[Freesurfer] recon-all error (Freesurfer)

86_64 x86_64 x86_64 GNU/Linux4) recon-all.log: see attached In addition, I'm seding information for error. ------- Gwang-Won Kim, Ph.D. Research FellowResearch Institute of Medical ImagingChonnam National University Medical School42 Jebongro, Donggu, Gwang

[Freesurfer] to evaluate volume and thickness of the amygdala using asegstats2table

Hello FreeSurfer Developers,   I have a question. I want to evaluate volume and thickness of the amygdala using asegstats2table. How do I obtain volume and thickness of the amygdala using asegstats2table? ___ Freesurfer mailing list Freesurfer@n

[Freesurfer] Recon-all error: -autrecon2 unrecognized

Hello FreeSurfer Developers,I saw UserContributions/FAQ of FreeSurfer as following:Q. I have already skull-stripped data. Can I submit it to recon-all?A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differentl

[Freesurfer] Question - how to smooth and transform into a template

-- Original Message -- Date: Wednesday, May 24, 2017 01:48:33 PM From: "Gwang-Won Kim" To: Subject: Question: how to smooth and transform into a template Hello FreeSurfer Developers,I read a sentence in a paper associated with Free Surfer as following: Before statistical

[Freesurfer] How to process ANCOVA with age as covariate

Hello FreeSurfer Developers, To compare cortical thickness between groups, I want to process analysis of covariance (ANCOVA) adjusting for age.When "mri_glmfit" process, do I insert "0 0 1 -1" in .mtx file?Would you please tell me how to process ANCOVA with age as covariate. FSGD FILEClass Group1Cl

[Freesurfer] How to process ANCOVA with age as covariate

Hello FreeSurfer Developers,To compare cortical thickness between groups, I want to process analysis of covariance (ANCOVA) adjusting for age.When "mri_glmfit" process, do I insert "0 0 1 -1" in .mtx file?Would you please tell me how to process ANCOVA with age as covariate.FSGD FILEClass Group1Clas

[Freesurfer] I have a question for "Segmentation of thalamic nuclei."

External Email - Use CautionDear there, I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version.I filled out “segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR]”.In two computer, there were massages “segmentThamicNuclei.sh: Command not found”

[Freesurfer] I have a question for "matlabruntime"

External Email - Use CautionDear there, I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version(freesurfer-linux-centos6_x86_64-dev.tar.gz).The OS of my notebook CentOS (6.10).MATLAB --> /usr/local/MATLAB/R2017bMRCv84 --> /usr/local/frees

[Freesurfer] I have a question for "matlabruntime"

/local/freesurfer/MCRv84I filled out “segmentThalamicNuclei.sh bert [SUBJECTS_DIR].In my notebook, there were the messages below.Best,Gwang-W

[Freesurfer] Problem for LGI

External Email - Use CautionDear there,I tried to process "recon-all -s -localGI"But, there were messages below.Thank you.-               < M A T L A B (R) >                  Copyright 1984-2017 The Mat

[Freesurfer] I have a question for subthalamic nucleus ROI.

External Email - Use Caution  Hi there,   I would like to make a ROI for subthalamic nucleus. But, there is not label name for subthalamic nucleus in FreeSurferColorLUT. How do I make a ROI for subthalamic nucleus in T1 image?   Thank you. Gwang-Won __

[Freesurfer] Substancia-Nigra ROI

External Email - Use CautionHi there,   I would like to make a ROI for a left Substanci Nigra. It is possible to make the ROIs for thalamus, putamen, caudate, etc. But, it is not possible to make the left Substanci Nigra  ROI as follows: mri_binarize --i $SUBJECTS_DIR/$subj/mri/a

[Freesurfer] Clusterwise correction for multiple comparisons

pheres and subcortical structures.I have a question. How can I do if I use p-values corrected only for subcortical structure? Good luck,Gwang-Won Kim  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

[Freesurfer] (Revised) Clusterwise correction for multiple comparisons

pheres and subcortical structures.I have a question. How can I do if I use p-values corrected only for subcortical structure? Good luck,Gwang-Won Kim  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

[Freesurfer] Using mask image

External Email - Use CautionHi there, I would like to show activation map in the thalamus, caudate nucleus, and hippocampus. activation.mgh : activation map in the subcortical areasmask.mgh: including the thalamus, caudate nucleus, and hippocampus How do I make the activation map in

[Freesurfer] mri_glmfit error

ol 3), Max=724.138794 (col 8) The scale is much different between columns 3 and 8, you may want to  normalize by subtracting the mean and dividing by the standard deviation.  What is the problem? Gwang-Won Kim ___ Freesurfer mailing list

[Freesurfer] (revised) mri_glmfit error

e mean and dividing by the standard deviation.  What is the problem? Gwang-Won Kim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Assign different number in FreeSurferColorLUT

UT in FreeView but 3 volumes (3 ROIs) have the color of number #1 in FreeSurferColorLUT. How do I assign different number of FreeSurferColorLUT in 3 volumes? Thank you,Gwang-Won Kim ___ Freesurfer mailing list Freesurfer@nmr.m

[Freesurfer] mask for cortical thickness

External Email - Use CautionHi there, I would like to analyze clusterwise correction for multiple comparisons using masks (exsample; superior frontal cortex and middle frontal cortex).I know that "2spaces" means adjust p-values for two hemispheres as follow; mri_glmfit-sim --glmdir

[Freesurfer] Thickness problem

External Email - Use CautionHi there, I obtained results for right thickness using aparcstats2table.Then, ANCOVA was used to compared right thickness between two group (age, sex, edu, ICV as covariates)using SPSS. A group showed higher right thickness in the superior fr

[Freesurfer] Recon-all

External Email - Use CautionHi there, I tried to process "recon-all" as follow: recon-all -autorecon-all -i A.nii.gz -s A -parallel But, there is the message for 4 days as follow (FREESURFER _HOME /usr/local/freesurfer/dev):#@# Fix Topology rhmris_fix_topology -maz -sphere qsphere.n

[Freesurfer] Problem for cortical thickness analysis

External Email - Use Caution Hi there, I obtained results for right thickness using aparcstats2table.Then, ANCOVA was used to compared right thickness between two group (age, sex, edu, ICV as covariates)using SPSS. AA group showed higher right thickness in the superior frontal gyrus

Re: [Freesurfer] Thickness problem

result of aparcstats2table Then look at the sig.table.dat Oftentimes, the SPSS analysis is not doing exactly the same thing as the mri_glmfit analysis. On 12/6/2019 11:25 AM, Gwang-Won Kim wrote: External Email - Use Caution Hi there, I obtained results for right thickness using aparcstats2ta

[Freesurfer] Problem for mri_glmfit

External Email - Use CautionDear Sir, I ran "mri_glmfit" commend.I had no problem when I used 3 covariates. But I'm having a problem with "mri_glmfit" when I used 4 covariates.I'm sending comment line, FSGD, and design matrix as the attached files. Thank you.Gwang-Won

[Freesurfer] Seed region in anatomical data for resting state fMRI data

External Email - Use CautionHi there,I obtained a seed region (left superior frontal)from anatomical data to process resting state fMRI data as follows: fcseed-sess -o lh.SFC.dat -segid 1028 -s session -fsd rest. I wonder if what the seed region is the left superior frontal was corr