[Freesurfer] Automated sub-region segmentation - Amygdala

Good afternoon, I am new to freesurfer - is it possible to auto-segment the Amygdala into sub-regions? Thank you for your time, Marc ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] corpus callosum

mostly, although the partial volume estimation will change it a bit. On Wed, 18 Jul 2012, Alfredo Damasceno wrote: Dear all,   The total corpus calllosum volume is not in the aseg.stats file, but instead I find CC post, mid post, central, mid ant, and anterior. Is it the same of the sum of the

Re: [Freesurfer] corpus callosum

yes, it is the sum doug On 07/18/2012 03:09 PM, Alfredo Damasceno wrote: > Dear all, > > The total corpus calllosum volume is not in the aseg.stats file, but > instead I find CC post, mid post, central, mid ant, and anterior. Is > it the same of the sum of these parts? > > Thanks > Alfredo > > >

[Freesurfer] corpus callosum

Dear all, The total corpus calllosum volume is not in the aseg.stats file, but instead I find CC post, mid post, central, mid ant, and anterior. Is it the same of the sum of these parts? Thanks Alfredo ___

Re: [Freesurfer] p-val from FDR

You would have to select the voxel-wise threshold found by FDR in the cluster analysis. This threshold (eg, 3.8) will not have a cached table, so you will have to run it hand. It does not make much sense to do it this way though. On 07/18/2012 01:37 PM, Antonella Kis wrote: > Sorry it was a sil

[Freesurfer] Longitudinal analysis question

Hello FS experts, I am running a group up subjects pre/post treatment. When trying to do group analysis, after converting data with the mri_slope command, when I made the long table into a cross table, I noticed in qdec it averaged my "time" variable and only supplies a mean and there is no lon

Re: [Freesurfer] retroicor

M is the number of regressor pairs. Leave out the others and it will figure them out. On 07/18/2012 01:43 PM, Caspar M. Schwiedrzik wrote: > and some more questions: in fast_retroicor(t,indpeak,M,peakamp,troughamp) > what is t / M? > how do I get peakamp and throughamp? > thanks again, caspar > >

Re: [Freesurfer] retroicor

If you don't specify them, I think it tries to figure them out. On 07/18/2012 01:36 PM, Caspar M. Schwiedrzik wrote: > great! > one more question: how do I choose fmin and fmax? > thanks, caspar > > 2012/7/18 Douglas N Greve > > > Try this > > ftp://surf

Re: [Freesurfer] retroicor

and some more questions: in fast_retroicor(t,indpeak,M,peakamp,troughamp) what is t / M? how do I get peakamp and throughamp? thanks again, caspar 2012/7/18 Caspar M. Schwiedrzik > great! > one more question: how do I choose fmin and fmax? > thanks, caspar > > 2012/7/18 Douglas N Greve > >> Try

Re: [Freesurfer] p-val from FDR

Sorry it was a silly question. Thanks, however, can I get the p val for each individual cluster after FDR if more than one survived at the same FDR threshold? Or this means that they have the same p-val? Thank you. Antonella From: Douglas N Greve To: freesu

Re: [Freesurfer] retroicor

great! one more question: how do I choose fmin and fmax? thanks, caspar 2012/7/18 Douglas N Greve > Try this > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/fast_retroicor.m > > > On 07/18/2012

Re: [Freesurfer] running trac-all -path missing files

Hi Rui - You can ignore the message about spline segments, it's fine. For the directory structure and where to find your files, I'll refer you to the trac-all wiki page (see section "Outputs from trac-all -path"): http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all Hope this helps, a.y

Re: [Freesurfer] retroicor

Try this ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > thanks for your advice. I am using > freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, while I have a > copy of peakfinder.m, fast_retro

[Freesurfer] running trac-all -path missing files

Hi FS users, I'm running “trac-all –path ” and when running it, it constantly gives the output ERROR: Degenerate spline segment 58 81 24 56 69 24 … But it runs until the end without exiting and says that it ran without errors. It’s normal? Plus, it seems that it fails to create the output

Re: [Freesurfer] retroicor

Hi Doug, thanks for your advice. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be part of the package. Could you let me know where to download it? Thanks, Caspar 2012/7/18 Douglas N Greve > Hi Caspar, I

Re: [Freesurfer] Sourcing error?

Hi Jeff, if you're going to use version 3, then you need to use an older version of FSL. Currently, you have FSLDIR pointing to the current version. Probably the "current" version changed over the last few months. if you look in /usr/pubsw/packages/fsl, you'll see all the versions we have. I do

Re: [Freesurfer] p-val from FDR

3.8 = -log10(1.5849e-04) On 07/18/2012 12:36 PM, Antonella Kis wrote: > Hi Doug, > > You mentioned that in my case when FDR found a voxel-wise threshold > of 3.8 means p<1.5849e-04. > > How exactly I you got this p-val? > > How I can get myp-vals for clusters after FDR? > > Many thanks. > An

Re: [Freesurfer] Sourcing error?

Hi Jeff, if you're going to use version 3, then you need to use an older version of FSL. Currently, you have FSLDIR pointing to the current version. Probably the "current" version changed over the last few months. if you look in /usr/pubsw/packages/fsl, you'll see all the versions we have. I do

Re: [Freesurfer] p-val from FDR

3.8 = -log10(1.5849e-04) On 07/18/2012 12:36 PM, Antonella Kis wrote: > Hi Doug, > > You mentioned that in my case when FDR found a voxel-wise threshold > of 3.8 means p<1.5849e-04. > > How exactly I you got this p-val? > > How I can get myp-vals for clusters after FDR? > > Many thanks. > Ant

[Freesurfer] Sourcing error?

