Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi Eugenio! Thank so much for your time and answers! Best regards; Cecilio. 2015-05-21 17:10 GMT+08:00 Eugenio Iglesias : > Hi again, > - Yes, if you want the whole hippocampal volumes, you can just add all the > substructures. > - If you compare such volumes with those from aseg.stats, you'll see that > they are 10%-15% smaller, but very highly correlated. We have observed that > the addition of the 5.3 subfields is a tiny bit better when it comes to > separating AD from controls based solely on hippocampal volume, though. > Cheers, > /Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > - Original Message - > From: "Cecilio C Baro Perez" > To: "Freesurfer support list" > Sent: Thursday, May 21, 2015 11:03:04 AM > Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 > > > > > > > > Hola Eugenio! > > Thank you so much for quick answer. Well telling from your response it > seems that the right way to proceed in order to achieve the absolute volume > is to sum up "ALL" given regions right? > And could you please also tell me, which of the hippocampal volumes is the > most correct one, the one given primarily by the "recon-all" or the > "segmented" one? > > Thank you in advance! > > Best regards; Cecilio. > > > > 2015-05-21 16:54 GMT+08:00 Eugenio Iglesias < e.igles...@bcbl.eu > : > > > Hola Cecilio, > Right-Hippocampus and Left-Hippocampus are generic labels for the > hippocampal regions that were not labeled as subiculum, CA, or fimbria in > the atlas. In practice, they correspond to the hippocampal tails. > Cheers, > /Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > > > - Original Message - > From: "Cecilio C Baro Perez" < cecilio.c.b...@gmail.com > > To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > > Sent: Thursday, May 21, 2015 4:35:31 AM > Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 > > > > > > > > > > Hi professor Bruce! > I got finally the segmentation of the hippocampus I was looking for. > Thought I have one more question I hope ypou could answer: > By using : > "kvlQuantifyPosteriorProbabilityImages > $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ > ? posterior_right_* posterior_Right-Hippocampus.mgz" > > I got the the fallowing answer: > right_CA1: 2499.75 > right_CA2_3: 7372.95 > right_CA4_DG: 4296.22 > right_fimbria: 665.066 > right_hippocampal_fissure: 390.295 > right_presubiculum: 3844.54 > right_subiculum: 4969.41 > Right-Hippocampus: 2709.7 > > I supposed the the total hippocampal quantification was done by summing > those up and multiplying it by 0,5^3 . But what is the last subfield (the > one by the name Right_Hippocampus)? Should I include it in the sum or is it > already the final Right hippocampus in mm3? > > Once again thank you so much for all your help! > > Best regards; Cecilio. > > > > > > > > > > > > > 2015-05-14 20:47 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu > : > > > Hi Cecilio > > all our measures are in native space and not corrected for head size. The > estimated total intracranial volume (etiv) is what we typically use for > correction, and it should be in the aseg.stats file. In general I think it > is preferable to use it as a regressor rather than divide, but perhaps > someone can comment on this. We also segment the whole hippocampus, and > which one you use is up to you (you could add up all the subfield volumes, > but you won't get the same volume as the hippocampus from the aseg as the > definitions are a bit different as are the algorithms). > > cheers > Bruce > > > > > > On Thu, 14 May 2015, Cecilio C Baro Perez wrote: > > > > Dear professor Bruce! > > Sorry for bothering you again! I'm about to extract the hippocampus volume > of a group of FS processed patients. Though, I have a few questions without > explicit answers on the Internet. > > As recommended on FS tutorials I'm using this commando on the terminal: > "recon-all -s -hippo-subfields". But will the hippocampus quantified > be > corrected for headsize or do I need to separately divide it with the total > head-size? In the case of yes, could you please tell me where the total > hea
