

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few questions regarding qdec
by Binod Thapa-Chhetry 19 Aug '13

19 Aug '13

HI all, We had submitted a paper based on cortical thickness analysis in Qdec. The reviewer's had couple concerns regarding the QDec analysis. We would appreciate your help to address/resolve those issues. Here are the concerns: (1) What was the rationale of using 10mm smoothing? The typical fMRI values for volumteric work is 2-3 x the original voxel size. What's the reason for this value? Our response so far: A smoothing kernel of 10 mm was chosen because this setting had been published recently in articles that performed similar analyses. 10 mm therefore was a typical parameter for this type of analysis. This setting was also the default in the QDEC GUI, also suggesting that it was a typical setting. We only performed analyses of the data for this project using this setting and did not iteratively test multiple kernel widths. Also, the FWHM for cortical thickness analyses is somewhat larger than that used in fMRI analyses because it is applied to surface, as opposed to volume-based data. Surface based data are not prone to the same artifacts of including white matter, csf or brain tissue on the other side of a sulcus as volume-based data are. (2) What's the p-value to get in for a cluster-wise analysis and what size is a significant cluster? It's important to know these non cluster-wise values to get a sense of the parameters that determine significance. Our response so far: QDEC does not have a parameter that can be adjusted for cluster size or extent as other whole brain analyses such as Statistical Parametric Mapping do. The researcher can only indicate a statistical cutoff. We used a p value cutoff of 0.05 after a correction for multiple comparisons that was based on the Monte Carlo permutation cluster analysis with 10,000 iterations. Additionally, our findings comprise of pretty large clusters. This obviates the reason for cluster-thresholding based on size. Thanks in advance for the response. Binod

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Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
by Francesco Siciliano 19 Aug '13

19 Aug '13

________________________________ From: Francesco Siciliano Sent: Monday, August 19, 2013 12:54 PM To: Francesco Siciliano Subject: RE: [Tracula] error running trac-all –path –c Configuration_file.txt I also noticed that even on those that appeared to finish, there was no dpath folder. Any help would be greatly appreciated! Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155 ________________________________ From: Francesco Siciliano Sent: Monday, August 19, 2013 12:13 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Tracula] error running trac-all –path –c Configuration_file.txt Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory?

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Two Inquiries
by Liane Hunter 19 Aug '13

19 Aug '13

1. Segmentation of partial brain Dear FreeSurfers, 1. Can I expect recon-all to work on a T1W image where only part of the brain is in FOV? The obvious answer is that I should just try, but it would help to know in case I get unexpected results. Perhaps a more appropriate question is: what should I expect to work and what should I expect to fail. Thank you, ---------------------- 2. Rotated segmentation Dear FreeSurfers, I start with a T1W image in NIFTI format. After running recon-all, I use mri_convert to convert aseg.mgz to aseg.nii. This aseg.nii image does not overlay the original T1W. It is slightly rotated. Is it normal? If I would like to make it overlay what should I do? Register using flirt? Thank you, -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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Orientation/Primary-Slice-Direction
by Mark Plantz 19 Aug '13

19 Aug '13

Hello freesurfers, I have an image that is in RAS orientation with the axial primary slice direction. Is there anyway to change this to LIA orientation with the coronal primary slice direction? I am assuming mri_convert would work, but I'm not sure which flags to use. Thanks in advance. MP

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Re: [Freesurfer] Antw: Re: [tracula] error running trac-all -prep
by Borsodi Florian 19 Aug '13

