Freesurfer

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21 participants
30070 discussions

long_stats results for group analysis
by Maria A Infante 17 May '17

17 May '17

Hi I run the commands listed below and I was wondering if there is a way to get the average pc1 for each group. I get an average for the entire sample. What should I use instead of --osgm? long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 --do-spc --time years --stack-rate ./qdec/long_3groups.aseg-rate.stack.txt --stack-pc1fit ./qdec/long_3groups.aseg-pc1fit.stack.txt --stack-pc1 ./qdec/long_3groups.aseg-pc1.stack.txt --stack-spc ./qdec/long_3groups.aseg-spc.stack.txt mri_glmfit --osgm --glmdir long_3groups.aseg-pc1 --table ./qdec/long_3groups.aseg-pc1.stack.txt

2 1

Number of subjects in data table
by Benjamin Ubani 16 May '17

16 May '17

Hello, I'm writing because I have had an issue with QDEC and it's ability to correctly read the number of subjects indicated on my data table. I have about 70 subjects listed, but the program is only reading three. This is a ".dat" file that was created via a .csv template using Libre Calc. Ben -- *Benjamin N. Ubani* *Research Assistant* *Department of Psychiatry* *University of Minnesota* *612-624-0197*

3 4

CA1 subfield extraction
by Stephanos Leandrou 16 May '17

16 May '17

Hello Freesurfer Developers, I want to perform texture analysis on the CA1 subfield of the hippocampus. Thus, I am using the recon-all command to generate the subfields. However, I want to perform texture analysis on the CA1 subfield only and I need to extract it from the original T1 image... How can I do this, what are the steps to save the CA1 subfield only? Thank you in advance... Stephanos

2 1

Re: [Freesurfer] GLM_Fit Question
by Mikael Novén 16 May '17

16 May '17

Dear Freesurfer experts, I also have this problem and can't seem to find the script. Would it be possible to get access to it? Thank you in advance, Mikael Novén

2 1

decimate overlay
by Dorothy Sincasto 16 May '17

16 May '17

Hi freesurfers, I have an overlay with 4k vertices and I want to decimate it to 1k. This overlay is actually an atlas with a label value for each vertex. My surfaces will have 1k vertices and I need the overlay to 1k so I know which areas each vertex belong to. I tried to decimate the atlas.mgh but it gives me this error: ERROR: MRISread: file '/Users/dsinc35/Desktop/projects/parcellation/MMP_atlas_L.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface! Maybe there is a way to project it? Any thoughts? Thanks, Dorothy

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Re: [Freesurfer] problem in extract subcortical volume as ROI
by Cong 16 May '17

16 May '17

Dear Doug I think my problem may caused by that extracted ROI have different coordination to original T1 image, although they match well in freeview. For example, one voxel is [148,144,131] in extracted left thalamus but [71,130,89] in original T1.nii and T1.mgz. So how to extract a ROI having same coordinate with T1? Regards Cong > > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > > > no idea. you'll proably have to contact the MRIcro group > > > On 5/16/17 8:28 AM, Cong wrote: >> Dear FSers >> I extracted left thalamus as ROI volume from aseg.mgz by this command: >> / mri_binarize --i control001/mri/aseg.mgz --match 10 --o >> control001/roi/l_thal.nii/ >> I overlaid l_thal.nii to control001.nii in MRIcro software in a >> Macbook and it looks well. >> However, when I overlaid l_thal.nii to control001.nii in Windows >> MRIcro, it comes a Warning: >> this NIFTI image includes an rotation transformation. >> When I open these two files same time, the left thalamus mismatch >> obviously to original T1 image. >> I attached an image to show my problem. I try to register this ROI >> volume to diffusion B0 image, >> and the registered left thalamus appears in the same wrong position >> as shown in attached image. >> Could someone tell me what?s wrong and how to solve it. >> >> Regards >> Cong

2 1

R: Thalamic seeds in FS-FAST
by stdp82＠virgilio.it 16 May '17

16 May '17

Please I wonder whether the thalamic seeds from 8001-8014 are available in FS 6.0 and, specifically for FS-FAST for functional connectivity?Thanks.Regards,Stefano

2 1

R: Thalamic seeds in FS-FAST
by stdp82＠virgilio.it 16 May '17

16 May '17

Please I wonder whether the thalamic seeds from 8001-8014 are available in FS 6.0 and, specifically for FS-FAST for functional connectivity?Thanks.Regards,Stefano

1 0

Thalamic seeds in FS-FAST
by stdp82＠virgilio.it 16 May '17

16 May '17

The thalamic seeds from 8001-8014 are available in FS 6.0 and, specifically for FS-FAST for functional connectivity.Thanks.Regards,Stefano

1 0

CA1 subfield extraction
by Stephanos Leandrou 16 May '17

16 May '17

1 0

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