[Freesurfer] memory requirement...

Hi: I installed Freesurfer v4.4.0 in a PC with 1 GB RAM... There will be any problem to run Freesurfer in that PC, or only it runs slow ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel

[Freesurfer] tksurfer error in ubuntu...

Plot.tcl Reading /home/image/bin/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-977

[Freesurfer] freesurfer in Ubuntu 8.1 or 9.04

Hi: I want to install FSL under Ubuntu 8.10 or 9.04... There exist any problem, or I must use CentOS ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] anatomic better image for Siemens Avanto...

Hi: Which is the better anatomical sequence for freesurfer that I could get using a Siemens Avanto scanner ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

[Freesurfer] aseg.stats columns...

Hi: In the "aseg.stats" file, some columns has the title: "normMean", "normRange", etc... What is the meaning of the word "norm" ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Sant

[Freesurfer] mesh file...

Hi: Where I can find the mesh file that freesurfer generates for each patient ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] MGZ to DICOM conversion...

Hi: How can I convert an MGZ (or Analyze or NIFTI) file to a DICOM one?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

[Freesurfer] skull strip...

Hi: The command: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s only runs the skullstrip procedure ?... Which is the "clone" tool ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santi

[Freesurfer] tkmedit "save main volume as.." option...

ssue, but it was not... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.m

[Freesurfer] difference between lh.aparc.a2005s.stats and lh.aparc.stats...

Hi: In lh.aparc.a2005s.stats and lh.aparc.stats files, the volume of the cuneus is different... Why ?.. Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

[Freesurfer] tkmedit "save main volume as.." option...

ssue, but it was not... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.m

Re: [Freesurfer] tkmedit "save main volume as.." option...

Hi: Yes... I am editing brainmask.mgz... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl Nick Schmansky escribió: > are you editing brainmask.mgz? i'm u

[Freesurfer] watershed error...

! Linux image 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 18:40:08 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Oct 7 15:29:31 CLT 2009 -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9

Re: [Freesurfer] watershed error...

Hi: Yes... the occipital white matter has value 110 in general... The frontal white matter has voxels with values 94 to 117 aprox... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9

Re: [Freesurfer] watershed error...

Hi: How can I put the control points in the nu.mgz image ?... Sincerely Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl Nick Schmansky escribió: > check if the whitematter

Re: [Freesurfer] watershed error...

Hi: Ok... I test it with the command that you told me, and I added the option "wsthresh 35"... Then I got a good skull stripped image... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170

[Freesurfer] reference paper of freesurfer...

Hi: I need to put in a paper the main reference of freesurfer... Which?... I am searching it in the freesurfer wiki, but it appears many papers related to freesurfer... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago

[Freesurfer] tkmedit File menu option in gray...

Hi: Why the options "Save Manin Volume" and "Save Main Volume as" in TkMedit' "File" menu appears in gray (disabled) ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. T

[Freesurfer] segmentation error

Hi: Which is the error of the volumes that appears in aseg.stats ?... are they quantifiable ?... Because I notice that the right-hippocampus (for example) that appears in aseg.auto.mgz is bigger than the right-hippocampus of T1.mgz image... Sincerely, -- Gonzalo Rojas Costa

[Freesurfer] corpus callosum bad segmentation...

Hi: I tried to segment a T1 volume of a 3 years old patient... It fails to segment the cortex in some specific regions, and the corpus callosum appears such as white matter... Why ?... Could I correct it ?... Sincerely -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic

Re: [Freesurfer] corpus callosum bad segmentation...

Hi Bruce: And, How can I send you ?... Sincerely Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl Bruce Fischl escribió: > Hi Gonzalo, > > we'll need to see th

Re: [Freesurfer] bad segmentation ?

Hi Bruce: Ok... I will send you the complete study... I think that it could be a better solution... Which is the web page to upload it ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

DOF)... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 11-01-2010 11:40, Bruce Fischl escribió: > it's 6 by default. Not sure if 12 is implemented yet, but I k

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: Forgot the e-mail that I sent you recently... I will try using --12... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 11-01-2010 11:55, Douglas N Greve

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: Yes... I think that it is better to use the original images, but the SPMT_0001 is in MNI 152 space... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 11-01

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

SPMT_0001 image to freesurfer ones... ii) apply the inverse transformation (that I use to normalize the PET of the patient to MNI 152) to SPMT_0001, and then use 6 DOF to corregister SPMT_0001 to freesurfer... Sincerely Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: I could use the original PET data to generate the registration, but I need to do the second method that I explain in my e-mail... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9

Re: [Freesurfer] modification of tksurfer and tkmedit palettes

Hi Bruce: Yes... I asking about the color palette for other overlays... the heat scale... Because, I am trying to display as an overlay an image that have five discrete valuesa, and for that, I need another type of color palette... Sincerely, Gonzalo Rojas Costa Department of

Re: [Freesurfer] modification of tksurfer and tkmedit palettes

register.dat file that I got with bbregister... but if I try to load as a segmentation file in tkmedit, I couldn't specify the register.dat file... How can I solve that problem ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago,

[Freesurfer] a freeview bug ?...

