[Freesurfer]  hippocampus subfields

Hi professor, I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the result that there was an obvious difference in left hippocampus, but no difference in right hippocampus. Then, I run segmentation of hippocampus subfields. The result showed there is no difference in to

[Freesurfer] hippocampus subfields

Hi professor, I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the result that there was anobvious difference in left hippocampus, but no difference in right hippocampus. Then, I run segmentation of hippocampus subfields.The result showed there is no difference in tota

Re: [Freesurfer] hippocampus subfields

Dear Zheng, Do you think you could provide us with some more detail on your analyses? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of 郑凤莲 <13181

Re: [Freesurfer] hippocampus subfields

Dear Eugenio, Thank you for your reply. I am sorry that I don't express it clearly. FIrstly, I ran egstats2label --subjects subjid --meas volume --segno 17 53 --tablefile $SUBJECTS_DIR/ASEGSTATS.txt' and acquired the volume value of left and right hippocampus. Then I used SPSS softwa

Re: [Freesurfer] hippocampus subfields

Hi again, Zheng, How many subjects do you have? Did you correct by intracranial volume? What is the age range? -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of 郑凤莲

[Freesurfer] Talairach of ROI

Hello FreeSurfer Developers, I have two questions about coordinate of ROI when running the QDEC module: (1) After drawing a ROI,the terminal demostrated the results like this: ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWPCWPLow CWPHi NVtxsWghtVtx Annot 1

[Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hello, I have posted several times about problems with skull-stripping with our dataset. We have tried gcut and multiple other options in other packages (AFNI, FSL, ANTS) to remove skull from structural images in our dataset with little success. Recently, a colleague suggested this may be due to

[Freesurfer] % overlap of multiple labels

Hello Freesurfer experts, I am using the mris_compute_parc_overlap command to compute the % overlap of two labels of the same region. Is there a way to do this for multiple labels? Best Idil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

[Freesurfer] CSF mask with aparc+aseg

Hello, I am attempting to generate a CSF mask from my aparc+aseg.nii image file. However, my mask seems to only encompass the ventricular system itself, ignoring any other CSF (see attached image). I attempted to make the mask using the following MRI_binarize command with FS labels. mri_binariz

[Freesurfer] cuda compile help

cuda v8 freesurfer git download from today (v6?), gtx1080ti gpus, brief env recap: 999 cd /usr/local/freesurfer-gpu.git/ 1001 export PATH=/usr/local/cuda-8.0/bin:$PATH 1002 export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64 1004 make clean 1008 ./setup_configure | tee -a setup_configure

Re: [Freesurfer] cuda compile help

I should have mentioned, i did not do any data dirs step, confused on this, just hoping to compile gpu code -Henk - Reply message - From: "Meij, Henk" To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] cuda compile help Date: Fri, Nov 17, 2017 6:24 PM cuda v8 freesurfer git

[Freesurfer] Local white and gray matter measures

Freesurfer Developers, I recently received FS data from a collaborator which included measures such for which, I as a FS user, I am familiar (i.e. GrayVol.lh.Frontal and GrayVol.rh.Frontal). Also included were the following 2 variables: Local_Gray_Matter and Local_White_Matter. I have not come

Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Hello Dear Sir/Madam, Please provide your expert suggestions to resolve the above-mentioned error. Thank you very much, Best regards Manoj On Sat, Nov 18, 2017 at 11:05 AM, Manoj Kumar wrote: > Hello Dear Sir/Madam, > > I am fairly new to the freesurfer and am getting an error "ERROR: > mpr2m

Re: [Freesurfer] hippocampus subfields

Hi Eugenio, Thank you very much. I have 54 subjects, aged from 21 to 71. I ran 'recon-all -all' and 'recon-all -qcache', and acquired the volume of hippocampus from the aseg.stats. Then I used SPSS to calculate correlation between age and volume without correcting by intracranial vol