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi again, - Yes, if you want the whole hippocampal volumes, you can just add all the substructures. - If you compare such volumes with those from aseg.stats, you'll see that they are 10%-15% smaller, but very highly correlated. We have observed that the addition of the 5.3 subfields is a tiny bit better when it comes to separating AD from controls based solely on hippocampal volume, though. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Cecilio C Baro Perez" To: "Freesurfer support list" Sent: Thursday, May 21, 2015 11:03:04 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hola Eugenio! Thank you so much for quick answer. Well telling from your response it seems that the right way to proceed in order to achieve the absolute volume is to sum up "ALL" given regions right? And could you please also tell me, which of the hippocampal volumes is the most correct one, the one given primarily by the "recon-all" or the "segmented" one? Thank you in advance! Best regards; Cecilio. 2015-05-21 16:54 GMT+08:00 Eugenio Iglesias < e.igles...@bcbl.eu > : Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Cecilio C Baro Perez" < cecilio.c.b...@gmail.com > To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : "kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz" I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu > : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: "recon-all -s -hippo-subfields". But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command "less aseg.stats" gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu >: Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruc
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hola Eugenio! Thank you so much for quick answer. Well telling from your response it seems that the right way to proceed in order to achieve the absolute volume is to sum up "ALL" given regions right? And could you please also tell me, which of the hippocampal volumes is the most correct one, the one given primarily by the "recon-all" or the "segmented" one? Thank you in advance! Best regards; Cecilio. 2015-05-21 16:54 GMT+08:00 Eugenio Iglesias : > Hola Cecilio, > Right-Hippocampus and Left-Hippocampus are generic labels for the > hippocampal regions that were not labeled as subiculum, CA, or fimbria in > the atlas. In practice, they correspond to the hippocampal tails. > Cheers, > /Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > - Original Message - > From: "Cecilio C Baro Perez" > To: "Freesurfer support list" > Sent: Thursday, May 21, 2015 4:35:31 AM > Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 > > > > > > > > > > Hi professor Bruce! > I got finally the segmentation of the hippocampus I was looking for. > Thought I have one more question I hope ypou could answer: > By using : > "kvlQuantifyPosteriorProbabilityImages > $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ > ? posterior_right_* posterior_Right-Hippocampus.mgz" > > I got the the fallowing answer: > right_CA1: 2499.75 > right_CA2_3: 7372.95 > right_CA4_DG: 4296.22 > right_fimbria: 665.066 > right_hippocampal_fissure: 390.295 > right_presubiculum: 3844.54 > right_subiculum: 4969.41 > Right-Hippocampus: 2709.7 > > I supposed the the total hippocampal quantification was done by summing > those up and multiplying it by 0,5^3 . But what is the last subfield (the > one by the name Right_Hippocampus)? Should I include it in the sum or is it > already the final Right hippocampus in mm3? > > Once again thank you so much for all your help! > > Best regards; Cecilio. > > > > > > > > > > > > > 2015-05-14 20:47 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu > : > > > Hi Cecilio > > all our measures are in native space and not corrected for head size. The > estimated total intracranial volume (etiv) is what we typically use for > correction, and it should be in the aseg.stats file. In general I think it > is preferable to use it as a regressor rather than divide, but perhaps > someone can comment on this. We also segment the whole hippocampus, and > which one you use is up to you (you could add up all the subfield volumes, > but you won't get the same volume as the hippocampus from the aseg as the > definitions are a bit different as are the algorithms). > > cheers > Bruce > > > > > > On Thu, 14 May 2015, Cecilio C Baro Perez wrote: > > > > Dear professor Bruce! > > Sorry for bothering you again! I'm about to extract the hippocampus volume > of a group of FS processed patients. Though, I have a few questions without > explicit answers on the Internet. > > As recommended on FS tutorials I'm using this