[Freesurfer] Longitudinal difference...
Hi: We have GE 1.5T MRI fspgr volumetric acquisition of a MS patient (39 years old) and a Siemens 3T MRI mprage acquisition of the same patient three years after (42 years old)... we processed that images to got the volume of some structures that we need and compare... but, we found that multiple brain structures are bigger in the 42 year old images: right hypocampus (3187-3755), right cerebral white matter (151164-172448), right Cerebellum-White-Matter (12652-14902), right Cerebellum-Cortex (48812-51935), etc... And a similar situation occurs in left hemisphere... The Intracranial volumen 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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal study... analyze of results....
Hi: I want to do a longitudinal study between two time points of a patient... I want to compare the volume of the hypocampii, white matter, etc... I did the computation of both time points, I created the "base" image, and the "long" ones... How can I analyze the aseg.stats 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 Cel: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 Laboratory 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] (no subject)
Hi: Which is the optimal parameters for a morphometric sequence (fspgr?) n a 1.5 T MR OPTIMA 450w GE MRI equipment ?... Because, we are using an fspgr 1mm isotropic sequence, but we got wrong defined borders in some structures... for example, hypocampus, cortex-wm... I think it could be because 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 Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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, 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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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: 56-9-97771785 www.clc.cl El nov 15, 2013 11:12 AM, "Bruce Fischl" escribió: > Hi Gonzalo > > recon-all -s -balabels > > should do the trick > > cheers > Bruce > On Fri, 15 Nov 2013, Gonzalo Rojas Costa wrote: > > >> 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, >> >> >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Cl?nica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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 Medical Image Processing Department of Radiology Clinica 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 22
Hi Martin: But, between version 5.3 and 6.0 there are any differences in the algorithms for subcortical volume, cortical thickness, etc., or only additions to that, such as the hippocampus or brainstem subfields ?... and in general, if I segment for example the same healthy control in 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, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl On Wed, Nov 11, 2015 at 7:57 AM, wrote: > -- > > Message: 24 > Date: Tue, 10 Nov 2015 16:57:43 -0500 > From: Martin Reuter > Subject: Re: [Freesurfer] 5.3 vs 6.0 volumetric differences... > To: Freesurfer support list > Message-ID: <56426857.3030...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi Gonzalo, > > of course. > > There is even a difference when running the same FS version with a > different operating system (due to differences in the numerical > libraries, optimizations etc). > > Are changes big or small? > In a single case they can be very big (it could be a case that failed in > 5.3 and works with 6.0 - or the other way) > > Are changes directional (significantly larger or smaller volumes/thickness)? > Hard to say and hard to detect if small, but it can happen due to a new > algorithm that measurements are consistently larger (/smaller) than in > another version. We try to avoid this, but it can theoretically happen. > > That is why it is so important to stick with the same version and > operating system when processing data. > > Best, Martin > > On 11/10/2015 04:48 PM, Gonzalo Rojas Costa wrote: >> 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 >> > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tip and tricks with patient with one big ventricle...
Hi: I has the MPRAGE of a patient with one big ventricle, and the other has normal shape and size... Any tip and tricks to process it ?... Because freesurfer fails from the beggining of the process (VERY BAD talairach registration)... I test -bigventricle option of recon-all, but I got the same 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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 > Bruce > > On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: > >> Hi: >> >> I has the MPRAGE of a patient with one big ventricle, and the other >> has normal shape and size... Any tip and tricks to process it ?... >> Because freesurfer fails from the beggining of the process (VERY BAD >> talairach registration)... I test -bigventricle option of recon-all, >> but I got the same 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 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 believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. -- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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, at 2:16 PM, Gonzalo Rojas Costa > wrote: > >> 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 >>> Bruce >>> >>> On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: >>> >>>> Hi: >>>> >>>> I has the MPRAGE of a patient with one big ventricle, and the other >>>> has normal shape and size... Any tip and tricks to process it ?... >>>> Because freesurfer fails from the beggining of the process (VERY BAD >>>> talairach registration)... I test -bigventricle option of recon-all, >>>> but I got the same 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 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 believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> >> >> >> -- >> 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 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.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 want > > Bruce > On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: > >> 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, at 2:16 PM, Gonzalo Rojas Costa >>> wrote: >>> >>>> 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 >>>>> Bruce >>>>> >>>>> On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: >>>>> >>>>>> Hi: >>>>>> >>>>>> I has the MPRAGE of a patient with one big ventricle, and the other >>>>>> has normal shape and size... Any tip and tricks to process it ?... >>>>>> Because freesurfer fails from the beggining of the process (VERY BAD >>>>>> talairach registration)... I test -bigventricle option of recon-all, >>>>>> but I got the same 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 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 believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>> in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>> >>>> >>>> >>>> >>>> -- >>>> 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 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.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/ > > the centos6_x86_64 build is there now. the others will appear as they > finish their builds, which can take quite a bit of time... so check back > every day or so.... > > n. -- 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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] white matter volume per lobe...
Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh Which commands (sintaxis) must I use to compute the white matter volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats 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.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 the instructions that you told me... But, why I get the gray >> colored region (red arrow) ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >>> Message: 15 >>> Date: Mon, 27 May 2013 22:41:41 -0400 >>> From: Douglas Greve >>> Subject: Re: [Freesurfer] white matter volume per lobe... >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> you will need to run mri_annotation2label and specify the output to be >>> an annotation file instead of a segmentation. Then you will have to run >>> mri_aparc2aseg, specifying your lobes annotation as well as --labelwm >>> (look in the recon-all.log file for an example of how wmparc.mgz is >>> created). Then run mri_segstats (you can also get an example from the >>> recon-all.log file). >>> doug >> >> -- >> 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 > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 the region that is more than 5mm away from cortex. In the > wmparc it should be labeled as wm-lh-unknown > > doug > > > On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote: >> >> Hi Doug: >> >>I used the instructions that you told me to get the white matter per >> each lobule... But, I got the grey colored region (red arrow)... Which >> neuroanatomical area is ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >>> Message: 15 >>> Date: Mon, 27 May 2013 22:41:41 -0400 >>> From: Douglas Greve >>> Subject: Re: [Freesurfer] white matter volume per lobe... >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> you will need to run mri_annotation2label and specify the output to be >>> an annotation file instead of a segmentation. Then you will have to run >>> mri_aparc2aseg, specifying your lobes annotation as well as --labelwm >>> (look in the recon-all.log file for an example of how wmparc.mgz is >>> created). Then run mri_segstats (you can also get an example from the >>> recon-all.log file). >>> doug >> >> -- >> 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 > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] white matter volume per lobe...
Hi Doug: The command is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200 and the terminal output is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200 SUBJECTS_DIR /usr/local/freesurfer/subjects subject OAS1_0001_MR1 outvol mri/lobulitos_2.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 200.00 RipUnknown 1 Reading lh white surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot reading colortable from annotation file... colortable with 8 entries read (originally none) Reading rh white surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot reading colortable from annotation file... colortable with 8 entries read (originally none) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7659 vertices from left hemi Ripped 7544 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz ASeg Vox2RAS: --- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; - Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 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 you send me your full command line as well as the terminal output? > > On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote: >> >> 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 -- 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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 drop? > doug > > On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote: >> >> Hi Doug: >> >>The command is: >> >> mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown >> --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200 >> >> and the terminal output is: >> >> mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown >> --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200 >> >> SUBJECTS_DIR /usr/local/freesurfer/subjects >> subject OAS1_0001_MR1 >> outvol mri/lobulitos_2.mgz >> useribbon 0 >> baseoffset 0 >> labeling wm >> labeling hypo-intensities as wm >> dmaxctx 200.00 >> RipUnknown 1 >> >> Reading lh white surface >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white >> >> Reading lh pial surface >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial >> >> Loading lh annotations from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot >> reading colortable from annotation file... >> colortable with 8 entries read (originally none) >> >> Reading rh white surface >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white >> >> Reading rh pial surface >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial >> >> Loading rh annotations from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot >> reading colortable from annotation file... >> colortable with 8 entries read (originally none) >> Have color table for lh white annotation >> Have color table for rh white annotation >> Loading ribbon segmentation from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz >> Loading filled from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz >> Ripping vertices labeled as unkown >> Ripped 7659 vertices from left hemi >> Ripped 7544 vertices from right hemi >> >> Building hash of lh white >> >> Building hash of lh pial >> >> Building hash of rh white >> >> Building hash of rh pial >> >> Loading aseg from >> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz >> ASeg Vox2RAS: --- >> -1.000 0.000 0.000 128.000; >> 0.000 0.000 1.000 -128.000; >> 0.000 -1.000 0.000 128.000; >> 0.000 0.000 0.000 1.000; >> - >> >> Labeling Slice >>0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 >> 18 19 >> 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 >> 38 39 >> 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 >> 58 59 >> 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 >> 78 79 >> 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 >> 98 99 >> 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 >> 118 119 >> 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 >> 138 139 >> 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 >> 158 159 >> 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 >> 178 179 >> 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 >> 198 199 >> 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 >> 218 219 >> 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 >> 238 239 >> 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 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 you send me your full command line as well as the terminal output? >>> >>> On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote: >>>> >>>> Hi Doug: >>>> >>>> But, in the mri_aparc2aseg command, I test with the "--wmparc-
[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 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tracula error...
