[Freesurfer] Create a surface overlay with statistic results using AAL ROI

Hi all,   I have some statistical results for AAL 90 coordinates (correlation coefficients from network measurements x clinical data).   I would like to create an overlay to visualize in FreeSurfer standard (fsaverage) space, showing the areas with positive and negative correlations (and the scale

[Freesurfer] qdec

Hello FS experts,   I am trying to run qdec. When I load my data table it appears the following error message:   Loading data table /Users/carolinamrimkus/Documents/Cross_sectional_RRMS_RM1.dat... Number of columns:  290 fsid column:        1 Number of factors:  289 Number of subjects: 0 ERROR: Qd

[Freesurfer] QDEC longitudinal analysis

Hello Freesurfers,   I am trying to run QDEC for a longitudinal analysis.   I've run the command  "long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat" to adjust my qdec table to the right format for QDEC (with only one line / subject). I've also created the

[Freesurfer] long_mris_slopes error

Hi FreeSurfer experts,   I am trying to run Longitudinal Two Steps analysis.    In the long_mris_slopes I run the following command:   long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time y

[Freesurfer] Longitudinal post processing

Hello,   I am trying to make the Two Stage Longitudinal processing and when I give the command to prepare the data with QCACHE.   I've already set up the environment for FREESURFER_HOME, but it keeps appearing the error message:    ERROR: FREESURFER_HOME not defined in environment ERROR 1 : mri_lab

[Freesurfer] Mac OS X update

Hi all,   I have a simple doubt: I am updating my MAC OS X from Snow Leopard to Mavericks.   I am worried if FreeSurfer is going to run perfectly in the new OS X?   Thank you,  Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma

[Freesurfer] Image acquisition in different head coils

Hello,   Is it possible to compare FreeSurfer segmentation of images with similar protocol but acquired in different head coils (8 channel x 32 channel)? What are the possible bias and problems?   Thank you, Carolina  ___ Freesurfer mailing list Freesurf

[Freesurfer] image resolution

Hello, Someone asked me if it is possible to process T1 images with a 5mm slice / 1mm gap with FreeSurfer. Is it feasible to analyse? The person who asked used ITK tools to interpolate the images and reconstructed an isotropic voxel. I do not know if the post processed image with ITK can be validat

[Freesurfer] editing segmentation

Hello, The corpus callosum (CC) segmentation in my aparc+aseg.mgz file is not OK. It has included the fornix and ventricular areas within the CC. I erased with edit tool in the tkmedit and saved the new segmentation. How do I do to reprocess the subject and correct the stats (volume, etc)? Is the

[Freesurfer] qdec

Hello, In the qdec analysis the default smoothing factor is 10. What does it mean? For other technics such as fMRI we generally use a lower smoothing factor (~3 or lower). What would happen if I low down the FWHM? Thank you, Carolina ___ Freesurfer mail

[Freesurfer] Image resolution and reliability of freesurfer measurements

Hello, I would like to know if it is possible to process T1 images with a slice tickness of 5mm / 0.5mm of gap in freesurfer and obtain reliable cortical tickness measurements and parcelations? Thank you, Carolina Rimkus ___ Freesurfer mailing list Free

[Freesurfer] tracula

Hello,Is it possible to track fibers with TRACULA from the cortical parcelation masks obtained from recon-all or do we have to use the white matter parcelation to do so?Another question: if I use QDEC to find the areas with significant difference in the cortical tickness between two groups, is

[Freesurfer] TRACULA

Hello,Is it possible to track fibers with TRACULA from the cortical parcelation masks obtained from recon-all or do we have to use the white matter parcelation to do so?Another question: if I use QDEC to find the areas with significant difference in the cortical tickness between two groups, is it p

[Freesurfer] mri-convert

Hi, all,I would like to convert my DTI images from the REC-PAR format to .nii, so I could use in TRACULA and also other tools from freesurfer.Is it possible? What is the right comand line to do so?After the transformation, which image I use to register in the freesurfer domain?Thank you, Carolina _

[Freesurfer] WM hypointensities

Hello, How can I describe the method for WM hypointhensities segmentation and volume calculation? Can you suggest a reference? Thank you, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

[Freesurfer] corpus callosum segmentation

Hi,How is the segmentation of the corpus callosum is done? What are the proportions used? Are they equal in longitudinal lenth or it follows some a special segmentation?Do you know how to access the map (color map / visualization) of this segments?Thank you, Carolina ___

[Freesurfer] QDEC results and stats

Hello, all,I have 2 questions:- Does anybody know which structure is represented or correspond to "left ventral IDC" in aseg segmentation?- In QDEC analysis, when we obtatin the significant clusters and see the linear regression or correlation curve, what does it mean the "value" of the curve? Is

[Freesurfer] volumes 2

Hi, all,One more thing about the aseg: what does the CSF volume includes (the supratentorial arachnoid space? suprat + infrat?).Thank you, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

[Freesurfer] Intracranial volume

Hi, all,Does anybody know what the intracranial volume and supratentorial volume include? Does it include only the parenquima volume (white matter / gray matter volumes) or it includes the ventricules and CSF? What about the WM hhypointensities? Are they included in the WM Volume measurement or in

Re: [Freesurfer] Freesurfer Digest, Vol 90, Issue 54

Date: Fri, 12 Aug 2011 11:51:11 -0400 (EDT)From: "Nick Schmansky" Subject: Re: [Freesurfer] Fwd: qdecTo: "carolina.mr" Cc: freesurfer@nmr.mgh.harvard.eduMessage-ID: <50022.128.148.107.167.1313164271.squir...@mail.nmr.mgh.harvard.edu>Content-Type: text/plain;charset=iso-8859-1Car

[Freesurfer] Fwd: qdec

Mensagem originalDe: carolina.mr < carolina...@uol.com.br >Para: freesurfer-requ...@nmr.mgh.harvard.eduAssunto: qdecEnviada: 12/08/2011 00:43 Hello, When I load my qdec table it apears an error that I don't know how to solve. It says that there is not a nemline after my last su

[Freesurfer] freesurfer license

I have installed fressurfer and setup the environment for it, as it was described in freesurfer wikki. But I can't run the freesurfer. When I try any command it says that the command is not found. Probably, it is because I couldn't copy the license text to the .license file (I couldn't find it and