commando on the terminal: > "recon-all -s -hippo-subfields". But will the hippocampus quantified > be > corrected for headsize or do I need to separately divide it with the total > head-size? In the case of yes, could you please tell me where the total > head > volume could be found? > > I saw that the command "less aseg.stats" gives the hippocampal volume as > well, in that case what is the reason of performing point 1 (above)? > > Thank you in advance! > > Best regards; Cecilio. > > > 2015-05-01 0:06 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu >: > Hi Cecilio > > you need more computers, or run it on the amazon cloud. Pedro > Paulo has some utilities for this > > cheers > Bruce > > > On Fri, 1 May 2015, Cecilio C Baro Perez wrote: > > Oh thank you, that makes things much more clear! So > prefessor, that means > that there is any way possible to speed up the > freesurfer processing? I have > 30 patients and for each of the it takes like 25 h. > Best regards; Cecilio. > > 2015-04-30 23:33 GMT+08:00 Bruce Fischl > < fis...@nmr.mgh.harvard.edu >: > no, you need to run each subject separately. > What I was saying > is that you don't need to separate out the > importing into two > steps. You can run: > > > recon-all -s Pat1 \ > -i /9-2-1.dcm \ > -all > > for each subject > > cheers > Bruce > > > On Thu, 30 Ap
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Cecilio C Baro Perez" To: "Freesurfer support list" Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : "kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz" I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu > : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: "recon-all -s -hippo-subfields". But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command "less aseg.stats" gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu >: Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu >: no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i /9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i /9-2-1.dcm recon-all -s Pat2 \ -i /9-2-1.dcm and so on (2) recon-all -s -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu >: Hi Cecilio are Pat1 and Pat2 etc... different patients? If so, they need to be run separately. e.g. recon-all -s Pat1 -i http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Could that be an bug in the program? Once again! Thank you for your help! Best regards; Cecilio. 2015-04-29 1:09 GMT+08:
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : "kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz" I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl : > Hi Cecilio > > all our measures are in native space and not corrected for head size. The > estimated total intracranial volume (etiv) is what we typically use for > correction, and it should be in the aseg.stats file. In general I think it > is preferable to use it as a regressor rather than divide, but perhaps > someone can comment on this. We also segment the whole hippocampus, and > which one you use is up to you (you could add up all the subfield volumes, > but you won't get the same volume as the hippocampus from the aseg as the > definitions are a bit different as are the algorithms). > > cheers > Bruce > > > > > On Thu, 14 May 2015, Cecilio C Baro Perez wrote: > > Dear professor Bruce! >> >> Sorry for bothering you again! I'm about to extract the hippocampus volume >> of a group of FS processed patients. Though, I have a few questions >> without >> explicit answers on the Internet. >> >> As recommended on FS tutorials I'm using this commando on the terminal: >> "recon-all -s -hippo-subfields". But will the hippocampus quantified >> be >> corrected for headsize or do I need to separately divide it with the total >> head-size? In the case of yes, could you please tell me where the total >> head >> volume could be found? >> >> I saw that the command "less aseg.stats" gives the hippocampal volume as >> well, in that case what is the reason of performing point 1 (above)? >> >> Thank you in advance! >> >> Best regards; Cecilio. >> >> >> 2015-05-01 0:06 GMT+08:00 Bruce Fischl : >> Hi Cecilio >> >> you need more computers, or run it on the amazon cloud. Pedro >> Paulo has some utilities for this >> >> cheers >> Bruce >> >> >> On Fri, 1 May 2015, Cecilio C Baro Perez wrote: >> >> Oh thank you, that makes things much more clear! So >> prefessor, that means >> that there