[Freesurfer] mri segstats "masksign abs" syntaxis option

External Email - Use Caution Hi: Using "--masksign abs" option: which must be the syntax for "--maskthresh" option in mri_segstats command? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University Santiago Chile __

[Freesurfer] SUVr in PET neurological images

External Email - Use Caution Hi: Is it possible to compute SUVr in neurological PET images ? Using PETSurfer? How? Sincerely, Gonzalo Rojas Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

[Freesurfer] dt_recon, CC_Anterior (T1) and FA corregistration.

External Email - Use Caution Hi: I used the following commands: dt_recon --i sub-OAS30003_ses-d1631_run-01_dwi.nii.gz --b sub-OAS30003_ses-d1631_run-01_dwi.bval sub-OAS30003_ses-d1631_run-01_dwi.bvec --s OAS30003_MR_d1631 --o dt_recon_result cd dt_recon_result mri_vol2vol --mo

[Freesurfer] dt_recon and corregistration (2)...

External Email - Use Caution Hi: The error is in a misalignment between the FA and CC_Anterior section. Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University ___ Freesurfer mailin

[Freesurfer] hounsfield units based in some aseg.mgz labels

External Email - Use Caution Hi: I completed the co-registration of CT images to a freesurfer processed MRI image using the command: mri_coreg --mov sub-OAS30001_sess-d3132_CT.nii.gz --reg reg.lta --s OAS30001_MR_d0757 How can I get the mean and SD Hounsfield units (from co

[Freesurfer] hounsfield units for some aseg.mgz labels

External Email - Use Caution Hi: I completed the co-registration of CT to a freesurfer processed MRI image using the command: mri_coreg --mov sub-OAS30001_sess-d3132_CT.nii.gz --reg reg.lta --s OAS30001_MR_d0757 How can I get the mean and SD hounsfield units of some aseg.mgz

Re: [Freesurfer] freeview runtime error...

External Email - Use Caution Hi: I tested all the commands that you told me, but, I still have the error that I had specified to you: "gonzalorojascosta@gonzalobrain:~$ freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling th

Re: [Freesurfer] freeview runtime error...

External Email - Use Caution Hi: it is freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460, under Ubuntu 18.04.4 LTS. In a real physical ubuntu. Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

[Freesurfer] freeview runtime error...

External Email - Use Caution Hi: I tried to run freeview, but I got the following error: "This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, min

[Freesurfer] freeview runtime error...

External Email - Use Caution Hi: I got the following error running freeview in Ubuntu: "freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb

[Freesurfer] windows-based software to read freesurfer images...

External Email - Use Caution Hi: Is there any software for microsoft windows (and/or ubuntu) that allows you to read mgz file format images, and transformations in lta format? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae Universi

[Freesurfer] Freesurfer remotely processing

External Email - Use Caution Hi: Is there any free implementation that allows me to process images with freesurfer remotely? Sincerely Gonzalo Rojas Costa Medicine School Finis Terrae University ___ Freesurfer mailing list

[Freesurfer] remote access to freesurfer installation...

External Email - Use Caution Hi: Is there a freesurfer facility where an MRI study can be processed remotely? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] freeview error....

lling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb." How can I correct it? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list

[Freesurfer] online freesurfer

External Email - Use Caution Hi: Is there a freesurfer-based system that allows processing online an mprage image? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Longitudinal SAMSEG with multi-contrast data

utput outputDir/" ? Sincerely, Gonzalo Rojas Costa ___ 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 addres

[Freesurfer] fsl fmri thresh_zstat1.nii file showing in fsaverage pial surface

External Email - Use Caution Hi: I processed an fMRI task using FSL. I got the standard image coregistered result... How can I show the thresh_zstat1.nii file in fsaverage pial surface? Sincerely, Gonzalo Rojas Costa

[Freesurfer] mri_synthseg problem with CT... freesurver v 7.3.2

from 0-80 hounsfield units... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] automatic screenshots to all axial slices

External Email - Use Caution Hi: I need to take screenshots of all axial slices of a volumetric image that I am viewing using freeview (flair with a segmentation). How can I do it automatically? Sincerely, Gonzalo Rojas Costa

[Freesurfer] multiple axial slice screenshots

External Email - Use Caution Hi: I need to take screenshots to all axial slices of a volumetric image that I am viewing using freeview (flair with a segmentation). Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list

