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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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-openmp
by Jared Tanner 30 Oct '13

30 Oct '13

Hi, This might be answered somewhere but does -openmp work in 5.3 for OS X 10.8.x devices (I know online with the 5.2 release notes it says CENTOS only)? I ran recon-all with the -openmp flag and it finished without errors but did the flag actually do anything? Thank you, Jared

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SAG FSPGR BRAVO Sequence
by Ashley Hannah 30 Oct '13

30 Oct '13

Hello, Has anyone processed a SAG FSPGR BRAVO sequence successfully through FreeSurfer? When I run these images the program finishes without error however the output in tksurfer is grossly incorrect. Is there a way to adjust the parameters for reading white and gray matter by freesurfer (because BRAVO has a different contrast, not as defined) so that regions and boundaries are parceled correctly? Thanks, -- *Ashley*

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Issues with rh.white and rh.orig surfaces
by Jonathan Holt 30 Oct '13

30 Oct '13

FS experts, both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed? Jon

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Re: [Freesurfer] SAG FSPGR BRAVO Sequence
by Bruce Fischl 30 Oct '13

30 Oct '13

Hi Ashley what format are these in? They don't have an extension thanks Bruce On Wed, 30 Oct 2013, Ashley Hannah wrote: > Here are the tkmedit with overlay images. > > Thank you for your help! > > Ashley > > > On Wed, Oct 30, 2013 at 12:40 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > It's hard to tell anything from those images. We need to see > surfaces over volumes in freeview or tkmedit > Cheers > Bruce > > On Oct 30, 2013, at 12:01 PM, Ashley Hannah <ahannah1510(a)gmail.com> > wrote: > > For some reason the images will not display. > Hopefully this works.... > > > On Wed, Oct 30, 2013 at 11:31 AM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Ashley > > if you upload a dataset we'll take a look. I am > surprised to hear that you are having problems. Can > you post an example image? > > Bruce > On Wed, 30 Oct 2013, Ashley Hannah wrote: > > Hello, > Has anyone processed a SAG FSPGR BRAVO > sequence successfully through > FreeSurfer? > > When I run these images the program > finishes without error however the > output in tksurfer is grossly > incorrect. > > Is there a way to adjust the parameters > for reading white and gray matter by > freesurfer (because BRAVO has a > different contrast, not as defined) so > that > regions and boundaries are parceled > correctly? > > Thanks, > -- > Ashley > > > > > 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. > > > > > -- > Ashley M. Hannah > > <SAGBravo2_07.png> > > <SAGBravo1_07.png> > > > > > -- > > >

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Using glmfit with 2 different sequences
by celine＠nmr.mgh.harvard.edu 30 Oct '13

30 Oct '13

Hi freesurfer team, I am wondering if there would be a way to process a glm analysis between 2 surfaces from different modalities within one group of subjects. For example, within one population of patients, we would like to see if there is a spatial relationship between cortical thickness and another metrics (DTI metrics for example). What we have done so far is compute the mean cortical thickness for each parcellation, the mean FA for each parcellation, and we did a linear regression with all the subjects of our group. Would there be a way to do that at the vertex level instead of a whole region level? From what I understood, when we use glmfit, the regressors that we can put are single values like age, group, cognitive testing etc, but maybe not an entire surface? Thanks a lot Best, Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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Mac issue
by krista kelly 30 Oct '13

30 Oct '13

To all my fellow Freesurfers... Has anyone had any issues with doing recon-all on a Mac. I'm having a problem with the automatically generated labels V1, V2, and MT (when loaded in tksurfer there are holes in the mask) and I've been informed that this may be an issue because of running the program on a mac instead of using linux. I'm concerned that if the labels are incorrect, that there may also be a problem with the atlases and doing any whole brain analyses (although the atlas masks and surfs look fine). If anyone else has encountered this issue and can shed light on it for me, I would appreciate it! Best, Krista

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Re: [Freesurfer] Qdec Questions
by Douglas N Greve 30 Oct '13

30 Oct '13

In your case you have HC listed first, so red/yellow means HC>SAD, blue means SAD>HC doug On 10/29/2013 11:03 PM, Ashley Shurick wrote: > Hi Doug, > > Apologies, but I have a rather easy follow-up question that I can't > figure out: > > How do you interpret the effect in each significant region? A previous > post suggests using ctrl + left mouse click on a blob and examining > the plot of the data. However, for the model I am looking at ("Does > the thickness-ERQ correlation differ between HC and SAD?") I still > can't determine if cortical thinning represents HC<SAD or SAD<HC. I'm > attaching a representative plot here. > > Thank you, > > Ashley > > > On Tue, Oct 29, 2013 at 10:25 AM, Ashley Shurick > <ashley.shurick(a)gmail.com <mailto:ashley.shurick@gmail.com>> wrote: > > Thank you! > > > On Tue, Oct 29, 2013 at 10:19 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > On 10/29/2013 01:10 PM, Ashley Shurick wrote: > > Hi all, > > > > I'm running analyses in Qdec and want to verify a few things: > > > > 1. When comparing two groups (HC vs patients) I am including > mean > > cortical thickness as a covariate, using the following equation: > > > > > > bh.thickness = (lh.thickness*lh.surfarea + > rh.thickness*rh.surfarea) / > > (lh.surfarea + rh.surfarea) > > > > > > Is this the best way to calculate global mean thickness? > Yes > > > > > > 2. I want to regress out any effects of age, therefore I need to > > demean the ages for my groups as a whole, and not perform this > > calculation on each group separately, correct? > Yes, in which case the test of the difference between groups > will be > done at an age equal to the mean of the ages. > > > > 3. I'm including questionnaires as a covariate of interest - > do I need > > to demean these values as well? > When you do a test on a continuous covariate, that test will be > unaffected by demeaning of the covariate. Demeaning will > affect the > difference between groups if you use a separate covariate for each > group. If you have a single covariate across groups, demeaning > will have > no effect. > > doug > > > > > > Thank you in advance for your help! > > > > > > Ashley > > > > > > -- > > Ashley A. Shurick > > Ph.D. Candidate > > Department of Psychology > > Stanford University > > > > > > _______________________________________________ > > 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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