is any way possible to speed up the >> freesurfer processing? I have >> 30 patients and for each of the it takes like 25 h. >> Best regards; Cecilio. >> >> 2015-04-30 23:33 GMT+08:00 Bruce Fischl >> : >> no, you need to run each subject separately. >> What I was saying >> is that you don't need to separate out the >> importing into two >> steps. You can run: >> >> >>recon-all -s Pat1 \ >> -i /9-2-1.dcm \ >> -all >> >> for each subject >> >> cheers >> Bruce >> >> >> On Thu, 30 Apr 2015, Cecilio C Baro Perez >> wrote: >> >> Hi! >> Thank you for quick response! Yes, Pat1 >> and Pat2, >> etc are already imported >> into the freesurfer directory. So what I >> want to do >> do the further >> processing. Sorry, but I'm kind of >> confuse, I >> following the online >> tutorials: >> >> (1) >> >> recon-all -s Pat1 \ >>-i /9-2-1.dcm >> recon-all -s >> Pat2 \ >>-i /9-2-1.dcm >> and so on >> >> (2) >> >> recon-all -s -all >> >> Part (1) is completed for all my >> patients and I >> would like to do part (2) fo >> r >> all my patients at the same time. Isn't >> the right >> way to procede by typing i >> n the terminal as below? >> recon-all -s Pat1 -i Pat2 -i Pat3 -i >> Pat5 -i -all >>
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: "recon-all -s -hippo-subfields". But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command "less aseg.stats" gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl : Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl : no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i /9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i /9-2-1.dcm recon-all -s Pat2 \ -i /9-2-1.dcm and so on (2) recon-all -s -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl : Hi Cecilio are Pat1 and Pat2 etc... different patients? If so, they need to be run separately. e.g. recon-all -s Pat1 -i http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Could that be an bug in the program? Once again! Thank you for your help! Best regards; Cecilio. 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez : Thank you so much for your quick and helpful response!Best regards, Cecilio. 2015-04-26 20:27 GMT+08:00 Bruce Fischl
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: "recon-all -s -hippo-subfields". But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command "less aseg.stats" gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl : > Hi Cecilio > > you need more computers, or run it on the amazon cloud. Pedro Paulo has > some utilities for this > > cheers > Bruce > > > > On Fri, 1 May 2015, Cecilio C Baro Perez wrote: > > Oh thank you, that makes things much more clear! So prefessor, that means >> that there is any way possible to speed up the freesurfer processing? I >> have >> 30 patients and for each of the it takes like 25 h. >> Best regards; Cecilio. >> >> 2015-04-30 23:33 GMT+08:00 Bruce Fischl : >> no, you need to run each subject separately. What I was saying >> is that you don't need to separate out the importing into two >> steps. You can run: >> >> >>recon-all -s Pat1 \ >> -i /9-2-1.dcm \ >> -all >> >> for each subject >> >> cheers >> Bruce >> >> >> On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: >> >> Hi! >> Thank you for quick response! Yes, Pat1 and Pat2, >> etc are already imported >> into the freesurfer directory. So what I want to do >> do the further >> processing. Sorry, but I'm kind of confuse, I >> following the online >> tutorials: >> >> (1) >> >> recon-all -s Pat1 \ >>-i /9-2-1.dcm recon-all -s >> Pat2 \ >>-i /9-2-1.dcm >> and so on >> >> (2) >> >> recon-all -s -all >> >> Part (1) is completed for all my patients and I >> would like to do part (2) fo >> r >> all my patients at the same time. Isn't the right >> way to procede by typing i >> n the terminal as below? >> recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all >> Once again thank you for all your help! >> >> Best regards; Cecilio. >> >> >> 2015-04-30 22:35 GMT+08:00 Bruce Fischl >> : >> Hi Cecilio >> >> are Pat1 and Pat2 etc... different patients? >> If so, they need to >> be run separately. e.g. >> >> recon-all -s Pat1 -i > patient 1) -all >> recon-all -s Pat2 -i > patient 2) -all >> . >> . >> . >> >> cheers >> Bruce >> >> p.s. for the tcsh bug you should just get your >> sysadmin to >> update the version of tcsh you are using. >> >> On Thu, 30 Apr 2015, Cecilio C Baro Perez >> wrote: >> >> Dear professor