[Freesurfer] mri_synthseg error...

self._metric_methods[self._label_length].create(*args) tensorflow.python.framework.errors_impl.AlreadyExistsError: Another metric with the same name already exists." Which could be the problem ? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 44

[Freesurfer] mri_synthsr with CT images

/home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz --o /home/developer/Documents/OAS31367 --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 Killed What does "Killed" mean? Any log file? Sincerely, Gonzalo R

[Freesurfer] CT and mri_synthsr

/home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz --o /home/developer/Documents/OAS31367 --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 Killed What does "Killed" mean? Any log file? Sincerely, Gonzalo R

Re: [Freesurfer] SynthSeg with CT images.

External Email - Use Caution Ok... Thanks you very much... Gonzalo Rojas Costa On Wed, Mar 8, 2023 at 5:38 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > I added a flag (--ct) to mri_synthsr in FreeSurfer so people don’t need to > c

Re: [Freesurfer] SynthSeg with CT images.

External Email - Use Caution Hi Benjamin: I tested with the clipping, and it works ok with a CT image. Sincerely Gonzalo Rojas Costa El mié, 8 de mar de 2023, 14:39, Benjamin Billot escribió: > Yes, agreed. > > Gonzalo: Also, if SynthSeg still gives you a bad res

[Freesurfer] SynthSeg with CT images.

External Email - Use Caution Hi: I tried SynthSeg using CT images, but I got very bad results... CT images must have some specific characteristics? I tried with axial acquisition and volumetric one Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las

[Freesurfer] CT conversion from DICOM to MGZ

0 and rerun." Where can I find the FS_RESCALE_DICOM option ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail i

[Freesurfer] installation of two versions of freesurfer on same computer...

External Email - Use Caution Hi: How can I install two different versions of freesurfer on the same computer? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] trac-all error

r for model-based eddy-current distortion correction, ERROR: must specify PE direction" Why? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

[Freesurfer] infantFS computer requierements

? VRAM? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] T1 gadolinium

External Email - Use Caution Hi: SynthSeg is useful for T1-GD volumetric images? Another algorithm, software? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

[Freesurfer] convert .reg.lta linear transform to an ITK transform for 3DSlicer

External Email - Use Caution Hi: How can I convert a .reg.lta linear transform to an ITK transform for 3DSlicer? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

[Freesurfer] load PET.reg.lta freesurfer corregistration file in 3D slicer 4.11

External Email - Use Caution Hi: I coregistered a PET file to a freesurfer data using mri_coreg command. I imported the freesurfer-generated data to 3D Slicer. How can I import the PET.reg.lta file in 3D Slicer? Sincerely, Gonzalo Rojas Costa Department of Radiology

[Freesurfer] TRACULA question

External Email - Use Caution Hi: Is it possible to use input diffusion files in MOSAIC IMA Siemens file format directly? Or is it necessary to convert to nifti file format first? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of

[Freesurfer] "B0 distortion correction with reverse-polarity DWIs"

gMyCGFELAc-ReX5c6q891gCUl35SRXIWZUO0yvLGMBLAKZQpvywUwHckAUlf5_8SQ9ch05XQW5ockkLH0E_yaqNOGE5DPhCDJRX5qjywx1yF5JcMkcPbiNNbEc34hoNaOpP1Y0xmpNNirDZiIGlgBoFYRkmonGJsbGHxJHNnN8Vok295ZKv2AcDxmDMdvWQZIyAINNHpr5ixKNj5750wSN4LPTZHn8/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ftrac-all, but It was not clear to me how to solve the problem. Sincerely, Gonzalo Rojas Costa Department of Radiology C

[Freesurfer] “Illegal instruction (core dumped)” in mri_synthseg and mri_synthsr

External Email - Use Caution Hi: I tried to use mri_synthseg and mri_synthsr commands, but I got the error message "Illegal instruction (core dumped)". Any solution? I have the March 31st, 2022 version. Sincerely, Gonzalo Rojas Costa Department of Radiology C

[Freesurfer] "Vertex Talairach" in tksurfer?...

External Email - Use Caution Hi: "Vertex Talairach" in tksurfer: how does it relate to MNI coordinates? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-9777

[Freesurfer] MNI coordinates to vertex...