Hi: I ran "trac-all -prep -c dmrirc" and it finished ok... Then, when I tried to run the command "trac-all -bedp -c dmrirc", I got the error: ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/nodif_brain_mask.nii.gz ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/dwi.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri subjectdir is /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x27: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: 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 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html > > Hope this helps, > a.y -- 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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] white/gray surface and volumetric segmentation (aseg) difference...
Hi: With some mprage images, I got differences in the volumetric segmentation (aseg) of the cortex and the white/gray surface... Why ?... I know that both methods are totally different... In the aseg I got some bad segmentation of the cortex, but it in the white/gray surface I got very better 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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] GM and WM volume for each lobe...
Hi: I need to compute the GM and WM volume for each lobe... I know that for GM, I must use: mri_annotation2label --subject bert --hemi rh --lobesStrict lobesfile mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot bert 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 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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: > Content-Type: text/plain; charset=utf-8; format=flowed > > Try removing the --rip-unknown > > > On 09/12/2017 11:09 AM, Gonzalo Rojas Costa wrote: >> Hi: >> >>I created the following script (for freesurfer 5.3.0) to compute the >> lobes volume (including GM and WM). >> >>mri_annotation2label --subject pac --hemi rh --lobesStrict lobulos >> --seg lobulos --stat lobulos >>mri_annotation2label --subject pac --hemi lh --lobesStrict lobulos >> --seg lobulos --stat lobulos >>mris_anatomical_stats -a lobulos -f pac.lobulos.rh pac rh >>mris_anatomical_stats -a lobulos -f pac.lobulos.lh pac lh >>mri_aparc2aseg --s pac --labelwm --hypo-as-wm --rip-unknown >> --volmask --o $SUBJECTS_DIR/pac/mri/lobulitos.mgz --annot lobulos >> --wmparc-dmax 20 >>mri_segstats --seg $SUBJECTS_DIR/pac/mri/lobulitos.mgz --ctab >> /usr/local/freesurfer/LobulesColorLUT.txt --excludeid 0 --sum >> $i.lobulo.aseg.sum --id 1001 1004 1005 1006 2001 2004 2005 2006 3001 >> 3004 3005 3006 4001 4004 4005 4006 251 252 253 254 255 >> >>But, I didn't got the complete WM volume for each lobe (frontal lobe >> for example... see red arrow in attached image)... why ?... Any >> solution ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Cl?nica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> http://www.aribrain.info >> https://scholar.google.com/citations?user=LO7LZ3oJ >> https://www.researchgate.net/profile/Gonzalo_Rojas2 >> https://cl.linkedin.com/in/gonzalorojascosta >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta On Wed, Sep 20, 2017 at 5:47 PM, Douglas N Greve wrote: > We did not have a strong reason, just that it seemed to give maps that > looked reasonable > > > > On 09/20/2017 04:42 PM, Gonzalo Rojas Costa wrote: >> >> 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: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> http://www.aribrain.info >> https://scholar.google.com/citations?user=LO7LZ3oJ >> https://www.researchgate.net/profile/Gonzalo_Rojas2 >> https://cl.linkedin.com/in/gonzalorojascosta >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta On Thu, Sep 21, 2017 at 6:21 PM, Douglas N Greve wrote: > No, not for lobe volume. Have you seen the original wmparc paper? > > > > On 09/20/2017 04:53 PM, Gonzalo Rojas Costa wrote: >> >> 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, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> http://www.aribrain.info >> https://scholar.google.com/citations?user=LO7LZ3oJ >> https://www.researchgate.net/profile/Gonzalo_Rojas2 >> https://cl.linkedin.com/in/gonzalorojascosta >> >> >> On Wed, Sep 20, 2017 at 5:47 PM, Douglas N Greve >> wrote: >>> >>> We did not have a strong reason, just that it seemed to give maps that >>> looked reasonable >>> >>> >>> >>> On 09/20/2017 04:42 PM, Gonzalo Rojas Costa wrote: >>>> >>>> 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: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> http://www.aribrain.info >>>> https://scholar.google.com/citations?user=LO7LZ3oJ >>>> https://www.researchgate.net/profile/Gonzalo_Rojas2 >>>> https://cl.linkedin.com/in/gonzalorojascosta >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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? >Bruce >On Tue, 2 Sep 2014, Gonzalo Rojas Costa wrote: > >> >> 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 Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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.edu/mailman/listinfo/freesurfer
