Freesurfer

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30132 discussions

Posting to Freesurfer
by Herring, Elizabeth J. 17 May '17

17 May '17

Hello, I just subscribed to Freesurfer and I would like to be able to post to the list. My email is herring.75(a)osu.edu Thanks, Elizabeth Herring

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ERROR: must specify input table of b-values
by David Yang 17 May '17

17 May '17

Hello, I am trying to run the trac-all -prep command in TRACULA on a participant. However, every time I run the command trac-prepoc exits with errors and I get the message: 'ERROR:must specify input table of b-values'. I checked over the configuration file and everything seems correct: b-value table is specified and in the correct 1 column format, and there are the same number of b-values, b-vectors and DTI volumes. Does anyone know why I am getting this message? 1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) Platform: OS X Mavericks 10.9.5 3) trac-all -prep -c $VSDEVEL_DATA/VSDevel_outputs/dmric_1089001_06M.txt 4) Attached is the configuration file, b-values, b-vectors Thanks, David

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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

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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*

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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

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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

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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

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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

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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

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