Re: [Freesurfer] how does qdec make a contrast.mat file...?

of classes, and 0 0 1 will test it. I don't think that +1 -1 +1 tests anything meaningful. doug Cameron Ellis wrote: Hi, I have been running analyses in qdec and glmfit and comparing the results. I am puzzled by the results of one analysis that compares two groups. When I loaded a table.dat

[Freesurfer] how does qdec make a contrast.mat file...?

Hi, I have been running analyses in qdec and glmfit and comparing the results. I am puzzled by the results of one analysis that compares two groups. When I loaded a table.dat file in qdec and selected the variables of interest, an fsgd file containing only those variables was generated in the

[Freesurfer] variables and glmfit...

Hi all, I have two questions regarding glmfit and testing for effects of different variables. I have four groups. When testing for effects of age across all of the groups, will there be a difference when assigning each group a class in my fsgd file, with age as a variable, like so: Class PH Class

[Freesurfer] glm_fit question...

Hi all, Is it necessary to include a value in your contrast matrix for every class and variable in your fsgd file? It seems that this is the case. My understanding is that if you weight a variable 0 then it is automatically controlled for. So if am required to weight a variabe in the contrast

[Freesurfer] mri_glmfit...

Hi all, Does mri_glmfit run to correlate volume with a particular measure identify clusters on a voxel by voxel basis or does it compare the aseg volumes of the different subcortical structures? Thanks, Cameron ___ Freesurfer mailing list

Re: [Freesurfer] analysis of covariance using qdec

Narly, I don't think simply including a variable in the qdec.table.dat file will automatically control for that variable. It is my understanding that selecting a variable will control for that variable in all effects of the analysis. Someone please correct me if this is wrong. Cameron OK

[Freesurfer] recon-all error @ mris_volmask...

Hi, I am receiving this error for every subject I send through recon-all. I am checking for edits that need to be made but it seems very odd that 30 subjects or so would all error out at the same step. Any suggestions? Cameron Subject 'Ponce_033d2': make all recon-all -s

Re: [Freesurfer] recon-all error @ mris_volmask...

if it runs. You may be missing a library (I recall having a similar error). 2) Running out of memory might be a factor. How much do you have? Padraig Cameron Ellis wrote: Hi, I am receiving this error for every subject I send through recon-all. I am checking for edits that need

[Freesurfer] recon-all error, COR-.info...

Hi, I keep getting an error when I submit jobs to seychelles that a COR-.info file cannot be found. Do you know why this would be? I pasted the full command and error log below. Thanks! Cameron recon-all -i /space/grouch/4/users/ponce/ponce_002d2/3danat/003 -i

[Freesurfer] create segmentation...

Hi All, Does anyone have any information on whether it is possible to create a segmentation based on custom volumetric labels one has created, and then extract functional values from that segmentation using mri_segstats? If so, how would one go about making the segmentation? Thanks, Cameron

Re: [Freesurfer] Cluster thresholding

Hi, Just th9ought I would chime in here. I have the same understanding as Pratap as long as by primary cluster forming threshold you are referring to is the vertex wise p-value. The cluster wise p-value you choose after the simulation does not have to be derived from this value. But perhaps both

Re: [Freesurfer] mris_preproc error for mc sim...

oops. I pasted the original error message incorrectly. below is the error with the corrected path. Hi, In anattempt to prepare to run a monte carlo cluster threshold simulation with a group of subjects in stable3, I run into the following error using mris_preproc: [troy:retrievalnewest]

[Freesurfer] mris_preproc error for mc sim...

Hi, In anattempt to prepare to run a monte carlo cluster threshold simulation with a group of subjects in stable3, I run into the following error using mris_preproc: [troy:retrievalnewest] (nmr-stable3-env) mris_preproc --fsgd SM2_glm_MC_controls.fsgd --target allsubavg --hemi lh --sf

Re: [Freesurfer] mris_preproc error for mc sim...

Hi, It looks like the error I was obtaining from mris_preproc looks like it was due to a failure in stxgrinder-sess that I did not realize had occurred. I have a feeling that once this problem is resolved mris_preproc will run correctly, but help here would be much appreciated...The error is

[Freesurfer] stats for average subject...

Hi, Does anyone know if it is possible to generate an aparc.stats file for an average subject? mris_anatomical stats does not seem like it will work because it requires wm.mgz which is not generated in the make_average_subject process. I would like to find the number of vertices and the surface

[Freesurfer] activation patterns and par files

Hi all, I have run two different group analyses in stable3. All of the analysis parameters between the two are identical except that one uses a paradigm file containing three conditions and the other uses a paradigm file containing five conditions. The first three conditions in the analysis using

RE: [Freesurfer] activation patterns and par files

the same relative result? Cameron Every time point not specified as a condition would be counted as baseline, right? So does that mean then, that you have a different baseline for your 3 and 5 condition analyses? From: Cameron Ellis [EMAIL PROTECTED] To: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] multiple surface overlays

