Re: [Freesurfer] FsFastIndividual Retinotopy - Polar Only

Hello again, Don't mean to be a bother. I was wondering if anyone had any thoughts on what possibly be going wrong during my retinotopic analysis that I posted. I'm at quite a loss and would appreciate a look. Thanks and best, Daniel On Fri, May 11, 2012 at 11:49 AM, Daniel Cole wrote: > Hello

Re: [Freesurfer] trac-all -path error

Hi Priti - Thanks for your help. The inter-subject registration seems to have run OK, but there must be something wrong with the intra-subject registration. When I try to view it using freeview, it's completely dark - I don't see a brain at all. Is there a way to troubleshoot this? Thanks, Kiely

Re: [Freesurfer] trac-all -path error

Hi Kiely - Looks like you used flirt for the intra-subject registration, so you can look in trac-all.log for the flirt command line that registers diffusion to anatomical and play around with the parameters. You can also use bbregister instead of flirt for the intra-subject registration - it

Re: [Freesurfer] trac-all -path error

Kiely, For flirt, try using corratio, cost function instead of mutualinfo (which is the default in trac-all) to see if that solves your registration problem. > Hi Kiely - Looks like you used flirt for the intra-subject registration, > so you can look in trac-all.log for the flirt command line tha

Re: [Freesurfer] trac-all -path error

Is this something I can change in my dmrirc file or do I need to run flirt on it's own? Thanks, Kiely On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < rspr...@nmr.mgh.harvard.edu> wrote: > Kiely, For flirt, try using corratio, cost function instead of mutualinfo > (which is the default in tr

Re: [Freesurfer] trac-all -path error

No, this is something you have to try yourself on the command line. If you want to make the change permanent, you can edit the relevant line in $FREESURFER_HOME/bin/trac-preproc. On Wed, 16 May 2012, Kiely Donnelly wrote: Is this something I can change in my dmrirc file or do I need to run

Re: [Freesurfer] trac-all -path error

you have to run flirt commandline separately to check if it solves your problem. > Is this something I can change in my dmrirc file or do I need to run flirt > on it's own? > > Thanks, > > Kiely > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Kie

Re: [Freesurfer] Inter-hemispheric registration issue

Irene, this is a problem with the script. The work-around is to run xhemireg before running surfreg with the --xhemi option. doug On 05/16/2012 01:56 AM, Irene Altarelli wrote: > Dear Doug, > > here is what I get. > > First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the > attached

[Freesurfer] Fwd: Re: FsFastIndividual Retinotopy - Polar Only

Hi Daniel, did you miss my responses from last week? doug Original Message Subject:Re: [Freesurfer] FsFastIndividual Retinotopy - Polar Only Date: Fri, 11 May 2012 12:49:32 -0400 From: Douglas N Greve To: freesurfer@nmr.mgh.harvard.edu Hi Daniel, answers below

Re: [Freesurfer] gzipRe: Fwd: Load Brodmann surface area into inflated surface

Thanks Bruce! Those are the main questions now (not only to V1, but also to the rest of the Brodmann areas). I really want to be sure where the measures come from. I want that the different measures (i.e. cortical thickness and area are really from the same region in the cortex), to know wh

Re: [Freesurfer] trac-all -path error

I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line look something like this if I am running it in this individuals dmri directory: flirt -in dwi_orig.nii.gz -ref

Re: [Freesurfer] trac-all -path error

The .mat registration matrix should be saved under dmri/xfms/. On Wed, 16 May 2012, Kiely Donnelly wrote: I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line

Re: [Freesurfer] Asegstat2 table error

Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats? Also, please remember to copy the list so that others can see the answer and so that others can help with the answer. thanks! doug On 05/16/2012 11:56 AM, Rashmi Singh wrote: > > Dough, > > Yes, the stat files exist with all its

Re: [Freesurfer] Asegstat2 table error

Doug, Attached are the aseg.stat files of the two different runs (AA262.G1 and AB054.G1) where I got the error message. Thanks Rashmi. On 5/16/12 11:41 AM, "Douglas N Greve" wrote: >Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats? >Also, please remember to copy the list so th

[Freesurfer] Different values for cortical thickness

Dear Freesurfer Friends I have a question about cortical thickness. I do not understand why these commands give us DIFFERENT values for "average cortical thickness". Can you please let me know if you have any idea. Thanks a lot mris_anatomical_stats N2207 lh number of vertices

