Freesurfer

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30132 discussions

Qdec Questions
by Ashley Shurick 29 Oct '13

29 Oct '13

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? 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? 3. I'm including questionnaires as a covariate of interest - do I need to demean these values as well? Thank you in advance for your help! Ashley -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University

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tksurfer command for saving multiple view tiff
by Jason Tourville 29 Oct '13

29 Oct '13

Is there a command for the "saving multiple views as TIFFs" function in tksurfer that can be used in a TCL script? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Power analysis for Qdec
by amirhossein manzouri 29 Oct '13

29 Oct '13

Hi Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power ! -- Best regards, Amirhossein Manzouri

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fast_selxavg3.m - ERROR: design is ill-conditioned
by preciado＠nmr.mgh.harvard.edu 29 Oct '13

29 Oct '13

I have two sets of identical blocks within each fMRI run, so conditions {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks. If I run the analysis treating each with the contrasts set up with this numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m ... ntptot = 687, nX = 136, DOF = 551 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat XCond = 2926.01 (normalized) However, if I want to treat the two sets of blocks separately, i.e., {1,2,3,4,5,6,7,8,9,10} so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then fast_selxavg3.m gives: ntptot = 687, nX = 146, DOF = 541 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat XCond = 4.33238e+08 (normalized) ERROR: design is ill-conditioned 1) why does nX increase by 10 in the 2nd case? 2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle 10 separate blocks? The entire log file in the 2nd case is attached.

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v4.5.0: How to obtain total gray matter volume?
by Natalie Garcia 29 Oct '13

29 Oct '13

Dear all, I've been using Freesurfer v4.5.0 for some time and have reconned about 100 participants. I am wondering if there is an automatic way to obtain the total gray matter volume for all the subjects I have run so far under this version, or would it be necessary to update to v5.2? Any help would be greatly appreciated! Best, Natalie -- Natalie V. Garcia Graduate Student, Cognitive Psychology Psychology Department The Pennsylvania State University 423 Moore Building nvg109(a)psu.edu

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Fwd: missing eTIV in asegstats2table
by Daniel Ferreira 29 Oct '13

29 Oct '13

Hi Douglas, You are right, sorry for not including the thread. Below I paste our previous conversation. I also attach again the files you asked me for. Thanks, best Daniel Message: 13 Date: Wed, 23 Oct 2013 10:49:44 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5267E208.4090305(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Daniel, what is this in reference to? If this is a follow up on a previous thread, please include the rest of the thread and the file in the same email. I go through way too many emails to keep track of who's doing what. thanks! doug On 10/23/13 4:13 AM, Daniel Ferreira wrote: Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel Message: 4 Date: Tue, 08 Oct 2013 11:39:11 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5254271F.4040508(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Can you send the aseg.stats file for subj1 and subj2? On 10/08/2013 07:53 AM, Daniel Ferreira wrote: Dear Douglas, I generated my table with version 5.3. Attached is an example for two subjects (in .txt and .xls formats). Best regards Dani Message: 18 Date: Mon, 07 Oct 2013 11:05:51 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5252CDCF.9050804(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed what version was the table generated with? 5.3 does not use ICV in the table anymore. It uses eTIV. Can you send an example of one of your tables? On 10/07/2013 03:12 AM, Daniel Ferreira wrote: Dear Douglas and Martin, Thanks for your replies. So far I have always been able to get eTIV when running asegstats2table (last column on the spreadsheet). But my current FreeSurfer version (5.3.0) is not grabbing it. I can found eTIV in the header and extract it for all the subjects with mri_segstats (as below in blue), but output is quite messy. I would rather prefer to get it as in asegstats2table format. Any idea? Thanks a lot, Dani for i in FAD*; do echo $i; mri_segstats --subject $i --etiv-only >> table_eTIV; done Message: 4 Date: Wed, 2 Oct 2013 08:50:23 +0200 From: Daniel Ferreira <danifer(a)ull.es> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CACNza6eGqfsZ2Sfj9EVJxDD4pQv8PW7=nbCYwwMEPtER0C0o7w(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear Douglas, Thanks for your quick answer. Yes, all my subjects have the measure " EstimatedTotalIntraCranialVol" in their "aseg.stats" file. The problem is that when I run "asegstats2table", this variable is not exported to the created text file. I wonder if there is some way to extract eTIV for all my subjects at the same time. I manage to do it with "mri_segstats", but what I get is individual values for all my subjects in the terminal, so it is quite boring to pass all the values to a table. Thanks a lot, Dani Message: 1 Date: Tue, 01 Oct 2013 11:58:57 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <524AF141.3060100(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed It should still be there. I changed the name to EstimatedTotalIntraCranialVol, eg the line now looks like # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1509814.835086, mm^3 On 10/01/2013 10:50 AM, Daniel Ferreira wrote: Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani -- Daniel Ferreira, PhD. Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics (Karolinska Institute, Sweden) daniferp(a)gmail.com | daniel.ferreira.padilla(a)ki.se