Bruce! >> Sorry for bothering again, well I did >> exatly as you >> told before in order to >> process different subject at the same >> time: >> >> recon-all -s Pat1 -i Pat2 -i Pat3 -i >> Pat5 -all >> >> there Pat 1 (and the rest) are subjid. >> thought I got >> this error message: >> >> ARNING: tcsh v6.17.06 has an exit code >> bug! Please >> update tcsh! >> >> ERROR: cannot find Pat2 >> Linux cecilio-N73SV 3.8.0-44-generic >> #66~precise1-Ubuntu SMP Tue Jul 15 >> 04:01:04 UTC 2014 x86_64 x86_64 x86_64 >> GNU/Linux >> >> recon-all -s Pat1 exited with ERRORS at >> Thu Apr 30 >> 22:17:19 CST 2015 >> >> For more details, see the log file >> To report a problem, see >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> Could that be an bug in the program? >> >> Once again! Thank you for your help! >> >> Best regards; Cecilio. >> >> >> 2015-04-29 1:09 GMT+08:00 Cecilio C Baro >> Per
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl : no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i /9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i /9-2-1.dcm recon-all -s Pat2 \ -i /9-2-1.dcm and so on (2) recon-all -s -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl : Hi Cecilio are Pat1 and Pat2 etc... different patients? If so, they need to be run separately. e.g. recon-all -s Pat1 -i http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Could that be an bug in the program? Once again! Thank you for your help! Best regards; Cecilio. 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez : Thank you so much for your quick and helpful response!Best regards, Cecilio. 2015-04-26 20:27 GMT+08:00 Bruce Fischl : sorry Cecilio, it is pretty compute intensive. If you have multiple cores you can use -openmp to speed things up a bit, or just run more than one recon-all at a time. Note that you don't need to invoke it twice - just run: recon-all -s - -i --- -all cheers Bruce On Sun, 26 Apr 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Thank you so much for your help, it help me a lot! I have a silly question, sorry for that, I'm using the Freesurfer to extract the hippocampal volume of two different groups. Right using this two commands: "recon-all -s - -i followed by"recon-all -s --all" Is taking like a day of processing for just one patient. Is there any faster way as I'm only interested on the hippocampal volume? Once again thank you for your help! Best regards; Cecilio. 2015-04-25 22:10 GMT+08:00 Bruce Fischl : Hi Cecilio what do you mean "224 scans"? I assume
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl : > no, you need to run each subject separately. What I was saying is that you > don't need to separate out the importing into two steps. You can run: > > > recon-all -s Pat1 \ > -i /9-2-1.dcm \ > -all > > for each subject > > cheers > Bruce > > > On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: > > Hi! >> Thank you for quick response! Yes, Pat1 and Pat2, etc are already >> imported >> into the freesurfer directory. So what I want to do do the further >> processing. Sorry, but I'm kind of confuse, I following the online >> tutorials: >> >> (1) >> >> recon-all -s Pat1 \ >>-i /9-2-1.dcm recon-all -s Pat2 \ >>-i /9-2-1.dcm >> and so on >> >> (2) >> >> recon-all -s -all >> >> Part (1) is completed for all my patients and I would like to do part (2) >> fo >> r >> all my patients at the same time. Isn't the right way to procede by >> typing i >> n the terminal as below? >> recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all >> Once again thank you for all your help! >> >> Best regards; Cecilio. >> >> >> 2015-04-30 22:35 GMT+08:00 Bruce Fischl : >> Hi Cecilio >> >> are Pat1 and Pat2 etc... different patients? If so, they need to >> be run separately. e.g. >> >> recon-all -s Pat1 -i > recon-all -s Pat2 -i > . >> . >> . >> >> cheers >> Bruce >> >> p.s. for the tcsh bug you should just get your sysadmin to >> update the version of tcsh you are using. >> >> On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: >> >> Dear professor Bruce! >> Sorry for bothering again, well I did exatly as you >> told before in order to >> process different subject at the same time: >> >> recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -all >> >> there Pat 1 (and the rest) are subjid. thought I got >> this error message: >> >> ARNING: tcsh v6.17.06 has an exit code bug! Please >> update tcsh! >> >> ERROR: cannot