Hello, I am having difficulty with an fMRI command line program that we have run successfully in the past, but which we haven't used in ~4 months. In response to the following command lines (from a csh script): "setenv FSL_DIR $FSLDIR source /usr/local/freesurfer/nmr-stable3-env source ${FSLDIR}/

[Freesurfer] p-val from FDR

Hi Doug, You mentioned that in my case when  FDR found a voxel-wise threshold of 3.8  means   p<1.5849e-04. How exactly I you got this p-val? How I can get myp-vals for clusters after FDR? Many thanks. Antonella ___ Freesurfer mailing list Freesurf

Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option

Thanks Doug, So I suppose should be the sig.mgh from running mri_glmfit: mri_glmfit \ --y lh.L_frontal.15.mgh \ --fsgd L_frontal.fsgd dods\ --C lh-Avg-thickness-Cor.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.L_frontal.glmdir Is this right? Thank you. Antonella

Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option

It should be the sig.mgh file in your contrast directory. doug ps. Please post to the list and not me directly. thanks! On 07/18/2012 11:56 AM, Antonella Kis wrote: > Hi Doug, > > Many thanks for your prompt response and your help. I have one more > question please. I searched for mri_surfcluster

Re: [Freesurfer] ask for help

Hi Haochuanxi, what is the context of this question? Are you running a qdec analysis? What are your variables? doug ps. Please post your questions to the freesurfer list instead of me directly. thanks! On 07/18/2012 11:55 AM, 传玺 wrote: > Dear Doulgus > Could you tell me the exactly meaning of "

Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option

Hi Doug, Many thanks for your prompt response and your help. I have one more question please. I searched for mri_surfcluster command and I am not sure what should be my input file. Can you please clarify this for me? Should this be  L-frontal.fsgd since I have more subjects? Thank you. Antonel

Re: [Freesurfer] mni152.register.dat

On 07/17/2012 05:17 PM, Garikoitz Lerma Usabiaga wrote: > Thanks Doug, > > I've done it with the one in SPM: > tkmedit -f $SPM8_DIR/canonical/avg152T1.nii -overlay ROI45.nii > -fthresh 0.5 > is this ok or should I test it with the one from FSL as well? My > partner is working with SPM and MarsB

Re: [Freesurfer] retroicor

Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfi

Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option

Hi Antonella, first of all, FDR and clusterwise correction are doing different things. Technically, you don't get clusters from FDR. FDR will choose a voxel-wise threshold for you, and any voxel above threshold can be interpreted as surviving FDR (but you should know how to interpret it -- see

[Freesurfer] retroicor

Hi! Has someone used retroicor (retroactive correction of physiological noise; Glover at al. 2000) with Freesurfer? I would like to create nuisance regressors for EPI data based on cardiac and respiratory signals. The AFNI version of retroicor produces slice-based regressors, and I am not sure how

[Freesurfer] FDR versus mri_glmfit-sim with --cache option

Dear FS team, I am doing a cortical thickness study using QDEC. I used FDR and got the following clusters: Generating cluster stats using min threshold of 3.8... Found 2 clusters Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX

Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Hi Sue, mri_segstats does not compute the eTIV itself, it just gets it from the transform matrix. doug On 07/18/2012 09:33 AM, Susan Ruiz wrote: > Hi Bruce, Nick, Muhammad et al., > > I noticed that there is an updated mri_segstats for download in the > release notes on the wiki, but that appear

Re: [Freesurfer] FWHM smoothing for surface based

I think that the LGI is a very smooth measure, so even if you only smoothed by 15mm, there is a lot of smoothness in the unsmoothed data. This is what fwhm.dat is picking up. What happens if you do not smooth the data? What fwhm do you get? doug On 07/18/2012 08:02 AM, jm wrote: > Dear Freesu

Re: [Freesurfer] Labels for comparison

sure. You can look at the papers by Kennedy, Caviness and Makris On Wed, 18 Jul 2012, John Drozd wrote: > Hi Bruce, > > Thank you very much for your clarifications. I will ask ADNI for their > permission and I will consult CMA for their definitions. > > Thank you, > Have a great day, > John > >

Re: [Freesurfer] Labels for comparison

Hi Bruce, Thank you very much for your clarifications. I will ask ADNI for their permission and I will consult CMA for their definitions. Thank you, Have a great day, John Sent from my iPhone 4S On 2012-07-18, at 6:42 AM, Bruce Fischl wrote: > Hi John > > we follow the conventions of the

Re: [Freesurfer] Flip brain

Thank you Doug! Tadeu On Mon, Jul 16, 2012 at 1:31 PM, Douglas N Greve wrote: > Hi Tadeu, I have updated the files. The only difference is that the > "mcc" file below is now > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz > < > ftp://surfer.nmr.mgh.ha

Re: [Freesurfer] Labels for comparison

Hi John we follow the conventions of the Center for Morphometric Analysis (CMA) here at MGH. I'm not actually sure what landmarks they use to separate what they call "inferior lateral ventricle" from the main one, but you can check with them. As for ADNI, we might have that data but I'm not su

Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Hi Bruce, Nick, Muhammad et al., I noticed that there is an updated mri_segstats for download in the release notes on the wiki, but that appears to be for the SupraTentorial Volume rather than the eTIV. If the patch is available, that would be greatly appreciated (and preferable to running ever

[Freesurfer] FWHM smoothing for surface based

Dear Freesurfer Team: I would like some information on FWHM.dat folder glmdir and its relationship with mri_glmfit-sim. It happens that when I use mri_glmfit-sim with --cache-in can't find the data for fwhm 51 - which is logical because they exist only to 1..30, but my data were smoothed previ