Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

retinotopy analysis viewing in Freesurfer 5
by Katie Bettencourt 16 Feb '12

16 Feb '12

I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing. I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in): tksurfer-sess -a rtopy.self.?h -s sessid it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code: tksurfer-sess -a rtopy.self.?h -s sessid -map angle but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5? For reference in freesurfer4.5, I would load retinotopy data by using this command: tksurfer subjname ?h inflated and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset. Can you help me figure out how to get my data to display correctly? Thanks, Katie

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Freeview Surface Editing
by Tina Jeon 16 Feb '12

16 Feb '12

Dear freesurfer experts, I am new to the freeview interface. How do I go about drawing a ROI on the surfaces to create my own label? Both the voxel edit and ROI edit buttons are not useful in this case. Thank you in advance, Tina Jeon PhD Candidate Advanced Imaging Research Center UT Southwestern Medical Center 2201 Inwood Rd Dallas, TX 75204 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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transforming aseg.mgz, brain.mgz to native scanner space and dimensions
by Mario Ortega 16 Feb '12

16 Feb '12

Hello Freesurfer Mailing list, I would like to know how to do the item mentioned in the subject> Ideally not just write out the brain and aseg regions into isotropic voxels in standard space, but also accomplish converting back to the *original*resolution, would I have to specify an inverse transform file? If I follow the directions in the mri_label2vol, I get volumes in a scanner like orientation, but not the correct x,y,z, dimensions. Ie, I get 256x 256 x 256 as x,y,z. When in fact we scan at 256x256x176 Thanks Mario

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Re: [Freesurfer] REPOST: Nearest Cortical Label Clusters locations
by Douglas N Greve 16 Feb '12

16 Feb '12

Hi Antonella, I have created a registration file that will allow you to get coordinates (this one assume that you performed your group analysis in CVS space). ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg.cvs-to-fs… You can pass this to mris_volcluster. This will allow volcluster to report the segmentation that the peak falls into, but this will not tell you the closest cortical label. I'm working on a solution to that for the CVS subject. doug Antonella Kis wrote: > > > Hi Doug, > > > > By "more exactly location" I want to say that I would like to have the > MNI coordinates and also the annotation location or the nearest > cortical label (for example precentral or lateraloccipital, etc). > Also,after I ran the mri_segstats I don't have the MNI coordinates. > > Thanks for helping. > Antonella > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, February 14, 2012 1:18 PM > *Subject:* Re: [Freesurfer] Clusters locations > > > > Antonella Kis wrote: > > Hi Doug, > > > > 1) I would like to report the MNI coordinates and also a more exactly > > region I mean if possible tto find exactly where in the > > Left-Cerebral-White-Matter and Right-Cerebral-White-Matter my cluster > > is located. > What do you me by "exactly where"? The nearest cortical label? The fiber > bundle? > > > > 2)Can you please tell me if for the mean diffusivity I should use the > > simulation with the perm (as I use for the FA due to the fact that is > > not so Gaussian) option or it is OK to use the grf option. > I think you can use GRF for this as it corresponds to a normal contrast > in a GLM. Note that the permutation is the stronger (but more > conservative) test. > > > > > > 3) Can you please explain what exactly means for my clusters if I hit > > the positive sign under DISPLAY in Qdec? I mean if I compare the > > cortical thickness between two classes: controls vs. Patients and > > I am not interested in the sex or age differences just differences > > between the two classes will positive mean clusters where cortical > > thickness graeter in Class 1 than Class2 (Class1>Class2)? > > > > I have C = +1 -1 and my Class 1 = controls while Class2 = PAtients. > Positive is Controls > Patients > > doug > > > > > > THANKS YOU. > > Antonella > > ------------------------------------------------------------------------ > > *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > free surfer > > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Tuesday, February 14, 2012 9:59 AM > > *Subject:* Re: [Freesurfer] Clusters locations > > > > Hi Antonella, what level of detail do you want? I think that most > > people are reporting MNI coordinates. > > doug > > > > On 2/13/12 2:44 PM, Antonella Kis wrote: > >> Hi Doug, > >> > >> I will be very grateful if you give me some directions regarding how > >> I can get my clusters location ( my output is too general telling me > >> just Left-Cerebral-White-Matter and Right-Cerebral-White-Matter) and > >> the coordinates (MNI) when I run the: > >> > >> mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask > >> GroupAnalysis_pos.glmdir/mask.mgh --no-fixmni --cwsig > >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum > >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn > >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh > >> .09 --seg cvs_avg35 aseg.mgz --csdpdf > >> GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd > >> GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig > >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh > >> > >> and > >> > >> > >> mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i > >> > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.nii.gz > > >> --avgwf fa.avg.dat --sum permcsd.sig.cluster.summary > >> > >> > >> Thank you. > >> Antonella > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] overlay question
by Ivan Alvarez 16 Feb '12

