Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

Dilated ventricles
by Victor Kovac 01 Nov '13

01 Nov '13

Dear Freesurfer experts, I have run recon-all and included the -bigventrcles flag on a number of brains with ventriculomegaly. This fixed the segmentation errors in a few cases; however, there are still brains with dilated ventricles for which recon-all is not providing accurate segmentation (see attached image). Are there any other tricks I can attempt to solve this issue? I was considering doing manual pial and white matter edits in conjunction with filling the ventricles by using the Edit Voxels Tool. Would this be advisable? Thank you! Victor

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funcroi calculating percent signal change
by Alexandra Tanner 01 Nov '13

01 Nov '13

Hi Doug and Freesurfers, I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions: funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated! Thanks, Alex

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preferred method for generating appropriate bvecs for tracula
by Salil Soman 01 Nov '13

01 Nov '13

Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under the impression tracula requires this to be converted to a n row by 3 column file. 1) is this correct, 2) is there a preferred way to perform this transformation on linux systems? Thanks you, -Sal

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mri_glmfit-sim with conjunction maps but without pre-cached data
by Caspar M. Schwiedrzik 01 Nov '13

01 Nov '13

Hi, I have a question regarding cluster size thresholding using mri_glmfit-sim. Namely, I have a sig.nii conjunction map that I made with mri_concat. The analyses that serve as input to the conjunction map are done on a custom surface template. If I want to run mri_glmfit-sim, how would that work? I obviously do not have precached data. Thanks, Caspar

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recon-all scripts w/ new GCA atlas
by Mark Plantz 31 Oct '13

31 Oct '13

Hello freesurfers, I am currently attempting to run recon-all on infant subjects with a newly created 'gca' atlas. I e-mailed the listserv a while back about a strange memory allocation error that occurred right at the beginning of the "subcortical segmentation" pipeline. For a while, we thought that it was an issue with the actual atlas. However, after talking with someone who created canine atlases, it seems like it is a particular bug in the recon-all scripts themselves. It appears as though the default recon-all script needs to be altered to accept the new gca atlas. I was wondering if anyone has had success getting Freesurfer to accept their gca atlas? Thank you! Best, Mark

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Volumes in native or normalized space, and eTIV
by Dorian P. 31 Oct '13

31 Oct '13

Dear all, Excuse if these are simple questions but I am a bit confused on the significance of the volume measures. 1. Are the volumes of ROIs calculated after normalization? 2. If volumes are calculated post-normalization, why is correction for eTIV needed? 3. What is the quickest way to correct for eTIV? Thank you. Dorian TJU

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improvement of segmentation qualitiy by setting control points
by Annemarie Brandhofe 31 Oct '13

31 Oct '13

Dear freesurfer community, we are conducting cortical-thickness analysis and we have encountered some problems with setting control points to improve segmentation quality. Mainly, white matter was classified as grey matter after completion of the first run that incorporated control points. Now we have several questions, we would be very thankful for your comments: 1. According to your expereince, how many control points for the overall brain are usually necessary to obtain good segmentation results? 2. Are control points necessary at all? Is there a way to control the segmentation quality? 3. Is there any visual example on how to best set control points? Thank you for your help, Annemarie

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Re: [Freesurfer] [martinos-tech] parametric modulation
by Douglas N Greve 31 Oct '13