Hi: I have freesurfer 4.4.0... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer

[Freesurfer] a freeview bug ?...

Hi: I load orig.mgz using freeview application, but when I try to load lh.thickness or rh.thickness file, freeview quits unexpectedly... it is a freeview bug ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile

Re: [Freesurfer] a freeview bug ?...

Hi: I load orig.mgz using "Load Volume" command, and I tried to download lh.thickness and rh.thickness using "Load Surface" in "freeview" application... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Cond

[Freesurfer] execute a freesurfer command at a specificed time/day...

Hi: How can I execute a freesurfer command at a specificed time/day ?... Any Ubuntu trick ?... Sincerely, -- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel

[Freesurfer] comparison between three MRI exams of same patient...

Hi: I have three MRIs of the same patient taken at different dates/years... I need to compare the hippocampus volume (for example) between the three MRI... I want to compare also the cortical thickness between the three MRI... How can I do such computation ?... Sincerely, Gonzalo

[Freesurfer] lobe volumes...

Hi: How can I get the volume of each lobe ?... each hemisphere ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] corpus callosum volumetry of some sagital slices only...

Hi: How can I get the volumetry of the corpus callosum in only some sagital slices ?... For example, 5 slices to the left and 5 to the right the medial line ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes

Re: [Freesurfer] other color map for a volume in freeview..

Hi: Thanks you very much for your answer... I need the GE-Color palette because that is the color palette used for PET images... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes

[Freesurfer] ICV meaning...

Hi: Which is the meaning of the Intracaranial Volume (ICV) ?... it includes only the brain, or also the skull ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile

[Freesurfer] ICV meaning...

Hi: In aseg.stats file, appears "lh-cerebral-white-matter" and "Left-Cerebral-White-matter": which are the difference between both values?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo

Re: [Freesurfer] corpus callosum volumetry of some sagital slices only...

sliced for example ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 19-03-2010 12:59, Bruce Fischl escribió: > mri_cc takes a &#

[Freesurfer] manual corregistration...

Hi: How can I do a manual corresistration with freesurfer ?... 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] cortical thickness more than 5 milimeters...

Hi: Sometime ago I asked about how to show cortical thickness more than 5 milimeters... Bruce answered me, but I could not find his answer... Could you please send me again ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology

Re: [Freesurfer] "Configure Overlay Display" tksurfer window...

Hi: I mean transparent... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 09-07-2010 14:25, Douglas N Greve

[Freesurfer] volume of temporal lobe, frontal lobe, etc...

Hi: How can I automatically compute, the volume of each brain lobe (temporal lobe, occipital lobe, etc) ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel

Re: [Freesurfer] volume of temporal lobe, frontal lobe, etc...

Hi: There is a tutorial related to the creation of labels ?... 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 El 13

[Freesurfer] ICV error and talairach registration bad outputs...

Hi: In the image that I am sending attach, there exist a not exact talairach registration in the superior part of the brain... That difference produce an important error in the ICV, or not ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer

[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

[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 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] 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] 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] 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

[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] 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] 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

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] 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] 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] 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

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] 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] 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

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 >

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: 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 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

[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] 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

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...

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 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

[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

[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] 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 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

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] 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

[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] 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] 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

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:

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: 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: 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

[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

[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

[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

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] 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] "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] 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] 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] 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] 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] 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] 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] WM and ASEG edition... recon-all continue command...

Hi I editted the wm.mgz and aseg.mgz files... Which recon-all command must I use to continue the processing ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] WM and ASEG edition... recon-all continue command...

g.mgz) ?... Sincerely, Gonzalo Rojas Costa El 25-07-2011 18:51, Bruce Fischl escribió: > -make all should work. > > cheers > Bruce > On Mon, 25 Jul 2011, Gonzalo Rojas Costa wrote: > >> Hi >> >> I editted the wm.mgz and aseg.mgz files... Which recon-all command

Re: [Freesurfer] WM and ASEG edition... recon-all continue command...

Hi Bruce: I ran with -make all, and I get good results... It seems that freesurfer uses the wm.mgz and aseg.mgz editions that I did... Sincerely, Gonzalo Rojas Costa El 27-07-2011 11:48, Bruce Fischl escribió: > Hi Gonzalo, > > Nick can correct me if I'm wrong, but the i

[Freesurfer] xopts script...

Hi: In the web page "FSTutorial/TroubleshootingData - Free Surfer Wiki" appears "Try using an xopts script first to change the intensity thresholds being used"... What is a xopts script ?... How can I use a xopts script to change the intensity thresholds ?... Sincer

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