16 Feb '12

Following up on this topic, is it possible to display functional maps on a surface using Freeview? I have tried loading functional results as an overlay without much success. Kind regards, Ivan Alvarez On 16/02/2012 5:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Is this individual data or group? If individual, are you planning to do > a surface-based group analysis? If so, make sure that the fMRI data are > in the native functional space. > doug > > Bruce Fischl wrote: >> yes, use bbregister to register your functional maps, then >> mri_vol2surf to sample them onto the surface and load them in tksurfer. >> >> cheers >> Bruce >> On Thu, 16 Feb 2012, LAOUCHEDI MAKHLOUF wrote: >> >>> hi all >>> excuse me for this "simple question" but i am quiet new to >>> freesurfer >>> (i use it just for the parcellations). i've some functionnal maps (i've >>> used spm for that) that i want to use as an overlay on the pial >>> surface of >>> the subject. is there an easy way to do it >>> >>> thanks >>>

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Re: [Freesurfer] selxavg3-sess error
by Douglas N Greve 16 Feb '12

16 Feb '12

It does not look too bad to me. That is a significance map and it is covering most of the occipital region. If you want to see the angle, add -angle to your tksurfer-sess command. doug Daniel Cole wrote: > I was mistaken, I only have *Polar* (Rotating wedge) not Eccentricity > stimuli. > After running selxavg3-sess I view my results with "tksurfer-sess > -analysis rtopy.self.lh -sf sessid". > The retinotopic data shows up on the surface but looks incorrect... > I'm new to freesurfer so I'm not sure if it's simply the viewing > options causing the graphics to look incorrect or if the analysis > failed. Does the attached picture look correct to you? > > My apologies for the elementary questions. Thanks again for all of > your help, > Daniel > > On Thu, Feb 16, 2012 at 2:16 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > It can't create a fieldsign map from just the eccentricity. > doug > > Daniel Cole wrote: > > Hello, > Thanks for your reply. > You are right, I only have eccentricity. I reran all the > steps and tried your suggestion which worked! > However, now I'm having a different problem. > After running "mkanalysis-sess -analysis rtopy.self.lh > -surface self lh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5" > followed by "selxavg3-sess -analysis rtopy.self.lh -sf > sessid", I try running "fieldsign-sess -a rtopy.self.lh > -sphere -sf sessid", > > which gives me the error "ERROR: rtopy.self.lh is not > retinotopy". Will changing the analysis name for > mkanalysis-sess fix this? > > Many thanks, > Daniel > > On Thu, Feb 16, 2012 at 11:16 AM, Douglas N 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 Daniel, sorry for the delay. Is it the case that you > only have > eccentricity? The retinotopy tools are designed to work > with both > eccen and polar. You can still do the same analysis, just use > -abblocked instead of -retinotopy. > doug > > Daniel Cole wrote: > > Hello Doug, > I don't mean to rush your response, but, I was wondering if > you found any reason for why I'm getting this error? I've > been busy doing other analysis but I'm going to be > returning > to this data today and was hoping for your insight. > > Thanks again for taking the time, > Daniel > > On Fri, Feb 10, 2012 at 11:48 AM, Daniel Cole > <dcole10(a)u.rochester.edu > <mailto:dcole10@u.rochester.edu> <mailto:dcole10@u.rochester. > edu <mailto:dcole10@u.rochester.edu>> > <mailto:dcole10@u.rochester > <mailto:dcole10@u.rochester>. edu > > <mailto:dcole10@u.rochester. edu > <mailto:dcole10@u.rochester.edu>>>> wrote: > > Hi Doug, > Thanks for the response! > Here are the files you requested. > > Daniel > > > On Fri, Feb 10, 2012 at 11:44 AM, Douglas N 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>> > <mailto:greve@nmr.mgh.harvard > <mailto:greve@nmr.mgh.harvard>. edu > > <mailto:greve@nmr.mgh.harvard. edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Hi Daniel, can you send me the analysis.info > <http://analysis.info> > <http://analysis.info> > <http://analysis.info> and Xtmp.mat files? > > doug > > Daniel Cole wrote: > > > Hello Freesurfers, > > I think my last email failed to send so here > it is > again - > > > I'm running into problems using fs-fast for > a polar > only, > retinotopic analysis. > > > The error message I get is: > > > ********************* > > > Retinotopy dcole$ selxavg3-sess -analysis > rtopy.self.lh > -sf sessid > > Surface data self lh > > ------------------------------ > ------------------------------ -- > > selxavg3-sess logfile is > /rcbiUsers/dcole/Retinotopy/ > log/selxavg3-sess-bold-rtopy. > self.lh-120209144554.log > > ------------------------------ > ------------------------------ -- > > preproc-sess -s SUB01 -d > /rcbiUsers/dcole/Retinotopy -a > rtopy.self.lh -nolog > > ------------------------------ > ------------------------------ -- > > preproc-sess logfile is /dev/null > > ------------------------------ > ------------------------------ -- > > $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 > greve Exp $ > > dcole > > setenv FREESURFER_HOME /Volumes/RCBI/freesurfer > > setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/ > Retinotopy/Subjects/test > > Darwin commissure.local 11.2.0 Darwin Kernel > Version > 11.2.0: Tue Aug 9 20:54:00 PDT 2011; > root:xnu-1699.24.8~1/RELEASE_ X86_64 x86_64 > > /rcbiUsers/dcole/Retinotopy > > /Volumes/RCBI/freesurfer/ > fsfast/bin/preproc-sess > > -s SUB01 -d /rcbiUsers/dcole/Retinotopy -a > rtopy.self.lh > -nolog > > Thu Feb 9 14:45:54 EST 2012 > > instem f > mc 1 f fmcpr > stc 0 fmcpr > > sm 0 mask 1 brain > > SUB01 Template ----------------------------- > > mktemplate-sess -s SUB01 -d > /rcbiUsers/dcole/Retinotopy > -fsd bold -nolog -update > > Session: > /rcbiUsers/dcole/Retinotopy/ > SUB01 ---------------- > > > Thu Feb 9 14:45:54 EST 2012 > > Detected input format at nii > > SUB01 Update not needed > > Run: 001 ---------------- > > Thu Feb 9 14:45:54 EST 2012 > > SUB01 001 Update not needed > > Run: 002 ---------------- > > Thu Feb 9 14:45:54 EST 2012 > > SUB01 002 Update not needed > > Run: 003 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 003 Update not needed > > Run: 004 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 004 Update not needed > > Run: 005 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 005 Update not needed > > Thu Feb 9 14:45:55 EST 2012 > > mktemplate-sess completed > SUB01 Mask ------------------------ > > mkbrainmask-sess -maskstem brain -fsd bold > -s SUB01 -d > /rcbiUsers/dcole/Retinotopy -nolog -update > > ------------------------------ > ------------------ > > /rcbiUsers/dcole/Retinotopy/ SUB01 > Thu Feb 9 14:45:55 EST 2012 > > SUB01 Update not needed for session-level mask > > SUB01 Update not needed for run 001 mask > > SUB01 Update not needed for run 001 meanval > > SUB01 Update not needed for run 002 mask > > SUB01 Update not needed for run 002 meanval > > SUB01 Update not needed for run 003 mask > > SUB01 Update not needed for run 003 meanval > > SUB01 Update not needed for run 004 mask > > SUB01 Update not needed for run 004 meanval > > SUB01 Update not needed for run 005 mask > > SUB01 Update not needed for run 005 meanval > > Thu Feb 9 14:45:55 EST 2012 > > mkbrainmask-sess done > > SUB01 Registration ----------------------------- > > register-sess -s SUB01 -d > /rcbiUsers/dcole/Retinotopy -fsd > bold -dof 6 -per-run -nolog -update > > ------------------------------ > ------------------------------ -- > > register-sess logfile is /dev/null > > ------------------------------ > ------------------------------ -- > > Thu Feb 9 14:45:55 EST 2012 > > > setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/ > Retinotopy/Subjects/test > > cd /rcbiUsers/dcole/Retinotopy > > /Volumes/RCBI/freesurfer/ > fsfast/bin/register-sess -s > > SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd > bold -dof 6 > -per-run -nolog -update > > > freesurfer-Darwin-leopard- > i686-stable-pub-v5.1.0 > > > Darwin commissure.local 11.2.0 Darwin Kernel > Version > 11.2.0: Tue Aug 9 20:54:00 PDT 2011; > root:xnu-1699.24.8~1/RELEASE_ X86_64 x86_64 > > Session: > /rcbiUsers/dcole/Retinotopy/ > SUB01 ---------------- > > > Thu Feb 9 14:45:55 EST 2012 > > Run: 001 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 002 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 003 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 004 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 005 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Thu Feb 9 14:45:55 EST 2012 > > register-sess completed > SUB01 MC ----------------------------- > > mc-sess -fstem f -fmcstem fmcpr -s SUB01 -d > /rcbiUsers/dcole/Retinotopy -fsd bold -per-run > -nolog -update > > Logfile is /dev/null > > ------------------------------ ------------- > > /rcbiUsers/dcole/Retinotopy/ SUB01 > RunList: 001 002 003 004 005 > > SUB01 001 Update not needed > > SUB01 002 Update not needed > > SUB01 003 Update not needed > > SUB01 004 Update not needed > > SUB01 005 Update not needed > > > > Thu Feb 9 14:45:55 EST 2012 > > mc-sess completed SUCCESSFULLY > > SUB01 To Surface ----------------------------- > > rawfunc2surf-sess -fwhm 5 -s SUB01 -d > /rcbiUsers/dcole/Retinotopy -fsd bold -hemi > lh -self > -nolog -update > > instem fmcpr > > outstem fmcpr.sm5.self.hemi > > ------------------------------ > 1/1 SUB01 > > 1/1 SUB01 001 lh --------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 001 Update not needed > > 1/1 SUB01 002 lh --------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 002 Update not needed > > 1/1 SUB01 003 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > SUB01 003 Update not needed > > 1/1 SUB01 004 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > SUB01 004 Update not needed > > 1/1 SUB01 005 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > SUB01 005 Update not needed > > > Thu Feb 9 14:45:56 EST 2012 > > rawfunc2surf-sess completed > ------------------------------ ---------- > > Started at Thu Feb 9 14:45:54 EST 2012 > > Ended at Thu Feb 9 14:45:56 EST 2012 > > preproc-sess done > > ------------------------------ ------------- > > /rcbiUsers/dcole/Retinotopy/ SUB01 > Thu Feb 9 14:45:56 EST 2012 > > anadir = /rcbiUsers/dcole/Retinotopy/ > SUB01/bold/rtopy.self.lh > > DoGLMFit = 1 > > DoContrasts = 1 > > UpdateNeeded = 1 > > ------------------------------ ------------ > > ------- matlab output -------------------- > > Warning: Unable to open display 'iconic'. > You will > not be > able to display graphics on the screen. > > 2012-02-09 14:45:56.773 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.775 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.776 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.777 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.778 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.779 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.780 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.781 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.783 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.796 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.797 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.798 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.812 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.813 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:56.815 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > > < M A T L A B (R) > > > Copyright 1984-2010 The > MathWorks, > Inc. > > Version 7.10.0.499 (R2010a) > 64-bit > (maci64) > > February 5, 2010 > > > 2012-02-09 14:45:57.634 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.636 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.636 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.637 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.638 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.639 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.639 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.640 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.641 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.642 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.643 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.643 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.644 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.645 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.646 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.646 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.647 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.648 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.649 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.649 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.650 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.651 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.651 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.652 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.653 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.654 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.654 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.655 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.656 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.657 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.657 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.658 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.659 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.660 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.660 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.661 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.662 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.663 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.663 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.664 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.665 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.666 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.666 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.667 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.668 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.669 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.669 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > 2012-02-09 14:45:57.670 MATLAB[17738:7103] This > process is > attempting to exclude an item from Time > Machine by path > without administrator privileges. This is not > supported. > > To get started, type one of these: > helpwin, helpdesk, or > demo. > > For product information, visit > www.mathworks.com <http://www.mathworks.com> > <http://www.mathworks.com> > <http://www.mathworks.com> > <http://www.mathworks.com/>. > > > >> >> >> >> >> >> >> > /Volumes/RCBI/freesurfer/ > fsfast/toolbox/fast_selxavg3.m > > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > >> >> > >> >> > >> >> > > #@# SUB01 ############################## # > > /rcbiUsers/dcole/Retinotopy/ SUB01 > > > ------------------------- > > $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 > greve Exp $ > > /Volumes/RCBI/freesurfer/ > fsfast/toolbox/fast_selxavg3.m > > /Volumes/RCBI/freesurfer/ > fsfast/toolbox/fast_ldanaflac. m > > /Volumes/RCBI/freesurfer/ matlab/MRIread.m > > ------------------------- > > outtop = /rcbiUsers/dcole/Retinotopy > > Extension format = nii.gz > > nruns = 5 > > autostimdur = > > > outanadir = /rcbiUsers/dcole/Retinotopy/ > SUB01/bold/rtopy.self.lh > > Found 15746/149363 <tel:15746%2F149363> > <tel:15746%2F149363> > <tel:15746%2F149363> > <tel:15746%2F149363> (10.5) voxels in mask > > > Creating Design Matrix > > ... creation time = 0.011 sec > > DoMCFit = 1 > > ntptot = 1305, nX = 39, DOF = 1266 > > Saving X matrix to /rcbiUsers/dcole/Retinotopy/ > SUB01/bold/rtopy.self.lh/Xtmp. mat > > ??? Error using ==> svd > > Input to SVD must not contain NaN or Inf. > > > Error in ==> cond at 40 > > s = svd(A); > > > Error in ==> fast_selxavg3 at 254 > > XCond = cond(XtX); > > >> ------------------------------ > ------------ > > ERROR: fast_selxavg3() failed\n > > > ********************* > > > I think the problem is with the "??? Error > using ==> > svd... " error, not the matlab errors. I've > found that > many people were reporting this matlab error > but it's > presumably more of an annoyance than a > technical issue. > > > I'm following the tutorial at > http://surfer.nmr.mgh.harvard. edu/fswiki/ > FsFastIndividualRetinotopyAnal ysis > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > <http://harvard.edu/fswiki/> > FsFastIndividualRetinotopyAnal ysis > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > FsFastIndividualRetinotopyAnal ysis > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis>>> > . I'm pretty sure I have my directories set up > properly > and I've used Mricron's dcm2nii tool on my raw > functionals/structurals. I've also already > successfully > preprocessed my data and made the rtopy.par > files > (preproc-sess & mkanalysis-sess). > > I haven't been able to find a response that > fixed the > problem and was hoping for some suggestions. > > > Thanks so much, > > Daniel > > > -- > Daniel Cole > > University of Rochester > > Brain and Cognitive Sciences > > dcole10(a)u.rochester.edu > <mailto:dcole10@u.rochester.edu> > <mailto:dcole10@u.rochester. edu > <mailto:dcole10@u.rochester.edu>> <mailto:dcole10@u.rochester > <mailto:dcole10@u.rochester>. > edu <mailto:dcole10@u.rochester. edu > <mailto:dcole10@u.rochester.edu>>> > <mailto:dcole10@u.rochester > <mailto:dcole10@u.rochester> > <mailto:dcole10@u.rochester > <mailto:dcole10@u.rochester>>. edu > > <mailto:dcole10@u.rochester > <mailto:dcole10@u.rochester>. edu > <mailto:dcole10@u.rochester. edu > <mailto:dcole10@u.rochester.edu>>>> > > > ------------------------------ > ------------------------------ ------------ > > ______________________________ _________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh > <mailto:Freesurfer@nmr.mgh>. harvard.edu <http://harvard.edu> > > <mailto:Freesurfer@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard. > edu/mailman/listinfo/ > freesurfer > > <https://mail.nmr.mgh.harvard. > edu/mailman/listinfo/ freesurfer > <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > <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> > <mailto:greve@nmr.mgh.harvard. edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard > <mailto:greve@nmr.mgh.harvard>. edu > > <mailto:greve@nmr.mgh.harvard. edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> Fax: > 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: surfer.nmr.mgh.harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/> > <http://surfer.nmr.mgh. harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/>> fswiki/BugReporting > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > <http://harvard.edu/fswiki/> > BugReporting > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > FileDrop: www.nmr.mgh.harvard.edu/ > <http://www.nmr.mgh.harvard.edu/> > <http://www.nmr.mgh.harvard. edu/ > <http://www.nmr.mgh.harvard.edu/>> > facility/filedrop/index.html > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > > > > 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 > <http://www.partners.org/ complianceline > <http://www.partners.org/ complianceline > <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. > > > > > -- Daniel Cole > University of Rochester > Brain and Cognitive Sciences > dcole10(a)u.rochester.edu > <mailto:dcole10@u.rochester.edu> <mailto:dcole10@u.rochester. > edu <mailto:dcole10@u.rochester.edu>> > <mailto:dcole10@u.rochester > <mailto:dcole10@u.rochester>. edu > <mailto:dcole10@u.rochester. edu > <mailto:dcole10@u.rochester.edu>>> > > > > > > > -- Daniel Cole > University of Rochester > Brain and Cognitive Sciences > dcole10(a)u.rochester.edu > <mailto:dcole10@u.rochester.edu> <mailto:dcole10@u.rochester. > edu <mailto:dcole10@u.rochester.edu>> > <mailto:dcole10@u.rochester > <mailto:dcole10@u.rochester>. edu <mailto:dcole10@u.rochester. > edu <mailto:dcole10@u.rochester.edu>>> > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard. edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/> fswiki/BugReporting > <http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: www.nmr.mgh.harvard.edu/ > <http://www.nmr.mgh.harvard.edu/> facility/filedrop/index.html > <http://www.nmr.mgh.harvard. edu/facility/filedrop/index. > html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > > > -- > Daniel Cole > University of Rochester > Brain and Cognitive Sciences > dcole10(a)u.rochester.edu <mailto:dcole10@u.rochester.edu> > <mailto:dcole10@u.rochester. edu <mailto:dcole10@u.rochester.edu>> > > > -- > 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: www.nmr.mgh.harvard.edu/ facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Daniel Cole > University of Rochester > Brain and Cognitive Sciences > dcole10(a)u.rochester.edu <mailto:dcole10@u.rochester.edu> > > > ------------------------------------------------------------------------ > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