31 Oct '13

For condition 4 (posslope), the weight is always 0. You can't compute a slope if all the values are the same. doug On 10/29/2013 10:44 AM, Suzanne Oosterwijk wrote: > Hi Doug, > > Attached is the Xtmp.mat file for the analysis that gets the error. > > Thanks for your response on the second question. I am not sure what > you mean with demeaning, so I guess that I am not doing that :-) I > just wanted to make sure that not getting the same results does not > indicate a fundamental problem in my paradigm files. > > Thanks! > Suzanne > > > On Tue, Oct 29, 2013 at 3:31 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Suzanne, can you send me the Xtmp.mat file that gets created? > > On your second question, the answer might be a little tricky. > First, are you demeaning the modulation value? If not, then you > can certainly get different maps. The other part is that you can > get unpredicatable results because the design matrix is not > orthogonalbecause you have several event types. > > doug > > > > On 10/28/2013 12:30 PM, Suzanne Oosterwijk wrote: > > Hi Doug, > > I am running parametric modulation analyses in which I am > modeling 5 different ratings given by participants in response > to images. To model these ratings I made paradigm files > defining both the onset and the slope for each trial (see > email exchange below). Since I have 5 different ratings, I > made 5 different paradigm files per participant, per run. > These paradigm files hold the exact same trial sequence, only > with different numbers for the slope condition. When running > selxavg3-sess I get the following error: > > Input to SVD must not contain NaN or Inf. > > Error in cond (line 36) > s = svd(A); > > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > The strange thing is that selxavg3-sess stops running at a > particular participant when I am trying to model one > particular rating, whereas the exact same analysis for the > other three ratings I have run so far (for the same > participant) does not result in an error. I checked the > paradigm files over and over but I cannot find the mistake. > The paradigm files are all the same in terms of timing and > condition codes etc., the only thing that is different between > the files are the specific ratings per trial. So I really > don't understand why I get this error. I attached the paradigm > files for the erroneous analysis and also for the analysis > that runs successfully. I also attached the selxavg3-sess > logfile for the an erroneous analysis and for the successful > one. Maybe I am missing something here, but I just don't see it. > > Also, I have one other question concerning the parametric > modulation. As I understand it modeling the onset is the same > analysis as a normal contrast comparing a particular condition > against baseline. I compared the onset significance maps > (comparing onset to baseline) for each separate rating, and to > my surprise they are not the same. Since only the ratings > differ between the different analyses, and not the onset times > of the stimuli, I expected those maps to be completely > identical. Am I right in this assumption, or is there a reason > they can be different? > > Thanks! > Suzanne > > > > On Thu, Aug 15, 2013 at 4:28 PM, Douglas 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>>> wrote: > > Hi Suzanne, that is fine > doug > > > > On 8/14/13 7:13 AM, Suzanne Oosterwijk wrote: > > Hi Doug, > > Just a follow-up question. The ratings that I > collected for the > parametric modulation analysis have a range from 0 to > 1. This > means that the weights for some stimuli will have the > value 0. Is > this a problem? I am asking just to make sure that a > weight of 0 > does not exclude the corresponding data-point. > > Thanks, > Suzanne > > > On Fri, Jul 26, 2013 at 7:14 PM, Douglas 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>>> wrote: > > Hi Suzanne, yes that looks correct. > doug > > > > On 7/26/13 9:27 AM, Suzanne Oosterwijk wrote: > > Hello all, > > I want to perform a parametric modulation > analysis in > Freesurfer and I have a question about how to > adapt my > paradigm file. I understand how to code the > offset and the > slope (by adding the individual ratings as the > slope > weight), but I just want to check whether I am > correctly > modelling the trials of no interest. > > I have presented people with negative, > positive and neutral > images all preceded by a fixation cross. I > have individual > ratings for the negative images that I want to > use for the > parametric modulation analysis, but I don't > have any ratings > for the positive and neutral images. I do want > to model > these images and the fixation cross, however, > to make sure > that do not become part of the null. Based on > the wiki I > adapted my paradigm file like this: > > (1 = offset for the negative image; 2 = slope > for the > negative image; 3 = neu/pos image of no > interest; 4 = fixation) > > 00121NULL > 12431fix > 15131negoffset > 1523.79negslope > 18431fix > 21331neu/pos > 24431fix > 27131negoffset > 27231.00negslope > 30431fix > 33131negoffset > 3323.49negslope > 36091NULL > etc. > > Is this correct? > > Thanks so much for responding! > Suzanne > > > > -- > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> > <http://va.nl> > > > https://sites.google.com/site/suzanneoosterwijk/ > > __._,_.___ > Reply via web post > > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwM2ltbGk0BF9TA…> > Reply to sender > <mailto:suzanne.oosterwijk@gmail.com > <mailto:suzanne.oosterwijk@gmail.com>?subject=Re%3A%20parametric%20modulation> > Reply to group > <mailto:martinos-tech@yahoogroups.com > <mailto:martinos-tech@yahoogroups.com>?subject=Re%3A%20parametric%20modulation> > Start a New Topic > > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlMGwxMWZ1BF9TA…> > Messages in this topic > > <http://groups.yahoo.com/group/martinos-tech/message/5830;_ylc=X3oDMTM0bWtjc…> > > > (1) > > Recent Activity: > > Visit Your Group > > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlNWFnMGY0BF9TAzk3Mz…> > > Yahoo! Groups > > <http://groups.yahoo.com/;_ylc=X3oDMTJkNzk1aW9nBF9TAzk3NDc2NTkwBGdycElkAzQ5O…> > > Switch to: Text-Only > > <mailto:martinos-tech-traditional@yahoogroups.com > <mailto:martinos-tech-traditional@yahoogroups.com>?subject=Change%20Delivery%20Format:%20Traditional>, > Daily Digest > <mailto:martinos-tech-digest@yahoogroups.com > <mailto:martinos-tech-digest@yahoogroups.com>?subject=Email%20Delivery:%20Digest> > • Unsubscribe > > <mailto:martinos-tech-unsubscribe@yahoogroups.com > <mailto:martinos-tech-unsubscribe@yahoogroups.com>?subject=Unsubscribe> > • Terms of Use > <http://docs.yahoo.com/info/terms/> • Send us > Feedback > <mailto:ygroupsnotifications@yahoogroups.com > <mailto:ygroupsnotifications@yahoogroups.com>?subject=Feedback%20on%20the%20redesigned%20individual%20mail%20v1> > . > > __,_._,___ > > > 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. > > > > > -- > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> > <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > -- > 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/ > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu>va.nl <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > -- 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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tracula bvec flipped sign
by Cat Chong 30 Oct '13

30 Oct '13

Dear Experts, I was hoping you could help me with the following problem. Tracula failed when I attempted to use Siemens (Skyra) dicoms as input for the configuration file, so I converted the dicoms to niftii format using dcm2nii. I used the gradient information of the bvec file created by dcm2nii ( after re-assembling it into the appropriate 3 column format) and specified it as the bvec.txt file to run Tracula. All post- processing worked fine and the fiber paths look ‘ok’ as far as I can tell. Here is the conundrum: When I compared the bvec gradients from the dcm2nii conversion to the SIEMENS hardwired protocol, the sign of the ‘z’ direction appears to have been flipped? I am not sure why this happened and whether to choose the “hardwired” Siemens scanner bvecs or the ones created by the niftii conversion. Which ones are correct to use? Very best regards, Catherine

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-autorecon2 -cp vs -autorecon2 without -cp
by Adam Mezher 30 Oct '13

30 Oct '13

Hi all, Just curious to know what would happen to the image if, after making control point edits, I do not include the -cp flag to the run command? Conversely, what would happen if I include the -cp flag without having made edits? Thanks, Adam *Adam Mezher* Staff Research Associate Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864

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Freesurfer October 2013