[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 Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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://mail.nmr.mgh.harvard.edu/mailman/listinfo/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/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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] library to show freesurfer data embedded in a web page (mesh and axial, coronal, sagital slices)
External Email - Use Caution Hi: Do you know any library that allows to show freesurfer generated data (mesh and axial, coronal, sagittal slices) embedded in a web page? We were working using "BrainBrowser Volume Viewer" (brainbrowser.cbrain.mcgill.ca) and "AMI 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/listinfo/freesurfer
[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/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM and ASEG edition... recon-all continue command...
Hi Bruce: Maybe I didn't explain clearly my question... I did a complete processing of a patient, then I must edit wm.mgz and aseg.mgz because I found some segmentation errors... Which recon-all command must I run to reprocess the study to use the edited files (wm.mgz and aseg.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 >> 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/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 intent of -make all is to > detect which steps need to be rerun based on file timestamps. All edits > should also be detected and kept, so it should do the right thing (right > Nick?) > > cheers > Bruce ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 ?... 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] processing OASIS database using freesurfer 5
Hi: I need to reprocess some images of the OASIS database using freesurfer 5... Should I use only the command "recon-all -s OAS1_0074_MR1 -all", or I must add the option "-expert expert.opts" ?... In the first case freesurfer automatically use thresholds specified 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 > Subject: Re: [Freesurfer] tkmedit bus error > To: Carolina Valencia > Cc: Freesurfer Mailing List > > Hi Carolina, > > does this happen every time? Can you run freeview on the volumes and see > if it can display them properly? > > cheers > Bruce > On Thu, 15 Sep 2011, Carolina Valencia > wrote: > >> Hi FSusers >> >> I run recon-all in a patient without problems, but when I tried to view it >> in tkmedit, an error pops up. >> >> I appreciate your help! >> >> Best regards, >> Carolina >> >> recon-all -s CORBIC_vol01 finished without error at Tue Sep 13 12:42:43 COT >> 2011 >> done >> cvalencia-Precision-WorkStation-T3400:~> tkmedit CORBIC_vol01 brainmask.mgz >> -aux T1.mgz -surfs -segmentation aseg.mgz >> $FREESURFER_HOME/FreeSurferColorLUT.txt >> Bus error >> cvalencia-Precision-WorkStation-T3400:~> tkmedit CORBIC_vol01 brainmask.mgz >> -aux T1.mgz -surfs -segmentation aseg.mgz >> $FREESURFER_HOME/FreeSurferColorLUT.txt >> Bus error ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 was the hard disk space, I can open it now in the > views (tksurfer, tkmedit) > > Best regards, > > Carolina ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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_annotation2label with --lobesStrict to get a lobe > annotation. If that definition of "lobes" is good for you, then you can run > mris_anatomical_stats to get the volume for each lobe. > doug ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cuda error...
Hi: I installed CUDA 4 in a Ubuntu 10.10 based workstation... I tried to process a volume, but I got the following error: "writing output transformation to transforms/talairach_with_skull.lta... CUDA Error in file 'gcasgpu.cu' on line 159 : unspecified driver error. registration 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 this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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://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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 www.clc.cl ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] libtiff.so.3 instalaton error ?...