%2Farticles%2F10.3389%2Ffnins.2018.00235%2Ffull How to convert that MNI coordinates to vertex in the pial surface ? Sincerely Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 http://secure

[Freesurfer] resolution greater than 1 mm segmentation

? Especially hippocampal segmentation. Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Best mesh generation from hippocampus aseg segmentation

External Email - Use Caution Hi: Which is the best library or software to create the hippocampus mesh from aseg segmentation? Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] virtual disk image of freesurfer 7.1.1

External Email - Use Caution Hi: Where can I find the virtual disk image of freesurfer 7.1.1 ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] big difference between ICV same patient....

reprocess ? Other question... what do you mean with " You might be comparing dewarped vs not dewarped" Sincerely, Gonzalo Rojas Costa >Message: 6 >Date: Thu, 10 Sep 2020 12:42:41 -0400 >From: "Douglas N. Greve" >Subject: Re: [Freesurfer] big difference betwe

[Freesurfer] big difference between ICV same patient....

system in both cases... I reviewed the coregistration to MNI305 and it is reasonably good in both cases... The case was reviewed by an expert neuroradiologist, and she does not consider that there is a significant visual difference between both sizes. Sincerely Gonzalo Rojas Costa

Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...

External Email - Use Caution Hi: No... I don't have any specific issue... I have a previous freesurfer version installed that I want to continue using. So I want to install version freesurfer 7.0 on a virtual machine... Sincerely, Gonzalo Rojas Costa > Message:

[Freesurfer] freesurfer 7.0.0 in a virtual machine...

External Email - Use Caution Hi: How can install freesurfer 7.0.0 in a virtual machine ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] libpng12.so.0

I solve it ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?

External Email - Use Caution Hi: Where can I find the FreeSurfer 6.0 disk image for VirtualBox? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] library to show freesurfer data embedded in a web page (mesh and axial, coronal, sagital slices)

Medical Imaging (AMI) JS Toolkit" (https://fnndsc.github.io/ami), but I have some problems... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] web page library to show freesurfer data (mesh and axial, coronal, sagital slices)

External Email - Use Caution Hi: Do you know any library to show freesurfer data (mesh and axial, coronal, sagittal slices) embedded a web page? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer

[Freesurfer] Cortical thickness values more than 5 mm

External Email - Use Caution Hi: How can I get cortical thickness surface image with values more than 5 mm? Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] cortical thickness values in the insula...

External Email - Use Caution Hi: How can I get the different values of cortical thickness in the insula? Not the mean and SD... Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] curved reformat image....

External Email - Use Caution Hi: How can I get in an automatic way curved reformat images (for example, see paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009174/) Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology

[Freesurfer] "CorticalWhiteMatterVol" ?

External Email - Use Caution Hi: What is the meaning of the "CorticalWhiteMatterVol" measure? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e

[Freesurfer] myelination and freesurfer segmentation...

External Email - Use Caution Hi: Could you please tell me if Is there is a paper on myelination and segmentation? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes

[Freesurfer] local Gyrification Index

Hi: To compute local Gyrification Index is necessary Matlab... Complete installation or only runtime? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170

Re: [Freesurfer] lobes volume (WM and GM)

Hi Douglas: I am looking for that paper, but I couldn't found it... Which is it ? Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-21

Re: [Freesurfer] lobes volume (WM and GM)

Hi Douglas: I am looking for papers that used the volume of each lobe computed using freesurfer, but I couldn't found it... Do you know any?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441

Re: [Freesurfer] lobes volume (WM and GM)

Hi Douglas: Why you specified 5mm as the default value for the --wmparc-dmax option in mri_aparc2aseg command? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56

Re: [Freesurfer] lobes volume (WM and GM)

Hi Douglas: By removing --rip-unknown I got the same results... Why ?... Sincerely, Gonzalo Rojas Costa > Date: Tue, 12 Sep 2017 12:33:11 -0400 > From: Douglas N Greve > Subject: Re: [Freesurfer] lobes volume (WM and GM) > To: freesurfer@nmr.mgh.harvard.edu > Message-ID:

[Freesurfer] lobes volume (WM and GM)

Hi: I need the complete WM volume for each lobe... not only the WM up to 5mm beneath the lobes (default value) or 20 mm... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago

[Freesurfer] volumetric difference between 1.5 T and 3.0 T...