find Pat2 >> Linux cecilio-N73SV 3.8.0-44-generic >> #66~precise1-Ubuntu SMP Tue Jul 15 >> 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s Pat1 exited with ERRORS at Thu Apr 30 >> 22:17:19 CST 2015 >> >> For more details, see the log file >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> Could that be an bug in the program? >> >> Once again! Thank you for your help! >> >> Best regards; Cecilio. >> >> >> 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez >> : >> Thank you so much for your quick and helpful >> response!Best >> regards, Cecilio. >> >> 2015-04-26 20:27 GMT+08:00 Bruce Fischl >> : >> sorry Cecilio, it is pretty compute intensive. >> If you have >> multiple cores you can use -openmp to speed >> things up a >> bit, or just run more than one recon-all at a >> time. Note >> that you don't need to invoke it twice - just >> run: >> >> recon-all -s - -i --- -all >> >> cheers >> Bruce >> >> >> On Sun, 26 Apr 2015, Cecilio C Baro Perez >> wrote: >> >> Dear professor Bruce! >> >> Thank you so much for your help, it help >> me a >> lot! I have a silly question, >> sorry for that, I'm using the Freesurfer >> to >> extract the hippocampal volume >> of two different groups. Right using >> this two >> commands: >> >> "recon-all -s - -i followed >> by"recon-all >> -s --all" >> >> Is taking like a day of processing for >> just >> one patient. Is there any faster >> way as I'm only interested on the >> hippocampal >> volume? >> >> Once again thank you for your help! >> >> Best regards; Cecilio. >> >> 2015-04-25 22:10 GMT+08:00 Bruce Fischl >> : >> Hi Cecilio >> >> what do you mean "224 scans"? I >> assume >>
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i /9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i /9-2-1.dcm recon-all -s Pat2 \ -i /9-2-1.dcm and so on (2) recon-all -s -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl : Hi Cecilio are Pat1 and Pat2 etc... different patients? If so, they need to be run separately. e.g. recon-all -s Pat1 -i http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Could that be an bug in the program? Once again! Thank you for your help! Best regards; Cecilio. 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez : Thank you so much for your quick and helpful response!Best regards, Cecilio. 2015-04-26 20:27 GMT+08:00 Bruce Fischl : sorry Cecilio, it is pretty compute intensive. If you have multiple cores you can use -openmp to speed things up a bit, or just run more than one recon-all at a time. Note that you don't need to invoke it twice - just run: recon-all -s - -i --- -all cheers Bruce On Sun, 26 Apr 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Thank you so much for your help, it help me a lot! I have a silly question, sorry for that, I'm using the Freesurfer to extract the hippocampal volume of two different groups. Right using this two commands: "recon-all -s - -i followed by"recon-all -s --all" Is taking like a day of processing for just one patient. Is there any faster way as I'm only interested on the hippocampal volume? Once again thank you for your help! Best regards; Cecilio. 2015-04-25 22:10 GMT+08:00 Bruce Fischl : Hi Cecilio what do you mean "224 scans"? I assume you mean 224 slices in each scan? And do you have two different runs of the same scan type (e.g. mprage) for each subject? You can try: mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 and freeview /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 to find out the scan parameters and also visualize it. cheers Bruce On Sat, 25 Apr 2015, Cecilio C Baro Perez wrote: Hi Bruce! Thank you for your quick replay! I appreciate that! Well my data is T1 dicom images. And For every subject I have 224 scans. Though as I'm using freesurfer I'm trying by only using 2 of 224 scans. Please correct me if I'm wrong: File name: Pat1 Number of scans in Pat1: 2 (81334010 and 81334011) On
