Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

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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R: R: Re: R: Re: analysis on 4-6yrs pat
by crailo＠inwind.it 29 Oct '13

29 Oct '13

Hi Bruce, it seems I have uploaded the dir as well. Thanks for your help! Regards Antonio >----Messaggio originale---- >Da: crailo(a)inwind.it >Data: 25/10/2013 17.02 >A: <fischl(a)nmr.mgh.harvard.edu> >Cc: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: R: Re: analysis on 4-6yrs pat > >Hi Bruce, >I guess running from scratch is the easiest way. I tried to upload the whole >dir but it seems I cannot have access to it. >Thanks >Regards >Antonio > >>----Messaggio originale---- >>Da: fischl(a)nmr.mgh.harvard.edu >>Data: 25/10/2013 15.33 >>A: "crailo(a)inwind.it"<crailo(a)inwind.it> >>Cc: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] R: Re: analysis on 4-6yrs pat >> >>Hi Antonio >> >>I need the whole subject directory to diagnose what happened with the FS >>analysis. Or I can try rerunning it from scratch here instead if you >>prefer >>Bruce >>On Fri, 25 Oct 2013, crailo(a)inwind.it wrote: >> >>> Hi Bruce, >>> thanks for the reply. I have uploaded two images, the original one and the >one >>> preprocessed via 3D slicer N3. >>> Thanks >>> Regards >>> Antonio >>> >>>> ----Messaggio originale---- >>>> Da: fischl(a)nmr.mgh.harvard.edu >>>> Data: 25/10/2013 14.07 >>>> A: "crailo(a)inwind.it"<crailo(a)inwind.it> >>>> Cc: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] analysis on 4-6yrs pat >>>> >>>> Hi Antonio >>>> >>>> it's tough to diagnose from one slice. Is the top of the head in general >>>> darker than the bottom? It looks like it, but that might also be lower >>>> myelin content. If you upload the subject we'll take a look. >>>> >>>> cheers >>>> Bruce >>>> On Fri, 25 Oct >>>> 2013, crailo(a)inwind.it wrote: >>>> >>>>> >>>>> Dear Freesurfer experts, >>>>> >>>>> I am trying to run cortical thickness analysis on 4-6 yrs old patients >but >>> I >>>>> have some problem to get nice cortical gray matter. I have tried to run >>>>> several N3 but with no success so I would need to ask whether you could >>> give >>>>> me hints to improve that. Please find attached a screenshot of what I do >>>>> get. >>>>> >>>>> >>>>> Many thanks for any help. >>>>> >>>>> >>>>> Best Wishes >>>>> >>>>> Antonio >>>>> >>>>> >>>>> >>>> >>>> >>>> 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 >> > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Tracula preprocessing error: cannot find dwi_frames.nii.gz
by Michael Datko 28 Oct '13

28 Oct '13

Hello, I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead of the slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice? Thanks, Mike Datko

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Re: [Freesurfer] Freeview
by Lindsay Squeglia 28 Oct '13

28 Oct '13

It was definitely from freeview. These are the notes I wrote for creating figures previously, and I didn't have a problem: **Type freeview in command line in file where Freesurfer fsaverage brain is, will open file, go to File--> Load Surface -->fsaverage-->surf. Choose lh.pial; then do again for rh.pial for the pial surfaces. Go to View--> Show Control Panel, click on 1x1 view (white box at top of control panel), click on face (says 3D ALT3, at top of control panel, next to MRIs), Change Edge thickness=0 (to remove yellow lines), Change curvature=off (to make brain gray), (Must do all of this for L and R hemis separately). Label: load brain region (Label--> Load from file) you want from your Labels_from_parc file. Then you can change color accordingly. On Mon, Oct 28, 2013 at 11:58 AM, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu>wrote: > Was that from freeview or tksurfer? > > On 10/28/2013 02:06 PM, Lindsay Squeglia wrote: > > Hi Ruopeng, > > Thanks for your response! I used to do it all the time in the previous > versions of FreeSurfer (see attached). I am not sure why the new version is > different. > > Thanks! > Lindsay > > > > > On Mon, Oct 28, 2013 at 11:01 AM, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu > > wrote: > >> Hi Lindsay, >> >> I think there was no such option to display multiple surface labels at >> once even in the old version. However, we will add it in the future. >> >> Best, >> Ruopeng >> >> >> On 10/28/2013 01:48 PM, Lindsay Squeglia wrote: >> >> Hi all, >> >> I recently updated to FreeSurfer version 5.3.0, and I am now having >> problems with freeview that I didn't have on the older versions. When I go >> to "Surfaces" and "Load Labels", it only shows one label at a time. >> Previously, I could add several labels and all would appear on the Figure. >> Does anyone know a fix for this? >> >> Thanks! >> Lindsay >> >> >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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. >> > > > > -- > Lindsay M. Squeglia, Ph.D. > Postdoctoral Fellow > University of California San Diego > office phone: 858-822-2306 > email: lsquegli(a)ucsd.edu > > > -- Lindsay M. Squeglia, Ph.D. Postdoctoral Fellow University of California San Diego office phone: 858-822-2306 email: lsquegli(a)ucsd.edu

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2009

2008

2007

2006

2005

2004

Freesurfer October 2013