[Freesurfer] vertex-wise correlation

Dear Freesurfer experts, I have fMRI data that are processed in AFNI that I would like to examine the relationship with cortical thickness measures. In particular, I am interested in vertex-wise correlation of thickness and BOLD % signal change. The problem is I am new to Freesurfer. So far I h

Re: [Freesurfer] asegstats2table error

Do those files exist? Do they have content in them? doug On 05/15/2012 05:51 PM, Rashmi Singh wrote: > Hello, > I am trying to get the asegmentation information after the recon-all > run in the table form, but I am continuously getting the following error > > asegstats2table --subjects AA262.G1

[Freesurfer] asegstats2table error

Hello, I am trying to get the asegmentation information after the recon-all run in the table form, but I am continuously getting the following error asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile asegstats.txt SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the

Re: [Freesurfer] qdec.table.dat file

The last line does not end in a new line. Open it in your text editor, go to the last line, hit return, save it, and try again. doug On 05/15/2012 05:15 PM, Fidel Vila wrote: > Hi Freesurfer experts, > > A newbie question regarding working with QDEC. When I try to upload > the qdec.table.dat fil

[Freesurfer] qdec.table.dat file

Hi Freesurfer experts, A newbie question regarding working with QDEC. When I try to upload the qdec.table.dat file (attached) an error messages pops up "Error loading the data table". To the best of my knowledge I've followed the guidelines on the tutorial in terms of formatting. What would

Re: [Freesurfer] mri_segstats for T2-relaxation time data?

Hi Carl, those are all that are in the aseg.mgz. What more did you expect? doug On 05/15/2012 03:44 PM, Carl Anderson wrote: > Dear Freesurfer Folks, > > I have returned to the problem of trying to extract T2 values from a > T2-map using aseg & mri_segstats. > When I attempt mri_segstats it only

Re: [Freesurfer] mri_segstats for T2-relaxation time data?

p.s. what format is the attachment? It doesn't have an extension On Tue, 15 May 2012, Carl Anderson wrote: Dear Freesurfer Folks, I have returned to the problem of trying to extract T2 values from a T2-map using aseg & mri_segstats. When I attempt mri_segstats it only returns a small subs

Re: [Freesurfer] mri_segstats for T2-relaxation time data?

Hi Carl, you can ftp it or filedrop it (both are detailed on the fs wiki site) cheers Bruce On Tue, 15 May 2012, Carl Anderson wrote: Dear Freesurfer Folks, I have returned to the problem of trying to extract T2 values from a T2-map using aseg & mri_segstats. When I attempt mri_segstats it

[Freesurfer] mri_segstats for T2-relaxation time data?

Dear Freesurfer Folks, I have returned to the problem of trying to extract T2 values from a T2-map using aseg & mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb lim

Re: [Freesurfer] average lGI for each subject's hemipshere

That looks right. You can also run something like: mri_segstats --slabel subject lh ../label/lh.cortex.label --in lh.thickness --sum sum.dat --id 1 The output is sum.dat doug On 05/15/2012 02:14 PM, Inês Violante wrote: > I think I got it, but it would be great if someone could tell me if > th

[Freesurfer] mri_robust_template

Dear all, For a longitudinal analysis I need to have within subject templates. After some preprocessing that included FSL's BET, and linear registration of all time points to time-point 1, I fed images to mri_robust_template: mri_robust_template --mov tp1 tp2 tp3 --template --satit It runs fine

Re: [Freesurfer] average lGI for each subject's hemipshere

I think I got it, but it would be great if someone could tell me if this is wright: mris_anatomical_stats -l lh.cortex.label -t lh.pial_lgi -log file.txt SUBJECT lh pial thanks, ines On Tue, May 15, 2012 at 6:58 PM, Inês Violante wrote: > Dear all, > > How can I obtain an average lGI for each

[Freesurfer] average lGI for each subject's hemipshere

Dear all, How can I obtain an average lGI for each subject's hemipshere? I've tried: mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ lgi.annot.ctab -t pial_lgi $SUBJECT lh but I had the following error: ERROR: stating file .../label/lh.aparc.annot It cal

Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

Hi Bruce and Michael, That would be very nice. Do I just email you the hi-res *whole-brain*mprages, or is their another way to get the images to you? On the other hand, I'm a fair hand at scripting. I'd be willing to experiment with any scripts that you might provide. Last, and on an unrelated n

Re: [Freesurfer] Inter-hemispheric registration issue

Hi Irene, can you send the log file for the command that is failing? doug On 05/15/2012 01:28 PM, Irene Altarelli wrote: > Dear all, > > I'm trying to use the new script for the inter-hemisphere analysis, in > Fs version 5.0. I have downloaded the files as suggested > (http://www.mail-archive.com/

[Freesurfer] Inter-hemispheric registration issue

Dear all, I'm trying to use the new script for the inter-hemisphere analysis, in Fs version 5.0. I have downloaded the files as suggested (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html). Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym --lh), but

Re: [Freesurfer] Clusters size treshold question

Keep changing the --cwpvalthresh until all clusters smaller than 50 are gone. doug On 05/15/2012 12:43 PM, Antonella Kis wrote: > Dear All, > > I would like to know if there is a way to eliminate from my > significant clusters (grf.th3.pos.sig.cluster.mgh) obtained after > running mri_glmfit-s

[Freesurfer] Clusters size treshold question

Dear All, I would like to know if there is a way to eliminate from my significant clusters (grf.th3.pos.sig.cluster.mgh) obtained after running  mri_glmfit-sim with grf option and using mri_volcluster the clusters with a size smaller than 50 mm^3 or in other words to keep only clusters with a v

