[Freesurfer] Problem of Volumes differ in dimension in Longitudinal pipeline

command of dcm2nii and begin with "co". However, data of s12002_MRI2 was the file which begin with "o". But, when I used the file which begin with "co", they did not have same dimension. How could I solve the problem? (PS: have processed hundreds of data for subje

Re: [Freesurfer] How to extract significant result for each subject

Dear Douglas I try the analysis of volume and other indexes, not just thickness. I was confused that why the data of volume for each subject was so small (data in the file of cache.th13.pos.y.ocn.dat, e.g 1.39463 1.50616 2.53250) after using the command of mri_glmfit-sim (mri_glmfit-sim --

[Freesurfer] why the size become larger after fdr correction

Dear experts I use the following command and the Size(mm^2) was28.65. mri_surfcluster --in leg.volume.lh.20/g2v2/sig.mgh --thmin 3.7190 --no-adjust --sign abs --subject fsaverage --hemi lh --annot aparc.a2009s --mask leg.volume.lh.20/mask.mgh --sum leg.volume.lh.20/g2v2/sig.z3.7190.txt # Clus

[Freesurfer] unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim

small ( e.g 1.39463 1.50616 2.53250).Data of thickness was same as volume (e.g 1.83629 3.01648 2.16078). Could you tell the unit of each index? And could the data be used as further analysis, e.g correlation with IQ or other behaviors? Thank you Wang kangcheng

Re: [Freesurfer] unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim

Thank you doug Data of thickness: 1.83629 3.01648 2.16078 corresponds to lateraloccipital, frontalpole and superiorparietal. Why the number of volume (e.g 1.39463 1.50616 2.53250) was also so small ? was the unit cm^3? Wang Kangcheng

Re: [Freesurfer] unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim

3.984 46872 1185.43 -7.7 -71.9 50.4 0.06375 0.05929 0.06820 2487 precuneus 3 3.960 57039 3597.23 -10.6 64.4 -5.0 0.00020 0.0 0.00040 5545 frontalpole Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No

[Freesurfer] Why conn't find subject in Segmentation of hippocampal subfields

Dear experts When I do Segmentation of hippocampal subfields, it report that ERROR:connot find /nfs/preproc/muti_first/s What should I do next? THe scripts was following: SUBJECTS_DIR=/nfs/preproc/multi_first subject_list=${SUBJECTS_DIR}/scripts/check/hipp.list ## Get subjects

[Freesurfer] tkmedit error

: Setting global interpreter 00: 00: Wang Kangcheng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is

Re: [Freesurfer] tkmedit error

Thank you very much. I solve it using the method. Wang Kangcheng From: Z K Date: 2014-07-31 22:00 To: Freesurfer support list CC: kangchengwang0808 Subject: Re: [Freesurfer] tkmedit error The XQuartz upgrade from v2.7.5 to v2.7.6 broke some of the FreeSurfer GUIs. Please reinstall XQuartz

[Freesurfer] No voxel in mask using mri_binarize

But it found 0 voxels in final mask. How should I do ? Thank you Wang Kangcheng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only

[Freesurfer] how to extract the individual cortical thickness or volume value of significant cluster after RFT correction

Dear experts I have question regarding extracting the individual cortical volume value of significant cluster after RFT correction. I have 209 subjects in an analysis and G_pariet_inf-Angular showing significant correction with score of autism after RFT correction using command of mri_surfrf

Re: [Freesurfer] how to extract the individual cortical thickness or volume value of significant cluster after RFT correction

Dear experts I am sorry. There was some wrong with previous description. The results showed that G_pariet_inf-Angular was significantly positive correlated with score of autism after RFT correction using command of mri_surfrft_jlbr. With best Regards,kangcheng Wang ___

Re: [Freesurfer] how to extract the individual cortical thickness or volume value of significant cluster after RFT correction

Dear experts I run mri_glmfit-sim with the following command : mri_glmfit-sim --glmdir autistic.rh.volume.20 --cache 1.3 ${corr} --cwp 0.5 --2spaces did it right? In the creating files, I found cache.th13.pos.sig.ocn.annot. But I don't know how to load it in to freeview or tksurfer. Could y