Dear Pedro Paulo: I got the following error when I processing the autorecon2 stage... " 4281 Left-non-WM-hypointensities 0 4382 Right-non-WM-hypointensities 0 4485 Optic-Chiasm 187 187 45 251 CC_Posterior 540 540 46 252 CC_Mid_Posterior 182 182 47 253 CC_Central 131 131 48 254 CC_Mid_Anterior 162 162 49 255 CC_Anterior 219 219 Reporting on 49 segmentations # #...@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 /home/image/bin/freesurfer/subjects/rezende/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] libtiff.so.3 instalaton error ?...
Hi: But the sysadmin forgot the password of the superuser... I created the link in the /home/image directory, and in /home/image/freesurfer/bin, but freesurfer didn't find the lib... How can I solve the problem... How can I specify to freesurfer that the lib is in another folder ?... Any 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 works if you have write access to /usr/lib.. > otherwise you could contact your sysadmin. > > Krish > > On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote: > >> Dear Pedro Paulo: >> >> I got the following error when I processing the autorecon2 stage... >> >> " 4281 Left-non-WM-hypointensities 0 >> 4382 Right-non-WM-hypointensities 0 >> 4485 Optic-Chiasm 187 187 >> 45 251 CC_Posterior 540 540 >> 46 252 CC_Mid_Posterior 182 182 >> 47 253 CC_Central 131 131 >> 48 254 CC_Mid_Anterior 162 162 >> 49 255 CC_Anterior 219 219 >> >> Reporting on 49 segmentations >> # >> #...@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 >> /home/image/bin/freesurfer/subjects/rezende/mri >> >> mris_volmask --label_left_white 2 --label_left_ribbon 3 -- >> label_right_white >> 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende >> >> mris_volmask.bin: error while loading shared libraries: libtiff.so. >> 3: cannot >> open shared object file: No such file or directory >> Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 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.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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, >> >> I'd like to extract the left and right hippocampus from aseg.mgz, so >> basically what I want is a volume where left hippocampus have value >> (or label) 17 and right hippocampus have value (or label) 53, all the >> other place are zero. >> >> How can I do it? Using mri_threshold or mri_label2vol? >> >> Thanks a lot! >> >> Guang >> >> >> >> >> Hotmail: Free, trusted and rich email service. Get it now. >> <http://clk.atdmt.com/GBL/go/171222984/direct/01/> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >gr...@nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >In order to help us help you, please follow the steps in: >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] memory error
Hi: I got the following fatal error: CORRECTING DEFECT 61 (vertices=98413, convex hull=24013) Excessive topologic defect encountered: could not allocate 896316630 edges for retessellation Cannot allocate memory Linux image 2.6.28-16-generic #55-Ubuntu SMP Tue Oct 20 19:48:24 UTC 2009 i686 GNU/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
Hi: I got the following fatal error: CORRECTING DEFECT 61 (vertices=98413, convex hull=24013) Excessive topologic defect encountered: could not allocate 896316630 edges for retessellation Cannot allocate memory Linux image 2.6.28-16-generic #55-Ubuntu SMP Tue Oct 20 19:48:24 UTC 2009 i686 GNU/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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] skull strip question...
Hi: The tissue located in volume index coordinates (164, 54, 137) approx in the skull stripped volume that I am sending, could produce an error in the cortical thickness values for example, or any other parameters that freesurfer computes ?... I uploaded the files through your upload web 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...
Hi: In the temporal lobe I got a white matter "erroneous" segmentation (that I know that I could correct it using control points)... In the aseg.auto.mgz file the white matter appears as cerebral cortex... The cortical thickness computation is related to that segmentation ?... 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 Santiago Chile ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] conitnue longitudinal processing...
Hi: I was processing a longitudinal processing (previous the 8.8 earthquake) using a command line like: recon-all -base -tp -tp ... -all but it couldn't finished because the power cut... How can I continue the processing without starting again from the beginning ?... 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
[Freesurfer] continue longitudinal processing...
Hi: I was processing a longitudinal processing using a command line like: recon-all -base -tp -tp ... -all but it couldn't finished because the power cut produced by a 8.8 magnitude earthquake here in Chile... How can I continue the processing without starting again from the beginning ?... 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-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal Stream...
Hi: I processed a Longitudinal Stream between two MRIs of same patient taken in different dates... I used the following commands: i) recon-all -all -s , recon-all -all -s ii) recon-all -base -tp -tp -all iii) recon-all -long -all Which information was stored in the .long. folder ?... 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] realiability of cortical thickness...