Hi: There exist any difference between the volumetric values obtained using 1.5T and 3.0T images ? Any paper about it ? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile

Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 22

freesurfer 5.3 and 6.0 in the same operating system, there will be any difference in subcortical volumes and/or cortical thickness ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago

[Freesurfer] 5.3 vs 6.0 volumetric differences...

Hi: There are any difference between subcortical structures volume, cortical thickness, supratentorial volume, gray matter volume, etc. computed with freesurfer 5.3 and 6.0 ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing

[Freesurfer] 1.5T vs 3.0T longitudinal study...

Hi: I have two timepoints of the same patient: the first is in 1.5T and the second in 3.0T... Is it possible to do the longitudinal study (subcortical volumes) using the Workflow Summary described in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ?... Sincerely, Gonzalo Rojas

[Freesurfer] comparison of subcortical volume with 1.5 T and 3T...

Hi: I have some longitudinal study of a patient with 1.5 T images... now, we have 3T mprage images of the same patient... how can I do the comparison of the subcortical volume of the patient ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image

[Freesurfer] options for 7T images...

Hi: Must I use any recon-all option for 7T images ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

[Freesurfer] Ubuntu 14.04 LTS 64 bits

Hi: Which freesurfer version must I install in Ubuntu 14.04 LTS 64 bits ?... Sincerely... Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2

[Freesurfer] Longitudinal study: analyze results

Hi: For example: if I want to compare the volume of left hyppocampus in two time points, could I compare the volume in aseg.stats file of both "long" folders?... Sincerely, Gonzalo Rojas Costa -------- Gonzalo Rojas Costa Advanced Medical Image Processing

[Freesurfer] Longitudinal study... analyze of results....

files in each "long" folder ?... Sincerely, Gonzalo Rojas Costa -------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170

[Freesurfer] Longitudinal difference...

in both cases is: 1348899,976 and 1332590,755197... Why is the difference in volumen in the structures in both studies ?... Why is always bigger at 42 years old than 39 years old?... Any technical problem ?... We got a similar difference by normalizing with ICV... Sincerely, Gonzalo Rojas Costa

Re: [Freesurfer] Nframes greater than 1...

Hi: I don't know it is an mprage got in our center using a Siemens Avanto equipment freesurfer specify that the images has two nframes and for that reason freesurfer could not process it... Sincerely Gonzalo Rojas Costa >Hi Gonzalo > >what is in the two frames? >Bru

[Freesurfer] Nframes greater than 1...

Hi: I have an mprage image with nframes = 2... how can I convert it to use it in freesurfer ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las

[Freesurfer] Pons and midbrain segmentation....

Hi: How can I segment the pons and midbrain using freesurfer ?... or any other segmentation software that do such task ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las

Re: [Freesurfer] Generation of brodmann area label and statistics..

Hi Bruce; Thanks you very much... It rans ok... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel

[Freesurfer] Generation of brodmann area label and statistics..

Hi: I have some freesurfer processed studies I used 5.1 version, and now I found that it don't has the brodmann area labels and statistics generated in some studies... How can I create it without doing again the complete recon-all ? Sincerely, Go

[Freesurfer] Newest freeview version...

Hi: Which is the freeview newest version ?... the one that is included in freesurfer 5.3.0 package ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla

[Freesurfer] (no subject)

the GE images appears smoothed in comparison with the Siemens Avanto mprage images that we also use... Any comments ? Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes

[Freesurfer] a second "subjcts" folder...

Hi: I has a "subjects" folder in one physical harddisk... How can I continue processing more images in another "subjects" folder in a new physical harddisk without erasing the first one ?... Sincerely Gonzalo Rojas Vosta -- Gonzalo Rojas Costa Laboratory for Ad

Re: [Freesurfer] white matter volume per lobe...

Hi Douglas: The file is the OAS1_0001_MR1 case of OASIS-BRAINS database that I re-processed using freesurfer 5.2.0... Sincerely, Gonzalo Rojas Costa On Fri, May 31, 2013 at 12:12 PM, Douglas N Greve wrote: > don't know what's going on. Can you upload the subject to our file

Re: [Freesurfer] white matter volume per lobe...