Re: [Freesurfer] confusion with tkregister2

Hi Mia, you'll have to give us more information, eg, what was your command line for tkregister2? On 05/15/2012 09:56 AM, Borzello, Mia wrote: > Morning all, > > I ran the recon yesterday, and it says it ran without error. I am now running > tkregister2, but for some reason when i compare the cor

Re: [Freesurfer] 1-way ANOVA: contrast specification

Hi Alexander, what you have there looks like an interaction test for a 2x2 ANOVA. If you are looking for an effect of level, then you will need something like 1 -1 0 0 1 0 -1 0 1 0 0 -1 Plus 12 zeros on each line for the covariates. I would also first test for an interaction in the covariates. I

Re: [Freesurfer] A doubt with the group analysis of longitudinal data

That will be fine. We are working on tools to perform mixed effects analysis on longitudinal, but they are not ready yet. I think Martin has some tools to exploit the fact that they are longitudinal (eg, computing a slope normalizing by the first time point or the average of the time points). B

Re: [Freesurfer] low eff and VRF values

You're getting very low VRFs because of the sub-TR estimation (TR=1.5, but TER=0.5), so you reduce your power to about 1/3. This is not a problem unless you analyze your data using an FIR. If you assume a shape, then the power will come back. doug On 05/15/2012 11:41 AM, Andrew Valdespino wrote

Re: [Freesurfer] lGI differences without variation in other cortical morphometric variables

Hi, Thank you so much for your reply. I am going to read the paper. However, if the increase in head size obscures the lGI, why this is not an overall variation? Meaning, why is only for the frontal and temporal lobes? thank you ines On Tue, May 15, 2012 at 4:30 PM, j janssen wrote: > Hi, >

[Freesurfer] low eff and VRF values

(1) Version: optseq2.c,v 2.21.2.1 (2) Computer operating system: Mac OS X Version 10.7.3 (3) Command line: optseq2 --ntp 230 --tr 1.5 --psdwin 0 24 0.5 --ev go 7 36 --ev nogo 7 12 --nkeep 4 --o gonogo --nsearch 1000 (4) Description of the problem: This is in reference to a go/no-go paradigm. I a

Re: [Freesurfer] lGI differences without variation in other cortical morphometric variables

Hi, I am comparing a group of patients with controls. I extracted: > cortical volume, surface area, cortical thickness and gyrification > index for each subject's lobe. > Comparisons between this variables with Total Intracranial Volume as a > covariate indicated a difference in frontal and tempor

Re: [Freesurfer] Problem creating longitudinal template file

Hi Corinna, you need a single folder with all subjects and all time point: so the subjects directory will look like: me1 me2 me3 you1 you2 ... You can create such a folder and insert symbolic links to the original subject folders if you want to keep your structure. Then create the base in this

Re: [Freesurfer] confusion with tkregister2

I'm not sure if this is it's similar to my problem yesterday in that I just need to choose a new set of dicoms- in this case, possibly a different set of CT dicoms? thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvar

[Freesurfer] lGI differences without variation in other cortical morphometric variables

Dear all, I am comparing a group of patients with controls. I extracted: cortical volume, surface area, cortical thickness and gyrification index for each subject's lobe. Comparisons between this variables with Total Intracranial Volume as a covariate indicated a difference in frontal and temporal

[Freesurfer] confusion with tkregister2

Morning all, I ran the recon yesterday, and it says it ran without error. I am now running tkregister2, but for some reason when i compare the coronal view, things look okay on the mri, but it looks like the axial view for the CT. I'm not sure in which step this happened? Thanks, Mia

Re: [Freesurfer] Problem creating longitudinal template file

Hi Martin, I think this is what you're looking for. If not, let me know. recon-all -base 137_S_0158_template -tp /Applications/freesurfer/subjects/corinna/ADNI/BL/137_S_0158/mri/norm.mgz -tp /Applications/freesurfer/subjects/corinna/ADNI/12mos/137_S_0158/mri/norm.mgz -tp /Applications/freesurfer/s

Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

Yes, I have a modified script working. For the white surface, the essentials are the same as Bruce's script but it has some additional stuff (e.g register T2w to T1w), and I call it in the middle of the recon-all rather than at the end. For the pial surface, I have done some more complicated stuf

Re: [Freesurfer] recon-all exiting with errors

Hi Julia I don't see any error messages. If you upload the dataset we'll take a look. Make sure you have enough ram in the machine (>2G) and free disk space. cheers Bruce On Tue, 15 May 2012, Richter, Julia wrote: > Dear FreeSurfer experts, > > I am trying to recon-all T1 images with the com

Re: [Freesurfer] Need some materials

Hi Bobo try this: http://www.ncbi.nlm.nih.gov/pubmed/22248573 cheers Bruce On Tue, 15 May 2012, bowan...@mail.ustc.edu.cn wrote: > Dear Freesurfer Experts, > I am a senior, and I am going to finish my graduation thesis which is about > the use of freesurfer.So I need some written materials

Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his vers

[Freesurfer] recon-all exiting with errors

Dear FreeSurfer experts, I am trying to recon-all T1 images with the command recon-all -s -i /path/to/subject/directory/subject.nii.gz. This command used to work with several images, but one of my images is always exiting with errrors, in my opinion without a reason. Any suggestions what is go

[Freesurfer] 1-way ANOVA: contrast specification

Dear Freesurfers, I'm going to run 1-way anova, followed by post hoc pairwise comparison. My "factor-of-interest" has 4 levels and, in addition, I would like to regress out the effects of 3 continious variables. I have attached my *fsgd-file. Therefore, my first *mtx-file should contain the fo

[Freesurfer] Need some materials

Dear Freesurfer Experts, I am a senior, and I am going to finish my graduation thesis which is about the use of freesurfer.So I need some written materials,such as the development history of Freesurfer, the achievement of Freesurfer and so on. But I don't know. Can you help me? Or give me som