Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

Error -FSGD file for clinical correlations please help
by Rajagopalan, Venkateswaran 27 Sep '11

27 Sep '11

Dear All, I am trying to correlate clinical disability measure ALSFRS score with cortical thickness in ALS patients. Attached is the fsgd file. I am not able to run mris_preproc with this fsgd file "ERROR message: is no subjects specified" what am I doing wrong here , also my design matrix contrast is 1 0 am I right. I am interested in seeing whether there any correlation between cortical thickness changes in ALS patients with their ALSFRS score. Thanks Venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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recommended WM lesion filling procedure?
by Mishkin Derakhshan 27 Sep '11

27 Sep '11

Hi, I have a bunch of scans from patients with mulitple sclerosis. Since they all have substantial t2w hyperintensities I would like to automate the process of WM filling and re-running. Looking through the emails and the wiki, however, I am a bit confused. http://www.freesurfer.net/fswiki/FsTutorial/ControlPoints says I should NOT use control points for white matter lesions: "Control points should NOT be used to try and normalize a brain lesion to 110. Such defects should be fixed with white matter edits" BUT, http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes says I should: "mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. A potential work-around is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and lesions voxels in aseg.mgz to 77 (lesion mask can be derived manually or from an automated algorithm), then run recon-all -autorecon2-cp." I'm assuming that the guidance in the release notes supersedes the other wiki page but I wanted to make sure. thanks, mishkin

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QDEC stats table output
by Antonella Kis 27 Sep '11

27 Sep '11

Hi, After running QDEC, I would like to output in a table the thickness values within each clusters. I know this is a dependent variable and I can see the values on the plot but is there a way that I can get this values in a table? Thanks, Antonella ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc: carolina.mr <carolina.mr(a)uol.com.br>; David Kennedy <dave(a)nmr.mgh.harvard.edu>; freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, September 23, 2011 11:38 AM Subject: Re: [Freesurfer] QDEC results and stats The "value" is the dependent variable (eg, thickness). doug Bruce Fischl wrote: > Hi Carolina > > I'll leave the 2nd question for Doug and Nick. The first one, I think > you mean "ventral DC", which is short for "ventral diencephalon". It's > a grab bag of a bunch of stuff that we can't resolve. You would need > to check with someone like Dave Kennedy (ccd) to get the exact > description. > > cheers > Bruce > > On Fri, 23 Sep 2011, carolina.mr wrote: > >> >> Hello, all, >> >> I have 2 questions: >> >> - Does anybody know which structure is represented or correspond to >> "left ventral IDC" in aseg segmentation? >> >> - In QDEC analysis, when we obtatin the significant clusters and see >> the linear regression or correlation curve, what does it mean the >> "value" of the curve? Is it the regression coeficient? The level of >> correlation? How shall I describe it? >> >> Thank you, Carolina >> >> >> > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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retinotopy analysis: tksurfer-sess dimension error between mask and surf
by Michelle Umali 27 Sep '11

27 Sep '11

Dear Freesurfers, I am working on a retinotopy analysis and I got this error: ERROR: dimension mismatch between mask and surf when trying to look at map angle in tksurfer-sess Do I need to add --reshape flag? If so, where? Any help would be most appreciated. Thanks. Michelle Here are the analysis commands I used the error output for viewing the map is below it : mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj07 -fsd bold -force selxavg3-sess -a rtopy.self.lh -s sj07 -force selxavg3-sess -a rtopy.self.rh -s sj07 -force fieldsign-sess -a rtopy.self.lh -occip -s sj07 fieldsign-sess -a rtopy.self.rh -occip -s sj07 This is the output when I tried to view in tksurfer-sess BOTANICA:/usr/local/freesurfer/subjects/retinotopy> tksurfer-sess -a rtopy.self.lh -s sj07 -map angle Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux Tue Sep 27 06:37:33 EDT 2011 /usr/local/freesurfer/bin/tksurfer list eccen polar con/map eccen /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz con/map polar /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz maplist /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz mri_concat /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz --o /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii cd /usr/local/freesurfer/subjects/retinotopy setenv SUBJECTS_DIR /usr/local/freesurfer/subjects tksurfer ld07 lh inflated -overlay /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid 3.00000000000000000000 -fslope .50000000000000000000 -mask /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz -mask-thresh 2 -fthresh .01 Contrasts 0 eccen 1 polar setting colscalebarflag to 1 setting fthresh to 2.0000 setting fmid to 3.0000 setting fslope to 0.5000 mrismaskfile /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz... setting mrismaskthresh to 2.0000 setting fthresh to 0.0100 subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/retinotopy checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=156145, faces=312286 tkmedit: Trying to open /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.dat surfer: Interpreting overlay volume /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii as registered functional volume. surfer: curvature read: min=-3.127128 max=2.364444 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 8162 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(ld07) Reading mris mask /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz ERROR: dimension mismatch between mask and surf

