Re: [Freesurfer] Comparison of cortical thickness results

Falk, If you have the .annot file for a subject, you can break that apart into individual label files using mris_annot2label. Then knowing which labels compose the parietal lobe (for the Desikan-Killiany atlas, superior and inferior parietal, supramarginal, precuneus and postcentral compose the p

[Freesurfer] mris_preproc really averages?

Hello, I think my message got scrubbed from my last post with the pictures. I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two averag

Re: [Freesurfer] mri_convert problem

Rodrigo, These appear to be from a NeuroLogica CereTom scanner, and while they appear to be in dicom format, I cannot get mri_convert to recognize them. However, mricro does read them, and can convert them to analyze (which mri_convert can convert to .nii). Converting to analyze loses orientatio

Re: [Freesurfer] mris_glmfit annotation error

Devdutta, I've confirmed that in our tutorial data, the cluster annotations do correspond to their proper locations, so I can't say I've seen the problem you are seeing. Can you send me your .annot and .cluster.summary files? Send to: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

[Freesurfer] mris_glmfit annotation error

Hi, While going through the annotation of the clusters, we noticed that the regions that the cluster summary prints out do not correspond to the actual location in the brain. For example, in the summary one of the clusters is reported to be in the isthmus of cingulate. However, when I look at the

Re: [Freesurfer] White matter volumes for Gyrus and Sulcus

Sorry, I found the error in my script. The ‹ctxseg option cannot be used here, and we should use ‹a2005s option for mri_aparc2aseg command. Wayne On 27/04/09 10:25 AM, "Wayne Su" wrote: > Hello, > > Is there a way to get white matter volumes of gyrus and sulcus in Destrieux > atlas? I tried

Re: [Freesurfer] Convert image

mri_label2vol should do the trick On Mon, 27 Apr 2009, Kelly Silva wrote: Hello,    How can I convert one file *.label into *.img?     Thanks in advance.    Best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados

Re: RES: Re: Re: Re: [Freesurfer] Individual thickness data extraction from plot

Hi, finally I succeded.  I changed `seq 1 $numsubject` for `seq 0 52` and it worked properly! So, for some reason, numsubject that was previously defined as = 53, was not working the second issue was that my list started with 0 and thus, ended with 52 (instead of 1 to 53)Thanks for your help again!

[Freesurfer] White matter volumes for Gyrus and Sulcus

Hello, Is there a way to get white matter volumes of gyrus and sulcus in Destrieux atlas? I tried to use the same method used by white matter parcellation for Desikan-Killiany atlas, but no wm volumes were reported. Or we get the total volume of the label (how?), then subtract the gray volume to

Re: [Freesurfer] Convert image

Hi Kelly, I think you can use mri_label2vol. Try 'mri_label2vol --help' for more options. Sita. On Mon, 27 Apr 2009, Kelly Silva wrote: Hello,    How can I convert one file *.label into *.img?     Thanks in advance.    Best regards, Kelly Veja quais sã

[Freesurfer] Convert image

Hello,    How can I convert one file *.label into *.img?     Thanks in advance.    Best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ Freesurfer mailing

[Freesurfer] mri_convert problem

Hi, I'm trying to run mri_convert to convert CT dicoms into nifti format but I keep getting the following error: [multnomah:CT] (nmr-std-env) mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii file not found or

[Freesurfer] Comparison of cortical thickness results

Hi everyone, I’d like to compare the individual cortical thickness results of Freesurfer with the results of another software. The other software measures the cortical thickness for example across the whole left parietal lobe. So I have to get the according value of the whole left parietal lobe

[Freesurfer] Flattening marmoset cortex

Hi, I created a triangular mesh of a marmoset cortex (layer 4) from histological slices. Although the marmoset cortex is almost flat, it does have a very deep calcarine sulcus and I need to push it out. I am hoping that it is possible to feed the mesh to FreeSurfer so that it can be flattened.

RES: Re: Re: Re: [Freesurfer] Individual thickness data extraction from plot

You are not doing it right. That script is to be run inside a script. Create a file try.sh paste that lines in try.sh Execute chmod +x try.sh Run ./try.sh good luck PPJ Sent from my Nokia phone @E71 -Msg original- De: marina.lo...@crccorp.es Enviada: 27/04/2009 06:00:30 Assunto: Re:

Re: Re: Re: RES: [Freesurfer] Individual thickness data extraction from plot

Hi Nick and Pedro Paulo, Thanks a lot for your help and explanations. I have tried to do what you told me but still find only one asc file. I am copying to you what I did, just in case you could detect my mistake:mar...@linux4:~/FS$ export SUBJECTS_DIR=/data/User/marina/FS Where my subjects data fo