Hi all, Sourcing stable3, using tksurfer, does anyone know how to load more than one overlay at a time from the command line? (something like: tksurfer subject hemi surface -overlay1 ??? -overlay2 ??? overlay3 ???) Does this require scripting w/ tksurfer? Cameron

[Freesurfer] thickness and make_average_subject

Hi all, I am using make_average_subject to generate average subjects for two groups in a study. The average subjects' surfaces are created with no errors. However, I am curious why I cannot get the thickness file generated to appear on the surface. After I have the inflated average surface open,

[Freesurfer] mri_watershed problem

Hi everyone, I am trying to output bem surfaces using mri_watershed and I receive badly distorted surfaces. During the autorecon process there did not appear to be any errors generated, and the final surfaces look good, it is just in producing the bem surfaces independent from autorecon that

Re: [Freesurfer] fmri conjunction/correlation map

corresponding voxels from the two runs? what freesurfer tools would do this? Thanks in advance, Cameron Oh, you want a conjunction I think. Corrlation means something else. Try mergecontrasts-sess doug Cameron Ellis wrote: Hi Doug, We would like to compare, voxel by voxel, the activity between

[Freesurfer] fmri correlation map

Does anyone have an answer to this question? Hello, I am looking for a way to perform voxel-wise, within-subject correlations of two activation maps (in talairach space). The two existing maps reflect encoding and retrieval runs of a memory task. The idea would be to generate a correlation map

[Freesurfer] intergroup t-values

Hi all, I am trying to generate a t-map for an intergroup average. when I attempt to run stxgrinder the program looks for a fixed effects average. Since intergroupavg-sess assumes a random effects analysis is it possible to generate this statistic? Is there something statistically repugnant about

[Freesurfer] smoothing error...?

Hi, After sphreical resampling I attempted to smooth the spherical surface which seemed to work fine but when I try to perform a group average using the smoothed surface I receive this error: troy:cameo[99] isxavg-re-sess -group Controlssh+smvsnh -sf sessidcontrolsshvsnh -df sesspar -a

Re: [Freesurfer] preproc inorm question

, you just spec the motion corrected volume when you make a new analysis. You will need to re-run inorm, but you can do this outside of preproc with inorm-sess -funcstem fmc ... Cameron Ellis wrote: Hi all, If I were to perform a surface-based analysis, resampling to spherical space, and I did

[Freesurfer] topology fix error

Hi all, I received the following error while running autorecon. Has anyone come across this before who knows what to do to fix it? Cameron Command run: recon-all -subjid SM1S17_autoreconall -autorecon2 Error Script: [EMAIL PROTECTED] Fix Topology lh Wed Jan 17 04:00:20 EST 2007 cp

[Freesurfer] talairach registration

Hi, Hopefully this is something simple. When I try to check the talairach transform for my subjects I type: tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig and then I get this error: subject = SM1C2_autoreconall Reading lh surface orig

[Freesurfer] spherical smoothing

Hi, I am trying to smooth fucntional data on the spherical surface and I see that there are a few options for how this can be done and was wondering if anyone has any suggestions for an optimum smoothing technique. I see one option is implementing smoothing as a tag in mri_vol2surf but I also see

[Freesurfer] combining conditions

Hi, I have three conditions specified in my paradigm files that I have been comparing to one another. Two conditions I would like to combine and compare to the third in one contrast and was wondering if this would require modifying my paradigm files to refer to these two conditions with the same

Re: [Freesurfer] annotation2label problem

/rh.temporalpole.lab el 34800 SM2C1_autoreconall/label/rh.transversetemporal.label LabelWrite: saving to SM2C1_autoreconall/label/rh.transversetempor al.label Hi Cameron, can you give is more info? See surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for what is required. thanks doug Cameron

Re: [Freesurfer] ROI group analysis

I use the bhdr file that is in the same directory as the registration file? Cameron There should be a register.dat file in the bold dir of the average subject (or maybe in the bold/analysis/tal dir) doug Cameron Ellis wrote: Hi, I am trying to run mri_volcluster on a group ROI and am

[Freesurfer] ROI group analysis

Hi, I am trying to run mri_volcluster on a group ROI and am having some trouble. I was hoping someone had suggestion. I created individual ROIs and wanted to average them to obtain a group ROI. I ran isxavg-re-sess for each ROI but there is no registration file for mri_volcuster to reference. Have

[Freesurfer] roisummary and FIR

Hi, I am running roisummary with an FIR analysis with a 25s timewindow, 5s prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but shouldn't I receive 11 with these parameters? timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 timepoint: 01 2 3 4 5

[Freesurfer] roisummary question...

Hi, I am running an ROI analysis on a set of event-related data obtained through spmhrf analysis. When I run roisumamry-sess to obtain the values needed to calculate a percent signal change the number of estimations per condition is 1, which makes sense since I am looking at the entire time

[Freesurfer] preprocessing error

Hi, While attempting to preprocess a subjects data I am given an error message (pasted below) as the motion correction step is implemented does anyone have an idea of what the libvnl_algo.so file is and where it may be located? I am not sure why it cannot be loaded. Thanks in advance for the help!