Freesurfer May 2011

freesurfer@nmr.mgh.harvard.edu

120 participants
155 discussions

tkmedit
by Michelle Umali 12 May '11

12 May '11

Dear Freesurfers, I've noticed some problems in some inflated brains with the curvature displayed that I know will require manual intervention: -random spots of abnormally intense green or very intense red -tiny protrusions -falx cerebri obscuring parietal region -subcallosal splotches of red-green I've been reading the troubleshooting webpages, but I am not sure what is causing the above issues. Any suggestions on the appropriate edits would be greatly appreciated. Thanks. Michelle

2 3

Re: [Freesurfer] Interpreting results from Qdec
by Gallen, Courtney (NIH/NIDA) [F] 12 May '11

12 May '11

Thanks for the reply! I'm fairly certain that I'm using the same model. In Qdec: 2 discrete variables, 1 nuisance variable. In SPSS: a univariate ANOVA with 2 factors and 1 covariate. I understand the difference between Qdec and SPSS may be because Qdec looks at the entire cortex. Are there any realistic ways to work around this using something like SPSS? All I really want is to generate a figure with means for each of my groups, so I can understand what's driving the interaction. Any other suggestions about how to do so? -----Original Message----- From: greve(a)nmr.mgh.harvard.edu [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, April 28, 2011 9:06 AM To: Gallen, Courtney (NIH/NIDA) [F] Subject: Re: [Freesurfer] Interpreting results from Qdec Hi Courtney, a couple of suggestions: 1. make sure that QDEC and SPSS are using the identical model. 2. make sure that the values that you are extracting the same as the input to QDEC/glmfit (eg, don't use thickness for one and volume for another). It is possible for the ROI analysis to give very different results, but it usually requires that you select the voxels based on an unsigned statistic (eg, an F-test). This opens the possibility that positives and negatives in the ROI sum to 0. doug > Thanks Jesse. This does sound very similar to my issue. > > How did you resolve the problem? > > Thanks again! > > From: jessebledsoe(a)gmail.com [mailto:jessebledsoe@gmail.com] On Behalf Of > Jesse Bledsoe > Sent: Wednesday, April 27, 2011 1:19 PM > To: Gallen, Courtney (NIH/NIDA) [F]; Freesurfer Mailing List > Subject: Re: [Freesurfer] Interpreting results from Qdec > > Hi Courtney, > > I'm no expert but I recalled a post similar to yours awhile ago with the > same question you ask. Doug and Nick offered an answer that may be of > help: > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15586.html > > Jesse > On Wed, Apr 27, 2011 at 1:12 PM, Gallen, Courtney (NIH/NIDA) [F] > <gallencl(a)nida.nih.gov<mailto:gallencl@nida.nih.gov>> wrote: > Hi Doug > > Have a follow up question regarding significance levels in Qdec related to > extracting means from ROIs, etc. I'm posting to the entire mailing list in > case anyone else has ideas. > > Basically, I extracted mean volumes (from my set of participants) of ROIs > for which Qdec reports an interaction between two variables. I want to > look at these mean volumes in something like SPSS to see what is driving > the interaction/generate figures, etc. > > I'm having an issue with one such ROI, in that when I extract the mean > volumes and look for this interaction in SPSS, it is not significant (p ~ > 0.5, so really not significant at all). Is there any way that an ROI could > be significant in Qdec (p of 0.05, Monte Carlo sim), but not in SPSS when > I extract means for each participant? > > Let me know if this isn't clear. Any thoughts would be appreciated! > Courtney > > > Courtney Gallen > Post-baccalaureate IRTA > Neuroimaging Research Branch > National Institute on Drug Abuse (IRP) > 251 Bayview Blvd > Suite 200 > Baltimore, MD 21224 > Tel: (443) 740-2631<tel:%28443%29%20740-2631> > > -----Original Message----- > From: Douglas Greve > [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] > Sent: Tuesday, April 26, 2011 1:06 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Subject: Re: [Freesurfer] Interpreting results from Qdec > > Those are the values outside (first column) and inside (2nd col) the > ROI. You can add "--id 1" to only report the values inside the ROI. > > doug > > On 4/26/11 1:02 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >> It worked! >> Now, last question. The txt file has two separate values (?averages). >> What do they each represent? >> >> -----Original Message----- >> From: Douglas Greve >> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >> Sent: Tuesday, April 26, 2011 12:53 PM >> To: Gallen, Courtney (NIH/NIDA) [F] >> Subject: Re: [Freesurfer] Interpreting results from Qdec >> >> try "--slabel fsaverage lh ROI-drawn-on-QDEC-brain.label" >> >> >> On 4/26/11 12:52 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>> Actually, I hope I'm wrong about what I thought below. If I specify >>> individual subject's label and run: >>> >>> mri_segstats --in >>> /prot/Mprot/CTQ/freesurferDone/8579/surf/lh.volume.fwhm10.fsaverage.mgh >>> --slabel 8579 lh >>> /prot/Mprot/CTQ/freesurferDone/8579/label/lh.SupTemp_CTQxBDNFctrls.label >>> --avgwf lhSupTempctrls.txt >>> >>> I still get the same error about dimension mismatch >>> >>> >>> -----Original Message----- >>> From: Gallen, Courtney (NIH/NIDA) [F] >>> Sent: Tuesday, April 26, 2011 12:43 PM >>> To: 'Douglas Greve' >>> Subject: RE: [Freesurfer] Interpreting results from Qdec >>> >>> Ah I think I see the problem now. >>> >>> The label I originally specified is the general label created from the >>> ROI drawing in Qdec. Instead, I should use the individual subject's >>> label (from 'Map Label to Subjects') instead, right? >>> >>> Thank you! >>> >>> -----Original Message----- >>> From: Douglas Greve >>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>> Sent: Tuesday, April 26, 2011 12:38 PM >>> To: Gallen, Courtney (NIH/NIDA) [F] >>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>> >>> You have to use the subject that matches the input, fsaverage in this >>> case. How did you define your label? If you defined it on subject 123, >>> you can transfer it to fsaverage using mri_label2label. >>> doug >>> >>> On 4/26/11 12:28 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>>> Not a problem at all! >>>> >>>> If I use --in, I get an error saying that there is a dimension >>>> mismatch between input volume and seg. >>>> >>>> Any other thoughts? Thanks again! >>>> >>>> -----Original Message----- >>>> From: Douglas Greve >>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>> Sent: Tuesday, April 26, 2011 11:40 AM >>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>> >>>> >>>> Hi Courtney, sorry for the delay. If more than a few days go by >>>> without >>>> a response, feel free to repost -- I promise not to get annoyed! >>>> Sometimes, things get pushed up and out of my mail browser window, and >>>> I >>>> often don't get back to them. Sorry! >>>> >>>> To answer your question, try using --in where you have --seg. The >>>> "segmentation" is actually already specified because you've specified >>>> a >>>> label. >>>> >>>> doug >>>> >>>> On 4/26/11 11:03 AM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>> Hi Doug, >>>>> Sorry to keep bugging you but any thoughts about my response to your >>>>> e-mail from 2 weeks ago? I've given the exact command line I'm using >>>>> with mri_segstats. >>>>> Thanks again for all your help >>>>> Courtney >>>>> >>>>> -----Original Message----- >>>>> From: Gallen, Courtney (NIH/NIDA) [F] >>>>> Sent: Tuesday, April 12, 2011 10:59 AM >>>>> To: 'Douglas N Greve' >>>>> Subject: RE: [Freesurfer] Interpreting results from Qdec >>>>> >>>>> That may be the problem. ${sub} is an actual person's directory >>>>> >>>>> E.g., sub# 123--command line would be: >>>>> mri_segstats --seg >>>>> /prot/Mprot/CTQ/freesurferDone/123/surf/lh.volume.fwhm10.fsaverage.mgh >>>>> --slabel 123 lh \ >>>>> lh.SupTemp_CTQxBDNFctrls.label --avgwf lhSupTempctrls.txt >>>>> >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: Douglas N Greve >>>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>>> Sent: Tuesday, April 12, 2011 10:55 AM >>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>> >>>>> What is your full command-line? Without variables, just something >>>>> that >>>>> you could put directly into the terminal. Make sure that you are >>>>> specifying fsaverage as your subject (can't tell below because your >>>>> use >>>>> ${sub}). >>>>> >>>>> doug >>>>> >>>>> >>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>> Sorry, but I can't seem to figure out how to specify input data. I >>>>>> tried '--in' but get an error that the input vol and seg label are >>>>>> not the same dimensions. I've been looking at the help options for >>>>>> mri_segstats (http://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats) >>>>>> but don't see it >>>>>> >>>>>> -----Original Message----- >>>>>> From: Douglas N Greve >>>>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>>>> Sent: Friday, April 08, 2011 10:38 AM >>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>> >>>>>> The lh.volume.fwhm10.fsaverage.mgh should be your input. It is not >>>>>> a >>>>>> segmentation. You've already specified the seg with the the --slabel >>>>>> command. >>>>>> doug >>>>>> >>>>>> >>>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>> >>>>>>> One last question (hopefully). I'm specifying the input volume with >>>>>>> --seg, but am getting an error ('cannot do frame average without >>>>>>> input volume'). Am I missing something obvious? >>>>>>> >>>>>>> The entire command looks something like this: >>>>>>> mri_segstats --seg >>>>>>> /prot/Mprot/CTQ/freesurferDone/${sub}/surf/lh.volume.fwhm10.fsaverage.mgh >>>>>>> --slabel ${sub} lh \ >>>>>>> lh.SupTemp_CTQxBDNFctrls.label --avgwf lhSupTempctrls.txt >>>>>>> >>>>>>> Thanks again >>>>>>> -----Original Message----- >>>>>>> From: Douglas N Greve >>>>>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>>>>> Sent: Tuesday, April 05, 2011 4:21 PM >>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>> Cc: Nick Schmansky; Freesurfer Mailing List >>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>> >>>>>>> yes, something like ?h.volume.fwhm10.fsaverage.mgh >>>>>>> doug >>>>>>> >>>>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>>> >>>>>>> >>>>>>>> Hi Doug >>>>>>>> >>>>>>>> Thanks for helping me with this! >>>>>>>> >>>>>>>> First time around I did everything as is outlined in 'Define a >>>>>>>> Region of Interest' here: >>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis. >>>>>>>> >>>>>>>> I'll try your suggestion now. The input data would be something >>>>>>>> like ?h.volume.fwhm10.fsaverage.mgh, correct? >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Courtney >>>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: Douglas N Greve >>>>>>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>>>>>> Sent: Thursday, March 31, 2011 5:44 PM >>>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>>> Cc: Nick Schmansky; Freesurfer Mailing List >>>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>>> >>>>>>>> Hi Courtney, did you transfer the label to each individual subject >>>>>>>> using >>>>>>>> mri_label2label? A better way to replicate your qdec results is to >>>>>>>> run >>>>>>>> mri_segstats on the input data to qdec (y.mgh usually). Specify >>>>>>>> the >>>>>>>> label with "--slabel subject hemi yourlabel". Also specify >>>>>>>> "--avgwf >>>>>>>> subjectdata.txt". This will create this text file with a list of >>>>>>>> the >>>>>>>> input data for each subject averaged over your label. >>>>>>>> >>>>>>>> doug >>>>>>>> >>>>>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Hi Nick >>>>>>>>> >>>>>>>>> I'm revisiting this issue and have a few more questions. First, I >>>>>>>>> have a significant interaction between two variables on cortical >>>>>>>>> volume. I drew a label on this ROI and ran mris_anatomical_stats >>>>>>>>> on the label (thank you for that suggestion). >>>>>>>>> >>>>>>>>> For stats in the output table file, is the column 'GrayVol' the >>>>>>>>> same thing as the cortical volume I looked at in Qdec? I'm asking >>>>>>>>> because when I export GrayVol values into SPSS, there is no >>>>>>>>> longer a significant interaction between my variables (and if >>>>>>>>> this ROI is significant after multiple comparisons across the >>>>>>>>> brain, I'd expect the mean volume from the ROI to be very >>>>>>>>> significant in SPSS). >>>>>>>>> >>>>>>>>> Please let me know if my questions aren't clear. Thanks in >>>>>>>>> advance >>>>>>>>> Courtney >>>>>>>>> >>>>>>>>> >>>>>>>>> Courtney Gallen >>>>>>>>> Post-baccalaureate IRTA >>>>>>>>> Neuroimaging Research Branch >>>>>>>>> National Institute on Drug Abuse (IRP) >>>>>>>>> 251 Bayview Blvd >>>>>>>>> Suite 200 >>>>>>>>> Baltimore, MD 21224 >>>>>>>>> Tel: (443) 740-2631<tel:%28443%29%20740-2631> >>>>>>>>> >>>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: Nick Schmansky >>>>>>>>> [mailto:nicks@nmr.mgh.harvard.edu<mailto:nicks@nmr.mgh.harvard.edu>] >>>>>>>>> Sent: Thursday, January 13, 2011 3:08 PM >>>>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>>>> Cc: Freesurfer Mailing List >>>>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>>>> >>>>>>>>> Courtney, >>>>>>>>> >>>>>>>>> if i understand your question, i think one way to do that is to >>>>>>>>> use qdec >>>>>>>>> to draw a label on the blob of interest, and the run 'map label >>>>>>>>> to >>>>>>>>> subjects', which creates a label file in each subjects label dir, >>>>>>>>> then >>>>>>>>> you can run stats on that with mris_anatomical_stats. >>>>>>>>> >>>>>>>>> (btw, i'm putting this answer on the list, as others may have >>>>>>>>> better >>>>>>>>> ideas.) >>>>>>>>> >>>>>>>>> n. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) >>>>>>>>> [F] >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hi Nick >>>>>>>>>> >>>>>>>>>> Thanks for the prompt reply. Sorry if my questions seem a bit >>>>>>>>>> naïve--this is my first time using Freesurfer. >>>>>>>>>> >>>>>>>>>> A follow up question to your answer for question 1. I see that >>>>>>>>>> the group data will be plotted in Qdec for significant blobs, >>>>>>>>>> but say there is a significant interaction between two variables >>>>>>>>>> and it's not entirely apparent what is driving this interaction. >>>>>>>>>> Is there a way to extract the mean of this blob for each >>>>>>>>>> individual (i.e., treat it as an ROI or something similar) to >>>>>>>>>> determine what's driving the significance? >>>>>>>>>> >>>>>>>>>> Thanks in advance! >>>>>>>>>> Courtney >>>>>>>>>> >>>>>>>>>> -----Original Message----- >>>>>>>>>> From: Nick Schmansky >>>>>>>>>> [mailto:nicks@nmr.mgh.harvard.edu<mailto:nicks@nmr.mgh.harvard.edu>] >>>>>>>>>> Sent: Thursday, December 30, 2010 2:44 PM >>>>>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>>>>> Cc: >>>>>>>>>> freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>>>>> >>>>>>>>>> ans. 1. - the easiest way is to Ctrl- left mouse click on a >>>>>>>>>> blob, and a >>>>>>>>>> plot of the data at that surface vertex will appear. the group >>>>>>>>>> will be >>>>>>>>>> apparent from that (say, demented group is thinner than >>>>>>>>>> non-demented >>>>>>>>>> group). this data is significance data (log p, so '2' is 0.01), >>>>>>>>>> so mean >>>>>>>>>> and stdev wouldnt apply in that case. the file 'y.mgh' is the >>>>>>>>>> raw data >>>>>>>>>> of all subjects in the analysis, so you could extract mean and >>>>>>>>>> stdev >>>>>>>>>> from that. >>>>>>>>>> >>>>>>>>>> ans. 2. - slide the 'annotation' opacity slider to show the >>>>>>>>>> annotation >>>>>>>>>> data (cortical parcellation). the ctrl left click will also put >>>>>>>>>> the >>>>>>>>>> region info for that vertex on the lower left of the display. >>>>>>>>>> >>>>>>>>>> see also: >>>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis >>>>>>>>>> >>>>>>>>>> n. >>>>>>>>>> >>>>>>>>>> On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) >>>>>>>>>> [F] >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I'm currently running analyses in Qdec and have identified >>>>>>>>>>> areas that >>>>>>>>>>> show significant effects in my contrasts. I have two questions >>>>>>>>>>> related >>>>>>>>>>> to interpreting these results. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> 1. How can you interpret the effect in each "blob?" (i.e., >>>>>>>>>>> which >>>>>>>>>>> group has a greater cortical surface area, etc.). Right now, >>>>>>>>>>> all I >>>>>>>>>>> know is that there is an effect in certain areas. Can you >>>>>>>>>>> export this >>>>>>>>>>> data to get means and standard errors? >>>>>>>>>>> >>>>>>>>>>> 2. Is there a way to localize where these effects are? >>>>>>>>>>> E.g., a >>>>>>>>>>> tool that tells you this effect is located in __ area of the >>>>>>>>>>> brain? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Thanks in advance >>>>>>>>>>> >>>>>>>>>>> Courtney >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Courtney Gallen >>>>>>>>>>> >>>>>>>>>>> Post-baccalaureate IRTA >>>>>>>>>>> >>>>>>>>>>> Neuroimaging Research Branch >>>>>>>>>>> >>>>>>>>>>> National Institute on Drug Abuse (IRP) >>>>>>>>>>> >>>>>>>>>>> 251 Bayview Blvd >>>>>>>>>>> >>>>>>>>>>> Suite 200 >>>>>>>>>>> >>>>>>>>>>> Baltimore, MD 21224 >>>>>>>>>>> >>>>>>>>>>> Tel: (443) 740-2631<tel:%28443%29%20740-2631> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Jesse C. Bledsoe, M.A. > Ph.D. Candidate, Clinical Psychology > Consortium for Neurodevelopmental Study > Department of Psychology > 110E Psychology Building > Michigan State University > East Lansing, MI 48824 > ______________________________________ > > Note: Information contained in this electronic message and any attachments > to this message are intended for the exclusive use of the addressee(s) and > may contain proprietary, confidential or privileged information. If you > are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies > of > this message and any attachments. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 6