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Re: [Freesurfer] Thank you
by Douglas N Greve 27 Sep '11

27 Sep '11

You can't just go and regress out age. You first have to make sure that there is not an interaction between your age and group. That is done with the first step that I described using the DODS model. Both of the contrasts that you have below are for DODS, but you would only use the 2nd one. I know that you are not interested in age, but you have to test for an interaction with age first. If there is an interaction, then your contrast of interest (the difference between the group means) does not make sense. The first contrast below does test for a difference in the groups at age=0. If there is an interaction between age and group, then the difference between the groups becomes dependent on age. Eg, you can get a different difference if you test at age=0 vs age=50. If there is no difference between the age slopes of the groups, then you re-run the analysis using a DOSS model and test with a contrast of [1 -1 0]. doug Antonella Kis wrote: > Dear Doug, > > I'm very sorry to bother you so much but I am getting very confused > because on the GLM Group Analysis site I saw the following two situations: > > > Contrast 1 group.diff.mtx > > Null Hypothesis: is there a difference between the group intercepts? > Is there a difference between groups regressing out the effect of age? > 1 -1 0 0 > This is a t-test with Group1>Group2 being positive (red/yellow). > > > Contrast 2 group-x-age.mtx > > Null Hypothesis: is there a difference between the group age slopes? > Note: this is an interaction between group and age. Note: not possible > to test with DOSS. > 0 0 1 -1 > > So if I want to compare the two groups and consider age as a covariate (I am not interested in the effect of age on my cortical thickness) then should I go for the second case as you emailed me before? > I thought is the first case when we regress out the effect of age so we can see the differences in the cortical thickness between the two groups while age changes. > > I'm really sorry but I really > need your last advise. > > > Many, many thanks. > AK > > > > ------------------------------------------------------------------------ > *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, September 27, 2011 12:44 PM > *Subject:* Re: [Freesurfer] Thank you > > If you have two groups and you want to test for the differences in the > groups after you account for age, you need to do this in two steps. > First, set up a DODS model (ie, each group gets an intercept and a > slope). Use this to test for a difference between the slopes of the > groups ([0 0 1 -1]). If there is a difference, then you'll need to talk > to a statistician to figure out what to do. If there is no difference, > then set up a new DOSS model (ie, each group gets its own intercept but > they share a slope), then test the difference between the groups with [1 > -1 0]. > > doug > > Antonella Kis wrote: > > Thanks Doug, I followed your advise and it worked. > > I would like to ask you one more favour please: if using GLM I want to > > compare two groups and consider age as a covariate, does this mean > > that we account for age or we are regressing out the effect of age? Is > > this right? In this case can I consider the contrast matrix to be [1 > > 0] since we need to add zero for the variable which are covariate? > > > > Thank you. > > AK > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>> > > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Tuesday, September 27, 2011 11:17 AM > > *Subject:* Re: Clusters formation by FDR > > > > Why not run mri_glmfit-sim? It will give you the file that you want, > > and it will be easier than me explaining all the stuff you'd need to > > do to get it otherwise. > > doug > > > > Antonella Kis wrote: > > > Good morning Doug, > > > > > > > > > I will really appreciate if you can give me an advise on how I can > > get the mean average of the cortical thickness value for the FDR > > clusters so before Monte Carlo Simulation. > > > > > > Many thanks, > > > Antonella > > > > > > > > > > -- 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 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: 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 . 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 > FileDrop: 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] Thank you
by Douglas N Greve 27 Sep '11