Re: [Freesurfer] Asegstat2 table error

I was able to load both of those. Try this: cd /opt/freesurfer/subjects/AA262.G1/stats asegstats2table -i aseg.stats -t test.dat doug On 05/16/2012 01:25 PM, Rashmi Singh wrote: > Doug, > Attached are the aseg.stat files of the two different runs (AA262.G1 and > AB054.G1) where I got the erro

Re: [Freesurfer] Asegstat2 table error

It just loads in a single file and creates a "table" with one row. On 05/16/2012 02:02 PM, Rashmi Singh wrote: > Can you also let me know what does the following command do. > Thanks, > Rashmi. > > On 5/16/12 12:58 PM, "Douglas N Greve" wrote: > >> I was able to load both of those. Try this: >> >

[Freesurfer] Dependent measures qdec

Dear All, Could someone explain (or point me in the right direction) as to the meaning of the dependent measures (which can be used in qdec) - intensity_deep/intensity_superficial - intensity_deep.mgz/intensity_superficial.mgz - white K/H What do they represent ? Thanks. Mahinda __

[Freesurfer] Flip brain

Dear FS experts, How can I flip hemispheres? I read the mail list and Doug said that (2010): The problem with this is that you will get different results when you use the left hemi and the right-flipped-to-left hemi as compared to the right hemi and the left-flipped-to-right hemi. You'll actually

Re: [Freesurfer] Flip brain

Hi Tadeu, It will be available in 5.2. If you can't wait until then, then follow the instructions here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html doug On 05/16/2012 03:51 PM, Tadeu Kubo wrote: > Dear FS experts, > > How can I flip hemispheres? I read the mail list a

Re: [Freesurfer] Flip brain

Hi Doug Thank you! Tadeu On Wed, May 16, 2012 at 5:02 PM, Douglas N Greve wrote: > Hi Tadeu, It will be available in 5.2. If you can't wait until then, > then follow the instructions here: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html > doug > > On 05/16/2012 03:

[Freesurfer] aseg.stats not matching up

Suppose I were to open a subject aseg.mgz in tkmedit, and use the 3D fill tool to relabel the *entire* left hippocampus segmentation to 'MyNewImaginaryLabel'. If I then re-run the aseg stats, should the left hippocampus volume from the original aseg.stats be identical to the volume of MyImaginaryLa

Re: [Freesurfer] aseg.stats not matching up

Hi Joshua probabilities are computed internally, but not stored nor used in volume calcualtions. Are you actually doing a 3D fill? I don't think the hippocampus label is guaranteed to be connected. Can you try instead replacing every voxel in matlab with the hippocampus index to your new one?

Re: [Freesurfer] FsFastIndividual Retinotopy - Polar Only

Hey Doug, Sorry I did miss your response last time, thank you for the advice. I tried running the analysis again and this time it did create the angle file. However, now I'm running into a different problem. I can get the angle map to show up on the surface of my subject's brain but I can't get

Re: [Freesurfer] aseg.stats not matching up

Hi Bruce, First, let me add that if I run the mri_segstats without the --pv flag, the two will have identical volumes. This indicates to me that we captured all the voxels into the new label. Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of

Re: [Freesurfer] aseg.stats not matching up

hmmm, that is convincing. I don't think there's anything in mri_segstats that knows about the meaning of any of the indices, but maybe Doug can correct me? On Wed, 16 May 2012, Joshua Lee wrote: Hi Bruce, First, let me add that if I run the mri_segstats without the --pv flag, the two will ha

[Freesurfer] Question about DODS model and DOSS model

Hi all: I'm a little confused about the DODS model and DOSS model. I have two groups (patient and control) and one covariate (age), and I want to compare the diffirence of thickness between the groups with age as the covariate. In DODS model, is the process the analysis of variance substant

[Freesurfer] Problem in building FreeSurfer from source

I'm having a problem in building FreeSurfer from the source codes (both 'stable5' and 'release_5_1_0') downloaded from the CVS repository. When I run 'make', it stopped with the following error message: mri_convert.c:39:40: error: unwarpGradientNonlinearity.h: No such file or directory mri_conver

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

Oops i just realized I only sent this to Bruce: Thanks! It looks like this involves some manual intervention. Matt., I assume you're not manually making control points on 1000s of subjects (I imagine this is for the human connectcome project). Is your code public somewhere? Cheers, Michael On

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

Only because I was lazy! You can use surfaces for normalization too. I think the script I gave Matt probably had that in it On May 16, 2012, at 9:21 PM, Michael Waskom wrote: > Oops i just realized I only sent this to Bruce: > > Thanks! It looks like this involves some manual intervention.