251 252 253 254 255 nctx = 688931 Used brute-force search on 139 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to mri/lobulitos_2.mgz Sincerely, Gonzalo Rojas Costa On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve wrote: > can

Re: [Freesurfer] white matter volume per lobe...

Hi Doug: But, in the mri_aparc2aseg command, I test with the "--wmparc-dmax 200" option... I put that big value to test it, but I got the image that I sent you... Sincerely, Gonzalo Rojas Costa On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve wrote: > > It is probably th

Re: [Freesurfer] white matter volume per lobe...

Hi Doug: It is labeled as wm-rh-fusiform and wm-lh-fusiform Sincerely, Gonzalo Rojas Costa On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve wrote: > what is is labled? > > On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: >> >> Hi Doug: >> >>I use

[Freesurfer] white matter volume per lobe...

commans with different options, but I couldn't get the volume that I need... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.c

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Hi Nick: Ok... Tomorrow Sunday I will download and begin to test it... And which other new features has version 5.3.0 over 5.2.0 ?... Sincerely, Gonzalo Rojas Costa On Fri, May 3, 2013 at 5:46 PM, Nick Schmansky wrote: > this link is here: > > ftp://surfer.nmr.mgh.harvar

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Hi Bruce: Ok... I am interested in the 5.3 beta version... Sincerely, Gonzalo Rojas Costa On Fri, May 3, 2013 at 8:41 AM, Bruce Fischl wrote: > Hi Gonzalo > > version 5.3 is midway through the QA process. We can give you a beta of it > in the next couple of days if you wa

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Hi Bruce: And, where is version 5.3 ?... in the "nightly dev builds" ?... Sincerely, Gonzalo Rojas Costa On Thu, May 2, 2013 at 9:29 PM, Bruce Fischl wrote: > Hi Gonzalo > Try it with 5.3, or upload and I can r. It for you > Bruce > > > > On May 2, 2013,

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Hi Bruce: I tested 4.5 and 5.1 versions... with the first I processed complete, and with 5.1 only autorecon1 section... Sincerely, Gonzalo Rojas Costa On Thu, May 2, 2013 at 1:31 PM, Bruce Fischl wrote: > what version are you running? The newer ones are *much* better at this >

[Freesurfer] tip and tricks with patient with one big ventricle...

problems... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer

[Freesurfer] freesurfer 5.1 vs 5.2

Hi: How can install version 5.2 in a computer without uninstalling version 5.1 ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9

[Freesurfer] GM and WM volume for each lobe...

lh white And, for WM I know that I must use the commands: mri_aparc2aseg and mri_segstats, but I don't know the options of each command that I must use... Could you please send me the complete commands for WM?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical

[Freesurfer] default lateral extent corpus callosum

Hi: What is the default thickness of the corpus callosum?... 5 mm ?... 2 mm for each side from midline ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel

[Freesurfer] white/gray surface and volumetric segmentation (aseg) difference...

results... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer

Re: [Freesurfer] tracula error...

Hi Anastasia: And, which options do you think I must use with bedpostx ?... The default ?... Sincerely, Gonzalo Rojas Costa On Mon, Jul 30, 2012 at 5:36 PM, Anastasia Yendiki wrote: > > Hi Gonzalo - This has come up a few times recently. Please see here: > http://www.mail-ar

[Freesurfer] tracula error...

NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected That problem occurr because my PC is not a parallelized environment?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processin

[Freesurfer] tracula RAM memory ?...

Hi: How much memory needs tracula to process a DTI study ?... Because my PC (Ubuntu Linux, 4GB RAM) exit because it can't allocate memory in trac-preproc... There exist any tip & trick in such a case?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image P

[Freesurfer] tracula processing time ?...

Hi: How much time (aprox) take each step of tracula processing ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

[Freesurfer] pial mesh decimation...

Hi: How can I do a decimation to 1 polygons aprox to the pial surface ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

[Freesurfer] Corpus callosum aseg division...

Hi: Any reference about how freesurfer divides the corpus callosum in CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, CC_Anterior ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] mri_cc and CC thickness option...

Hi: For example, if I execute the mri_cc command with "-t 2", mri_cc shows me "setting callosum thickness to 5 mm"... Why ?... What exactly specify the -t option ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mai

[Freesurfer] WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...

Hi: In aseg.stats the WM hypointensities is included in left-cerebral (right-cerebral) white matter volume ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

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