Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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

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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 <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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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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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-gt2xlltn-6h/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-gt2xlltn-6h/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-gt2xlltn-6h/wvp/inv18_wvmp/?hs=false&tok=… -- (c) 2011, LinkedIn Corporation

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mri_convert error
by Andries R. Van Der Leij 27 Sep '11

27 Sep '11

Dear FS team, I'm working on some NIFTI images which I want to convert to mgz. When I try to do this, I get: mri_convert /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/NIFTI/sc0219-20101101-0003-T13DTFESENSE.nii.gz /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/FREESURFER/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/NIFTI/sc0219-20101101-0003-T13DTFESENSE.nii.gz... WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent (1,1) (1,1) (1,1.6) This is probably due to shear in the vox2ras matrix Input Vox2RAS ------ 0.013 0.018 1.600 -125.223; -1.000 -0.001 0.020 158.408; -0.002 1.000 -0.029 -85.678; 0.000 0.000 0.000 0.000; TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.012721, -0.999918, -0.00162597) j_ras = (0.0180632, -0.00139604, 0.999836) k_ras = (0.999756, 0.0127483, -0.0180439) writing to /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/FREESURFER/mri/orig/001.mgz... I'm not sure what's going on here, but I assume that something isn't right in the matrix, as my data (Phillips par/rec converted to NIFTI) are 1*1*1 mm (see below). I assume that our local conversion app does something fishy with the matrix. I'm completely in the dark on how to solve this. Any ideas would be greatly appreciated! Best, Andries avdleij1@debian:~/ID1000/ID1000_scans/CON_ID1000/NIFTI$ fslhd sc0219-20101101-0003-T13DTFESENSE.nii.gz filename sc0219-20101101-0003-T13DTFESENSE.nii.gz sizeof_hdr 348 data_type FLOAT32 dim0 3 dim1 256 dim2 256 dim3 160 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 16 nbyper 4 bitpix 32 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.0000000000 pixdim4 1.0000000000 pixdim5 0.0000000000 pixdim6 0.0000000000 pixdim7 0.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 0.012721 0.018063 0.999756 -125.222908 qto_xyz:2 -0.999918 -0.001396 0.012748 158.408218 qto_xyz:3 -0.001626 0.999836 -0.018044 -85.677658 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Anterior-to-Posterior qform_yorient Inferior-to-Superior qform_zorient Left-to-Right sform_name Aligned Anat sform_code 2 sto_xyz:1 0.012721 0.018063 1.599609 -125.222908 sto_xyz:2 -0.999918 -0.001396 0.020397 158.408218 sto_xyz:3 -0.001626 0.999836 -0.028870 -85.677658 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Inferior-to-Superior sform_zorient Left-to-Right file_type NIFTI-1+ file_code 1 descrip FSL4.1 aux_file

2 1

thickness_clinical_correlations
by Rajagopalan, Venkateswaran 26 Sep '11

26 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 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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Re: [Freesurfer] using isxconcat-sess for partial correlation coefficient map
by Douglas N Greve 26 Sep '11

26 Sep '11

Add "-m pcc" to the command line doug SHAHIN NASR wrote: > Hi, > > Would you tell me how can I use isxconcat-sess to calculate group > averaged "partial correlation coefficient map"? I have already > generated pcc.nii files for each individual subject. > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > -- 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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