non-white residuals in ROI-based contrast
by Pablo Polosecki 12 May '11

12 May '11

Hello List, I want to run an F-test on a ROI (I selected the voxels with some criterion). If I understand correctly the way to do it is by computing the F-statistic using: F=(roi_betas'*X'*M*X*roi_betas)/(Y'*R*Y)*(J-p)/p1 where: roi_betas are the average beta values across the roi X is the design matrix M is the projection matrix to the space generated by the reduced model given by my contrast matrix Y is the average time course of the ROI R is the residual generating matrix. J-p are the total degrees of freedom, and p1 are the degrees of freedom given by my contrast matrix I am noticing that the residuals are not whitened (the is noticeable auto-correlation in the ROI-averaged residuals that lasts ~10 timepoints). Could someone recommend a relatively simple way to correct for this auto-correlation (and avoid reinventing the weel in matlab)? Thanks in advance! Pablo

1 0

mri_nu_correct.mni segmentation fault
by Nikolas Borrel-Jensen 11 May '11

11 May '11

Hi all. I have two subjects where the mri_nu_correct.mni in the autorecon1 step is aborting: $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16617/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16617/nu0.mnc -odt float ncendef: ncid 3: No space left on device Error outputting volume: possibly disk full? Segmentation fault ... and there is plenty of space on the disk. Trying to run the command afterwards with mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2, I get a bit further mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22259/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22259/nu0.mnc -odt float mri_convert: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.22259/nu0.mnc... Abort ERROR: converting to minc It works for all other subjects. Can anybody help me with that? The orig.mgz file can be found here: http://freesurfer.nikolasborrel.com/ Kind regards, Nikolas