27 Sep '11

If you have two groups and you want to test for the differences in the groups after you account for age, you need to do this in two steps. First, set up a DODS model (ie, each group gets an intercept and a slope). Use this to test for a difference between the slopes of the groups ([0 0 1 -1]). If there is a difference, then you'll need to talk to a statistician to figure out what to do. If there is no difference, then set up a new DOSS model (ie, each group gets its own intercept but they share a slope), then test the difference between the groups with [1 -1 0]. doug Antonella Kis wrote: > Thanks Doug, I followed your advise and it worked. > I would like to ask you one more favour please: if using GLM I want to > compare two groups and consider age as a covariate, does this mean > that we account for age or we are regressing out the effect of age? Is > this right? In this case can I consider the contrast matrix to be [1 > 0] since we need to add zero for the variable which are covariate? > > Thank you. > AK > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, September 27, 2011 11:17 AM > *Subject:* Re: Clusters formation by FDR > > Why not run mri_glmfit-sim? It will give you the file that you want, > and it will be easier than me explaining all the stuff you'd need to > do to get it otherwise. > doug > > Antonella Kis wrote: > > Good morning Doug, > > > > > > I will really appreciate if you can give me an advise on how I can > get the mean average of the cortical thickness value for the FDR > clusters so before Monte Carlo Simulation. > > > > Many thanks, > > Antonella > > > > > > -- 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 > FileDrop: 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 . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Clusters formation by FDR
by Antonella Kis 27 Sep '11

27 Sep '11

Good morning Doug, I will really appreciate if you can give me an advise on how I can get the mean average of the cortical thickness value for the FDR clusters so before Monte Carlo Simulation. Many thanks, Antonella

2 1

ERROR running mkcontrast - in FsFastTutorialV5.1
by Carl Anderson 27 Sep '11

27 Sep '11

Dear Free Surfer, I have gotten to 3. Configure Contrasts in http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel When I run *mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1* I get the following result and error: vermisii:fsfast-functional carlanderson$ mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 INFO: Found 5 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 0 0 0 mkcontrast -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile my-workmem.sm05.lh/encode-v-base.mat nconds 5, wcond 1.00000000000000000000 0 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -no-octave Tue Sep 27 10:58:43 EDT 2011 Any suggestions? Thanks! <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

2 1

Longitudinal analysis - Qdec question
by Joana Braga Pereira 27 Sep '11

27 Sep '11

Dear Freesurfers, I'm doing a longitudinal analysis of cortical thickness using the newest version of Freesurfer and there is something i would like to ask you all. I have two time points and only one group of patients. I've finished the pre-processing and am now searching for differences between the two time points using Qdec. Since i only have one group my cross.qdec.table.dat file looks pretty much like this: fsid years template_M_b01 0.665 template_M_b02 0.665 template_b03 0.71 template_b04 0.79 template_b05 0.915 template_b07 0.665 template_b09 0.625 template_b10 0.625 template_b11 0.71 template_b13 1.04 template_b14 0.71 template_b15 0.665 template_b16 0.835 template_b17 0.665 template_b18 0.625 template_M_b19 0.71 template_M_b20 0.625 template_b21 0.71 template_b22 0.585 I selected the long.thickness.rate in Qdec interface and years as continuous covariate since it is the only variable that i have in my cross.qdec.table.dat (no groups or other covariates of interest). My question is: Is this the analysis i should be doing given that i want to know the differences between time point 1 - time point 2? Many thanks, Joana

3 4

Rejoindre mon réseau sur LinkedIn
by Mohan Boddu via LinkedIn 27 Sep '11

27 Sep '11

LinkedIn ------------ Mohan Boddu souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-gt2xmoou-3z/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-gt2xmoou-3z/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Mohan Boddu ? Les contacts de Mohan Boddu consulteront votre profil : Votre arrivée dans le réseau de Mohan Boddu attirera l'attention d'autres membres de LinkedIn. Voir qui a consulté votre profil. http://www.linkedin.com/e/-qq80um-gt2xmoou-3z/wvp/inv18_wvmp/?hs=false&tok=… -- (c) 2011, LinkedIn Corporation

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Freesurfer September 2011