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i /9-2-1.dcm recon-all -s Pat2 \ -i /9-2-1.dcm and so on (2) recon-all -s -all Part (1) is completed for all my patients and I would like to do part (2) for all my patients at the same time. Isn't the right way to procede by typing in the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl : > Hi Cecilio > > are Pat1 and Pat2 etc... different patients? If so, they need to be run > separately. e.g. > > recon-all -s Pat1 -i recon-all -s Pat2 -i . > . > . > > cheers > Bruce > > p.s. for the tcsh bug you should just get your sysadmin to update the > version of tcsh you are using. > > On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: > > Dear professor Bruce! >> >> Sorry for bothering again, well I did exatly as you told before in order >> to >> process different subject at the same time: >> >> recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -all >> >> there Pat 1 (and the rest) are subjid. thought I got this error message: >> >> ARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! >> >> ERROR: cannot find Pat2 >> Linux cecilio-N73SV 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 >> 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s Pat1 exited with ERRORS at Thu Apr 30 22:17:19 CST 2015 >> >> For more details, see the log file >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> Could that be an bug in the program? >> >> Once again! Thank you for your help! >> >> Best regards; Cecilio. >> >> >> 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez > >: >> Thank you so much for your quick and helpful response!Best >> regards, Cecilio. >> >> 2015-04-26 20:27 GMT+08:00 Bruce Fischl : >> sorry Cecilio, it is pretty compute intensive. If you have >> multiple cores you can use -openmp to speed things up a >> bit, or just run more than one recon-all at a time. Note >> that you don't need to invoke it twice - just run: >> >> recon-all -s - -i --- -all >> >> cheers >> Bruce >> >> >> On Sun, 26 Apr 2015, Cecilio C Baro Perez wrote: >> >> Dear professor Bruce! >> >> Thank you so much for your help, it help me a >> lot! I have a silly question, >> sorry for that, I'm using the Freesurfer to >> extract the hippocampal volume >> of two different groups. Right using this two >> commands: >> >> "recon-all -s - -i followed by"recon-all >> -s --all" >> >> Is taking like a day of processing for just >> one patient. Is there any faster >> way as I'm only interested on the hippocampal >> volume? >> >> Once again thank you for your help! >> >> Best regards; Cecilio. >> >> 2015-04-25 22:10 GMT+08:00 Bruce Fischl >> : >> Hi Cecilio >> >> what do you mean "224 scans"? I assume >> you mean 224 slices in >> each scan? And do you have two different >> runs of the same scan >> type (e.g. mprage) for each subject? You >> can try: >> >> mri_info >> /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> >> and >> >> freeview >> /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> >> to find out the scan parameters and also >> visualize it. >> >> cheers >> Bruce >> >> >> On Sat, 25 Apr 2015, Cecilio C Baro >> Perez wrote: >> >> Hi Bruce! >> Thank you for your quick replay! I >> appreciate that! >> Well my data is T1 dicom >> images. And For every subject I >> have 224 scans. >> Though as I'm using >> freesurfer I'm trying by only >> using 2 of 224 scans. >> Please correct me if I'm >> wrong: >> File name: Pat1 >> Number of scans in Pat1: 2 >> (81334010 and 81334011) >> >> On terminal: >> Input command: >> 1. recon-all -s Patient1 -i >> >> /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> (this is executed free >>
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi Cecilio are Pat1 and Pat2 etc... different patients? If so, they need to be run separately. e.g. recon-all -s Pat1 -i p.s. for the tcsh bug you should just get your sysadmin to update the version of tcsh you are using. On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering again, well I did exatly as you told before in order to process different subject at the same time: recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -all there Pat 1 (and the rest) are subjid. thought I got this error message: ARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: cannot find Pat2 Linux cecilio-N73SV 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Pat1 exited with ERRORS at Thu Apr 30 22:17:19 CST 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Could that be an bug in the program? Once again! Thank you for your help! Best regards; Cecilio. 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez : Thank you so much for your quick and helpful response!Best regards, Cecilio. 