2 1

Memory problem with mri_glmfit
by Ed Gronenschild 11 May '11

11 May '11

Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this. Ed

3 8

Error when loading qdec project file
by Natalia Francisca 11 May '11

11 May '11

Dear freesurfer list, I have got this message while trying to load the saved project file ln -s /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/fsaverage/label/*.aparc.annot /tmp/qdec_project_archive/fsaverage/label ln -s /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/qdec/lh-curva_aprendizaje-thickness-fwhm10 /tmp/qdec_project_archive ln -s /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/qdec/qdec.table.dat /tmp/qdec_project_archive cp /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/qdec/*.levels /tmp/qdec_project_archive cd /tmp; zip -r /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/qdec/lh-thickness-fwhm10.qdec qdec_project_archive > /dev/null rm -rf /tmp/qdec_project_archive Saving project file done. Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. When saving there is no error message, but when trying to load the saved project file, then the error pops up, any idea is appreciated. Natalia.

2 5

freeview
by swoodman＠nmr.mgh.harvard.edu 11 May '11

11 May '11

Hello all! I have a question regarding using freeview. When doing a 3D rengering of t-maps, there is a setting that allows you to view clusters with peak t scores. When we do this peak t scores are included in two clusters. We wish to only show ONE cluster for an image we are creating. How does one get rid of a cluster, ie only show the one of interest? Thank you! Sandra

1 0

Support for PPC Mac
by Ed Gronenschild 11 May '11

11 May '11

Hi, A while ago we were asked if still support was needed for FreeSurfer on a PPC Mac. I was one of the "happy" few who needed this. But I now can inform you that as far as I'm concerned you can discontinue this support. Thank you for all your support sofar. Ed

3 3

Temporal lobe tracing abnomality uncorrected by control points
by Moiyadi, Ammar 10 May '11

10 May '11

Dear Freesurfers, Freesurfer's autorecon is having trouble tracing both gray and white matter boundaries in the temporal region of one of my subjects (even after I added control points for the white matter). I have attached a png screen shot of this abnormality and was wondering if anyone has any ideas to correct this since I have never seen such a large tracing error before. Your input is much appreciated! Ammar

3 2

Testing FreeSurfer recon-all with 2 different head coils
by Gullett,Joseph M 10 May '11

10 May '11

Hello, Our University's MRI facility recently upgraded from an 8 channel to a 32 channel head coil. I have been doing some QC analyses to determine if this will affect our results with T1 enough to warrant a regression for the number of RF channels in the final study analysis. I ran FreeSurfer recon-all cortical measurements two times on the 8 channel T1's (I always do the recon-all with two consecutively acquired T1's), and two times on the 32 channel T1's. I did it twice on each because some members in our lab have mentioned that in the past they have re-ran the same analysis and got different results. This was not the case for me as I got identical results for both runs. I ran a t-test on all of the cortical results for 32 vs 8 channels and there is a significant difference p<.019 between the two in the LH aparc measurements, but no significant difference between the 8 and 32 channel scans in the RH aparc measurements (p<.280). Is there anything inherent to the method FreeSurfer uses for its' cortical measurements that would result in an inconsistency only in the left hemisphere, or is it safe to chalk this up to a difference between head coils? Also of note, the two sets of scans were done only 6 months apart on the same individual (me). Here is what I ran if it helps at all: recon-all -s FShc12_redo -i /data/birc/RESEARCH/DFITZGERALD_projects/664-2008/HC12/acqfiles/DICOM/T1-1/DICOM/o20101113_104703IM_0001T1W3DTFESENSE664-2008-HC12s601a1006.nii.gz -i /data/birc/RESEARCH/DFITZGERALD_projects/664-2008/HC12/acqfiles/DICOM/T1-2/DICOM/o20101113_104703IM_0001T1W3DTFESENSE664-2008-HC12s701a1007.nii.gz -autorecon-all and then, aparcstats2table --subjects FShc12_redo --hemi rh --meas thickness --tablefile aparc_rh_thickness_stats_May_10_2011.txt and aparcstats2table --subjects FShc12_redo --hemi lh --meas thickness --tablefile aparc_lh_thickness_stats_May_10_2011.txt Thank you in advance, Joe

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Freesurfer May 2011