Hi: Freesurfer Developer team: did you published any paper related to the reliability of cortical thickness ?... How you measure that reliability ?.. And, the reliability of the volumetry of different segmented brain structures (such as the hippocampus) ?... And, in the case of the cortical 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 intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] definition of some aseg.stats measures...
Hi: What is the definition of the following measures that appears at the beginning of "aseg.stats" file: "Brain Mask Volume", "Brain Segmentation Volume Without Ventricles" (BrainSegVolNotVent), "Brain Segmentation Volume" (BrainSegVol), "Intracranial 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.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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 11:07:01 +0100 > From: Andreas Berger > Subject: [Freesurfer] changing watershed threshold has no effect > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <68f948a91003260307g4fee4b69s9c04624544df2...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hello freesurfers, > > we are having a problem with insufficient skull stripping, in 66 out > of 200 subjects this affects the pial surface, as can be seen in the > attached screenshot1. since the problem is somewhat generalized in > location, i tried to change the watershed threshold as suggested by > the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean > -wsthresh n), but even 0 seems to have no effect (it looks different, > but not less skull), see screenshot2. am i doing it wrong? ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] normal value of "Brain Segmentation Volume Without Ventricles" value ?
Hi Bruce: I downloaded a study from OASIS dataset, but it didn't appears the BrainSegVolNotVent parameter in "aseg" datafile... I think because it was processed using a previous freesurfer version... Can I compute BrainSegVolNotVent without processing again the downloaded 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 > > > On Tue, 20 Apr 2010, Gonzalo > Rojas Costa wrote: > >> 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 >> ___ >> 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 believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 of scan is it? > > cheers > Bruce > On Thu, 22 Apr 2010, > Gonzalo Rojas wrote: > >> Hi: >> >> I got a WM segmentation error such as that I show in the attached image... >> The segmentation error include many coronal slices in size (more than 15)... >> How can I correct it ?... Besides, I got a very big mesh defect >> (vertices=21320, convex hull=9913) that freesurfer couldn't correct: could >> that defect be produced by that WM segmentation error?... >> >> If you want, I could send you more additional files... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 Clínica las Condes Santiago Chile ___ 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 believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] libpng12.so.0
External Email - Use Caution Hi: I tried to use the tkregisterfv command in Ubuntu 18.04.4 LTS, but I got the following error: "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory". How can 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/freesurfer
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: 4 > Date: Thu, 7 May 2020 12:43:56 +0200 (CEST) > From: Tim Sch?fer > Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine... > To: Freesurfer support list > Message-ID: <1445340988.123994.1588848236...@ox.hosteurope.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > There should be no difference to installation on a physical machine. Are you > running into any specific issues? > > Tim > >> On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa < gonzalo.rojas.co...@gmail.com> wrote: >> >> >> 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 > >-- > Dr. Tim Sch?fer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] big difference between ICV same patient....
External Email - Use Caution Hi: Why I got a big ICV difference between MPRAGE of the same patient (2019: 1775887.317631, 2020: 1566398.53576 mm3), one-year difference acquisition, and the same MRI Skyra 3T equipment? I used freesurfer 5.1.0 on the same computer, and operating 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] big difference between ICV same patient....
External Email - Use Caution Hi: I modified the coregistration using "tkregister2 --s subj1 --fstal --surfs". Then, I used "recon-all -make all -s subj1", but I got "Nothing to be done"... why ?... Which command must I run after tkregister2 to 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 between ICV same patient >To: >Message-ID: <0112a2be-2c41-a100-6ac7-e8d054e97...@mgh.harvard.edu> >Content-Type: text/plain; charset="utf-8" > >It all comes down to the registration. See >https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV >The image may have more-or-less neck and that can change the >registration and ICV. The contrast may be different. The scanner may >have had software updates. You might be comparing dewarped vs not dewarped. > >On 9/10/2020 2:16 PM, Gonzalo Rojas Costa wrote: >> >> External Email - Use Caution >> >> Hi: >> >> ? Why I got a big ICV difference between MPRAGE of the same patient >> (2019: 1775887.317631, 2020: 1566398.53576 mm3), one-year difference >> acquisition, and the same MRI Skyra 3T equipment? I used freesurfer >> 5.1.0 on the same computer, and operating 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