19 Aug '13

Hi Anastasia, Here are the bvec and bval files you asked me about. Sincerely, Florian >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> Hi Florian - Can you please also attach the bvecs/bvals files from the dmri directory? Thanks, a.y On Sun, 18 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thanks for your help. I renamed the directories and reran trac-all. It > worked for the moment. > However, then I got another error: "bvecs and bvals don't have the same > number of entries." > I don't know why, because they actually have the same number of entries. > > I attached the logfile so that you may see what is going on. The error > occours at line 1463. > > Thank you in advance for your help. > > Sincerely, > Florian > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > Hi Florian - I see what's going on. Can you please rename the directory > /data/physics/florian/nii into something that doesn't include "nii", and > rerun? Because "nii" is a file extension, this confuses some of the > scripts. > > Thanks, > a.y > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia > > > > I ran the command you sent me and it runs without any errors. > > I also attached the command line for you. > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > same kind of problems. > > > > sincerely > > Florian > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > >>> > > > > Hi Florian - Can you please run this command directly on the command line > > and see if there are any errors? > > > > flip4fsl > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > Thanks, > > a.y > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia > > > > > > Thank you for your answer. > > > > > > Yes, those files exist. > > > I also extracted the bvec an bval files with anotther software then > > dcm2nii > > > and i keep getting the same kind of error. > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > testdata for running tracula. > > > > > > sincerely > > > Florian > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > >>> > > > > > > Hi Florian - Do these files exist? > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > s > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > s > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > this > > > has nothing to do with the error you're getting) I have to warn you that > > > you may not be able to get good results running probabilistic > tractography > > > on this data. It looks like you're acquiring the same 6 diffusion > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > reconstructing the tensor model, but will probably not be sufficient for > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > tracula). Your scan time is better spent acquiring 48 different > > > directions, rather than the same 6 directions 8 times. > > > > > > a.y > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > Hello, > > > > > > > > I have been trying to run tracula on my data and i keep getting the > same > > > > kind of error repeatedly. > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > diffusion protocol. However, tracula cannot read the bvec and bval > data > > > out > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > the > > > > config file. > > > > After doing so, I got the error which says that tracula cannot find > the > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > I have tried many options, but still cannot find a solution. > > > > I am hoping to get some troubleshooting help. > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > files. > > > > To uphold patient confidentiality, I have encode the name patient's > data > > > as > > > > "AAAAAA". > > > > > > > > I believe the problems are the bvec and bval files or their > structures. > > > The > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > 268 > > > and > > > > 1480 - 1484. > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > With kind regards, > > > > > > > > Florian Borsodi > > > > Department of Neurology > > > > Medical University of Graz > > > > > > > > > > > > > > > > > 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. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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R: Re: Statistical concerns
by stdp82＠virgilio.it 19 Aug '13

19 Aug '13

Dear Doug, thank you very much for your reply!Point c, is now ok. Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 4-ago-2013 20.34 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Statistical concerns On 8/1/13 7:56 AM, stdp82(a)virgilio.it wrote: Hi list, I have some questions please. 1- I have carried out Monte Carlo Simulation to assess the difference among three groups (23, 24 and 32 subjects). Main results were confirmed also by FDR, but I prefer to shown the Monte Carlo becouse it better describes my thesis. Recently I have submitted my paper but a referee asked me "Why use cluster based Monte Carlo methods for correction of multiple comparisons instead of the more conventional vertex-wise FDR correction? I suspect the former is much less conservative than the latter. It would be interesting to know the results for FDR corrected thresholds (p<0.05), and whether the present results would remain statistically 'active'. Now, I'm looking literature and I'm noting that several recent articles published on top journals used Monte Carlo Simulation (Ehrlich et al., 2013 Schizophr Bull.; Sasamoto et al., 2013 Schizophr Bull). What do you think about it? How do you advise to reply to the referee? I'd like to show Monte Carlo results. This is a very surprising request by the reviewer. FDR is hardly "conventional", and the brain imaging community has been using clusterwise correction for 20 years. I'm not even sure what "voxelwise" FDR is. Is that different than the one introduced by Genovese in 2002? As for how to respond to the reviewer, I'm not sure. You can certainly make a case that doing the clusterwise correction is the "industry standard". You can also site a paper out of the Friston group from a few years back critisizing the Genovese-style FDR. Have you applied the Genovese-style FDR that we offer in FS? If that works out, then there is no need to fight with the reviewer. 2- I should do also correlation analysis. I'm using QDEC as recommanded in guideliness (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freev…) In one group, after fsgd creation, I'm performing correlation analysis between thickness and neuropsychiatric test scores (it has been put in covariete windows-it should be dipendent factor). I'm also putting some nuisance factors (they should be dipendent factor in the regression analysis) to exclude the their effect on data. a- Is this procedure corrected? b- Is corrected to talk regression analysis in the text of my manuscript? c- Is corrected whether I explain this correlation analysis as reported in the description performed above? I'm confused. If you are using qdec, then you put your factors (which are independent) in the qdec table, not in the FSGD file. Otherwise the procedure looks correct and you can talk about "regression analysis" in your ms. I don't understand (c). doug Thank you very much, Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Trouble with mris_label2annot
by Stephen Politzer-Ahles 19 Aug '13

