[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..

nzalo 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 mailing list Freesurfer@nmr.mgh.harvar

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...

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 www.clc.cl Gonzalo Rojas Costa Laboratory for Advanced

[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

[Freesurfer] processing OASIS database using freesurfer 5

fied in expert.opts ?... 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

[Freesurfer] optimal sequence in a 1.5 T MR OPTIMA 450w GE MRI equipment...

Hi: Which is the optimal parameters for a morphometric sequence in a 1.5 T MR OPTIMA 450w GE MRI equipment ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] tkmedit bus error

Hi Carolina: And did you tested the tksurfer command ?... for example: tksurfer CORBIC_vol01 rh pial Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile > Message: 4 > Date: Sun, 18 Sep 2011 10:25:26 -0400 (EDT) > From: Bruce Fischl >

Re: [Freesurfer] tkmedit bus error

Hi Carolina: Is it possible, but in my case when the hard disk is full at the moment of the processing, I got a fatal error from recon-all command... Sincerely, Gonzalo Rojas Costa El 19-09-2011 9:53, Carolina Valencia escribió: > Thanks for the answers. > I think the problem w

[Freesurfer] volume of different lobes of the brain....

Hi: How can I get the volume of the different lobes of the brain (occipital, parietal, temporal, etc) ?... White matter and gray matter?... Labels ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] volume of different lobes of the brain....

Hi Douglas: The solution that you sent me runs only in freesurfer 5... Do you have ay solution for freesurfer 4.5.0 to compute GM+WM volume for each lobule ?... Sincerely, Gonzalo Rojas Costa On Mon, Sep 26, 2011 at 11:01 AM, Douglas N Greve wrote: > You can run mri_annotation2la

[Freesurfer] paper related to subcortical volume in children...

Hi: There exist any paper related to the subcortical volume in children (below 15 years old)?... any image database ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] cuda error...

tration took 15 minutes and 1 seconds. Abort"... How can I correct it ?... Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in thi

[Freesurfer] cortical thickness values in a specified gyrus...

Hi: In rh.aparc.a2009s.stats file, appears the average cortical thickness (ThickAvg) value for frontal middle gyrus (G_front_middle): how can I get the values of the cortical thickness in that gyrus (for example), not the average value ?... Sincerely, Gonzalo Rojas Costa

[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

[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] 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] 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] continue from a specific stage of autorecon2

Dear Pedro Paulo: I need to continue the freesurfer professing from a specific stage of autorecon2 (careginv; stage 4 of autorecon2 in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStableTablev4).. Which is the command line to do it ?... Sincerely, Gonzalo Rojas Costa

[Freesurfer] libtiff.so.3 instalaton error ?...

42:44 UTC 2008 i686 GNU/Linux recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009" Which is the problem ?... How can install libtiff.so.3 ?.. Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] libtiff.so.3 instalaton error ?...

idea ?... SIncerely, Gonzalo Rojas Costa Krish Subramaniam escribió: > Hi > > On Ubuntu, you will need to do the following: > cd /usr/lib > sudo ln -s libtiff.so.4 libtiff.so.3 > ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download ) > > The second command only work

Re: [Freesurfer] how to extract segmented hippocampus

Dear Douglas: And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz with the mri_binarize command ?... Sincerely, Gonzalo Rojas Costa > mri_binarize with --match 17 or --match 53 will do it > > doug > > Guang Zeng wrote: >> Hi, there, >>

[Freesurfer] memory error

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

[Freesurfer] memory error 2

/Linux How can I correct it ?... I have a PC with 2.5 GB RAM, and iit is the first processing that fails with an error related to memory... Why ?... Is it really a memory problem ?... There is a tip and trick that allows me to correct it ?... Sincerely, Gonzalo Rojas Costa

[Freesurfer] skull strip question...

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

[Freesurfer] erroneous segmentation of white matter and cortical thickness...

... Or the segmentation and cortical thickness are computed in a independent way ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Hi: bbregister is for 6 or 12 DOF corregistration ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] modification of tksurfer and tkmedit palette...

Hi: I want to modify the color palette that tksurfer uses to display overlay data... How can i modify it ?... the same question for tkmedit... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] modification of tksurfer and tkmedit palettes

Hi: I will write my question in another way: in which file could I find the palette that tksurfer and tkmedit uses to display overlay data ?... because I want to create other palettes... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing

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

Hi: I have three MRIs of the same patient took during different months... I need to compare the hippocampus volume fof the three exams (for example), the cortical thickness, etc... How can I do such computation ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic

[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] lobe volumes...

Hi: There exist any tool that could show me the structures that differ between each hemisphere more than a given percentage (volume) ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] difference between structures...

Hi: There exist any tool that could show me the structures that differ between each hemisphere more than a given percentage (volume) ?... For example: the hippocampus... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer

[Freesurfer] conitnue longitudinal processing...

nzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] continue longitudinal processing...

nning ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-ma

[Freesurfer] Longitudinal Stream...

?... 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 addressed. If you

[Freesurfer] realiability of cortical thickness...

thickness less than 1 mm?... How you can measure it ?... 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

[Freesurfer] definition of some aseg.stats measures...

al Volume" (IntraCranialVol, ICV) ?... The cerebelum is included in the ICV ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica Las Condes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr

Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 64

Hi Andreas: As far as I know, the complete command is: recon-all -s subjid -skullstrip -no-wsgcaatlas -wsthresh 35 -clean-bm Sincerely, Gonzalo Rojas Costa Laboratory of Medical Imaging Processing Department of Radiology Clínica Las Condes Santiago Chile > Date: Fri, 26 Mar 2010 11

[Freesurfer] normal value of Bra

Hi: I need to know which is the normal value of BrainSegVolNotVent (Brain Segmentation Volume Without Ventricles) of patients with 70 years aprox ?... Any paper ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile

[Freesurfer] normal value of "Brain Segmentation Volume Without Ventricles" value ?

Hi: I need to know which is the normal value of BrainSegVolNotVent (Brain Segmentation Volume Without Ventricles) of patients with 70 years aprox ?... Any paper ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile

[Freesurfer] normal value of "Brain Segmentation Volume Without Ventricles" value ?

Hi: I need to know which is the value of BrainSegVolNotVent (Brain Segmentation Volume Without Ventricles) of healthy volunteers at different ages... Any paper ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile

Re: [Freesurfer] normal value of "Brain Segmentation Volume Without Ventricles" value ?

d OASIS dataset ?... Sincerely, Gonzalo Rojas Costa Bruce Fischl escribió: > Hi Gonzalo, > > I think the OASIS dataset is distributed with asegs on them, so you could download that and calculate it yourself, although of course it will be age-dependent. > cheers > Bruce > > &g

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

Hi: Freeview only has grayscale, heat and jet in the color maps for a volume... How can I specify another color map ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

Re: [Freesurfer] WM segmentation error...

Hi Bruce: The patient has 3 years old... The parameters of the sequence, are: TI = 1100 ms, TR=1870 ms, TE=3.25 ms, Number of averages=1, FOV 256x256, Avanto 1.5 T... Sincerely Gonzalo Rojas Costa Bruce Fischl escribió: > Hi Gonzalo, > > what age is this subject? And what type o

[Freesurfer] Hippocampus volume normalization relative to what other volume ?...

Hi: If we want to compare the hippocampus volume between different patients, which other volume could I use to normalize it ?... the ICV ?... the volume of each hemisphere ?... And, if I want to compare the amygdala, for example ?... Sincerely, Gonzalo Rojas Costa Department of Radiology

[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 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

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] 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] 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

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