mri_glmfit-sim with cache option
by Antonella Kis 16 Feb '12

16 Feb '12

Dear Doug, Is possible to get more clusters if I correct by multiple comparisons so I run: mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .999 \ --overwrite than the number of clusters in the sig.mgh so the uncorrected results? cwpvalthresh .999 allows me to see all the clusters. Are this all the clusters after multiple comparisons regardless of significance? Thank you. AK

2 1

bash freesurferstats2table script
by Fidel Vila 16 Feb '12

16 Feb '12

Hi there, I was wondering if it would be possible to obtain a copy of the freesurferstats2table script that is posted on the Wiki. When I try to access it it requests a user name and password (I tried my mailing list username and psswd, but didn't work). Greatly appreciate it, Fidel

1 0

whole brain volume
by Dana W. Moore 16 Feb '12

16 Feb '12

Hi everyone, Previous versions of FreeSurfer had a whole brain measure in the aseg.stats file called BrainSegVolNotVent. The newest version no longer has this. I am wondering where I can now find a measure of whole brain volume? Thanks, Dana -- Dana W. Moore, Ph.D. Instructor of Neuropsychology Department of Neurology & Neuroscience Weill Cornell Medical College 428 East 72nd Street, Suite 500 New York, NY 10021

2 6

Structural Group Analysis vs. DTI Group Analysis
by Antonella Kis 16 Feb '12

16 Feb '12

Dear all, I completed my DTI group analysis at subcortical level on the CVS space and found clusters that survived by multiple comparisons. The results shows that FA is decreasing in patients vs. controls. I used then the same subject to do a structural group analysis to compare the cortical thickness between the two classes. I found some clusters on the fsaverage but this time they different located then the clusters found in my DTI data. Is this right? I suppose it should be since I compare two different data sets for the same subjects: FA clusters on subcortical CVS space vs. structural data on the fsaverage. I still found that my cortical thickness is decreasing in patients vs. controls but is there any relation that I can established between the two studies? Can I merge my structural results with my subcortical results? I was reading about this on your webpage:http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastG… but I am not sure if in this case the structural analysis is using the same functional data set while in my case I have same subjects but structural data for the structural group analysis and DTI data for the subcortical analysis. Can you please make this a little clear for me? Thank you very much! Antonella

1 1

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Freesurfer February 2012