19 Aug '13

Hello, I have a set of custom labels and I want to plot them all at once on one brain, so I'm trying to use mris_label2annot for that. However, I'm getting several problems. Here is an example of what I get: http://i.imgur.com/Sw1Z9UT.png The labels I'm using were originally defined on a decimated source space (that was created using the MNE toolbox), so it's normal that most of them show up as lots of dots rather than contiguous areas. However, I don't know why some of them actually are showing up as contiguous areas; when I plot the labels one by one, all of them show up as series of dots rather than contiguous areas, so it seems that creating the annotation is messing something up. I also have a few other problems that you can't see in the image. Firstly ( and most seriously), the locations of the labels that show up when I plot this annotation do not at all match where the labels actually are--that is, if I hover my mouse over one of the labels in this, it doesn't match where the label actually should be if I plot that label by itself. Secondly, there seems to be some indexing issue with my color lookup table--I have 58 labels per hemisphere, so I created a color table that starts at label 0 and goes up to 57 (as per the example at http://ftp.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles and the automatically-generated annotations such as lh.aparc2009s.annot). In my color lookup table, label 0 is called 'amygdala' and label 1 is called 'anteriorcommisure'. But when I actually run mris_label2annot, the output seems to suggest that the program is 1-indexed instead of 0-indexed (because it skips the 0th label, andlooks for the 57th label, see output snippet below): Reading ctab /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab Number of ctab entries 58 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ ... cmdline mris_label2annot --ctab /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab --subject fsaverage --annot MRATparc --hemi lh --l lh.amygdala.label --l lh.anteriorcommissure.label --l lh.anteriornucleus.label --l lh.ba1.label --l lh.ba10.label --l lh.ba11.label --l lh.ba13.label --l lh.ba17.label --l lh.ba18.label --l lh.ba19.label --l lh.ba2.label --l lh.ba20.label --l lh.ba21.label --l lh.ba22.label --l lh.ba23.label --l lh.ba24.label --l lh.ba25.label --l lh.ba27.label --l lh.ba28.label --l lh.ba29.label --l lh.ba3.label --l lh.ba30.label --l lh.ba31.label --l lh.ba32.label --l lh.ba33.label --l lh.ba34.label --l lh.ba35.label --l lh.ba36.label --l lh.ba37.label --l lh.ba38.label --l lh.ba39.label --l lh.ba4.label --l lh.ba40.label --l lh.ba41.label --l lh.ba42.label --l lh.ba43.label --l lh.ba44.label --l lh.ba45.label --l lh.ba46.label --l lh.ba47.label --l lh.ba5.label --l lh.ba6.label --l lh.ba7.label --l lh.ba8.label --l lh.ba9.label --l lh.caudatebody.label --l lh.caudatehead.label --l lh.caudatetail.label --l lh.corpuscallosum.label --l lh.culmen.label --l lh.declive.label --l lh.hippocampus.label --l lh.hypothalamus.label --l lh.mammillarybody.label --l lh.medialdorsalnucleus.label --l lh.optictract.label --l lh.pulvinar.label --l lh.putamen.label ... subject fsaverage hemi lh SUBJECTS_DIR /media/LAPTOP_HD/WW3_newanalysis/subjects ColorTable /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab AnnotName MRATparc nlables 58 LabelThresh 0 0.000000 Loading /media/LAPTOP_HD/WW3_newanalysis/subjects/fsaverage/surf/lh.orig 1 3988503 anteriorcommissure 2 11811863 anteriornucleus 3 3957823 ba10 ... 56 1326221 pulvinar 57 14423183 putamen 58 -1 NOT_FOUND Does anyone have suggestions about any or all of these issues? Thank you, Steve Politzer-Ahles Stephen Politzer-Ahles New York University, Abu Dhabi Psychology Department http://www.nyu.edu/projects/politzer-ahles/

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error for autorecon3
by Troebinger, Luzia 19 Aug '13

19 Aug '13

Hi all, I am trying to run recon-all on a structural for one of my subjects, but freesurfer exited with errors during the last few stages (the ones covered by autorecon-3). It appears that it is just missing some label - the problem occurs at the following stage: painting output onto subject ME. processing subject lh.EC_average... MRISread (filename) could not open file I've used freesurfer before, same subject directory, but didn't get this error - it appears from the path after the MRISread command that it is just the subject directory, but not the directory for this particular subject. It appears freesurfer is looking for this file, which it can't find: /home/virtualuser/freesurfer/s_sub/lh.EC_average/surf/lh.sphere.reg where /home/virtualuser/freesurfer/s_sub is my subject directory. Can anyone advise as to how to fix this? Any help would be much appreciated. Best Luzia

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Freesurfer August 2013