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Re: [Freesurfer] [martinos-tech] parametric modulation
by Douglas N Greve 29 Oct '13

29 Oct '13

I mean to take all the values (eg, .68849, .31061, etc), compute their mean, then subtract the mean from each value. This will not affect the slope calculation but can affect the offset. Seeing differences in the offsets does not mean that anything is fundamentally wrong. 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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subcortical segmentation VS surface
by elisa veronese 29 Oct '13

29 Oct '13

Dear FS experts, I am not sure about the result of the recon-all on some subjects from my database. In particular, in the attached file there is an apparent disagreement betwee the surface red line and the parcellation of the GM. Should I consider this processed image as correct or not? The red regions in the correspondence of the insula seem correct, but the red line is uncorrect. Thank you for your help, Elisa -- Elisa Veronese - PhD * Research Unit on Brain Imaging and Neuropsychology (RUBIN) * * Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php *

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how to transfer .label file to .nii file
by Zhao Jingjing 29 Oct '13

29 Oct '13

Hi, Our lab have managed to generate ROIs in T1 images using Freesurfer, which led to .label files. We succesfully measured the cortical thickness in these ROIs for each subject in Freesurfer. Now we are aiming to track white matter fibers from these ROIs in a tractography software Trackvis. However, .lable files seem not be readable in Trackvis. Thus, we are wondering if .label files can be tranferred to .nii files easily in Freesurfer so that we can use the converted .nii ROI files to track fibers in Trackvis. Another related question is how can we coregister the ROIs drawn in T1 images with DTI images and make sure that those ROIs converted from T1 images are the still in the same regions in the DTI images? Thanks. Jingjing Zhao Postdoc scientist Laboratoire de Sciences Cognitives et Psycholinguistique Departement d’Etudes Cognitives Ecole Normale Superieure 29 rue d’Ulm, 75230, Paris Cedex 05, France Tel: +33 1 44 32 26 57 Fax: +33 1 44 32 26 30 *Email: *jingjing.jj.zhao(a)gmail.com

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Tksurfer abbreviations
by Harry Hallock [hhal5293＠uni.sydney.edu.au] 29 Oct '13

29 Oct '13

Hi all, Apologies for this basic question, but im quite the newbie. I'mcurrently using tksurfer and got this result: surfer: filling (ctrl-c to cancel).... done, 4646 vertices filled surfer: performing FDR on 1989 vertices MRISfdr2vwth(): np = 1989, nv = 163842, fdr = 0.05, vwth=2.24098 MRISfdr2vwth(rate=0.050000, sign=0, 1, only_marked=1) = 2.240980 surfer: MRISfdr2vwth with rate 0.05 and sign 0 returned threshold 2.240980 I was wondering what np, nv and vwth actually stand for? Also does anyone know how to get the T or F statistic? Thanks, Harry Harry Hallock | MPhil Candidate Regenerative Neuroscience Group | Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050 | Australia T +61 2 9114 4138 E hhal5293(a)uni.sydney.edu.au | W www.rng.org.au

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