2015-04-26 20:27 GMT+08:00 Bruce Fischl : sorry Cecilio, it is pretty compute intensive. If you have multiple cores you can use -openmp to speed things up a bit, or just run more than one recon-all at a time. Note that you don't need to invoke it twice - just run: recon-all -s - -i --- -all cheers Bruce On Sun, 26 Apr 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Thank you so much for your help, it help me a lot! I have a silly question, sorry for that, I'm using the Freesurfer to extract the hippocampal volume of two different groups. Right using this two commands: "recon-all -s - -i followed by"recon-all -s --all" Is taking like a day of processing for just one patient. Is there any faster way as I'm only interested on the hippocampal volume? Once again thank you for your help! Best regards; Cecilio. 2015-04-25 22:10 GMT+08:00 Bruce Fischl : Hi Cecilio what do you mean "224 scans"? I assume you mean 224 slices in each scan? And do you have two different runs of the same scan type (e.g. mprage) for each subject? You can try: mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 and freeview /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 to find out the scan parameters and also visualize it. cheers Bruce On Sat, 25 Apr 2015, Cecilio C Baro Perez wrote: Hi Bruce! Thank you for your quick replay! I appreciate that! Well my data is T1 dicom images. And For every subject I have 224 scans. Though as I'm using freesurfer I'm trying by only using 2 of 224 scans. Please correct me if I'm wrong: File name: Pat1 Number of scans in Pat1: 2 (81334010 and 81334011) On terminal: Input command: 1. recon-all -s Patient1 -i /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 (this is executed free from errors) 2. recon-all -s Patient1 -all My error becomes: #@# Talairach Failure Detection Сб. апр. 25 18:25:07 CST 2015 recon-all -s Patient1 exited with ERRORS at Сб. апр. 25 18:25:32 CST 2015 Besides if I try to use the tkmedit I get this following: Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Please do you possibly know how to go around this problem. Thank you in advance!
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Dear professor Bruce! Sorry for bothering again, well I did exatly as you told before in order to process different subject at the same time: recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -all there Pat 1 (and the rest) are subjid. thought I got this error message: ARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: cannot find Pat2 Linux cecilio-N73SV 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Pat1 exited with ERRORS at Thu Apr 30 22:17:19 CST 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Could that be an bug in the program? Once again! Thank you for your help! Best regards; Cecilio. 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez : > Thank you so much for your quick and helpful response! > Best regards, Cecilio. > > 2015-04-26 20:27 GMT+08:00 Bruce Fischl : > >> sorry Cecilio, it is pretty compute intensive. If you have multiple cores >> you can use -openmp to speed things up a bit, or just run more than one >> recon-all at a time. Note that you don't need to invoke it twice - just run: >> >> recon-all -s - -i --- -all >> >> cheers >> Bruce >> >> >> >> On Sun, 26 Apr 2015, Cecilio C Baro Perez wrote: >> >> Dear professor Bruce! >>> >>> Thank you so much for your help, it help me a lot! I have a silly >>> question, >>> sorry for that, I'm using the Freesurfer to extract the hippocampal >>> volume >>> of two different groups. Right using this two commands: >>> >>> "recon-all -s - -i followed by"recon-all -s --all" >>> >>> Is taking like a day of processing for just one patient. Is there any >>> faster >>> way as I'm only interested on the hippocampal volume? >>> >>> Once again thank you for your help! >>> >>> Best regards; Cecilio. >>> >>> 2015-04-25 22:10 GMT+08:00 Bruce Fischl : >>> Hi Cecilio >>> >>> what do you mean "224 scans"? I assume you mean 224 slices in >>> each scan? And do you have two different runs of the same scan >>> type (e.g. mprage) for each subject? You can try: >>> >>> mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >>> >>> and >>> >>> freeview /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >>> >>> to find out the scan parameters and also visualize it. >>> >>> cheers >>> Bruce >>> >>> >>> On Sat, 25 Apr 2015, Cecilio C Baro Perez wrote: >>> >>> Hi Bruce! >>> Thank you for your quick replay! I appreciate that! >>> Well my data is T1 dicom >>> images. And For every subject I have 224 scans. >>> Though as I'm using >>> freesurfer I'm trying by only using 2 of 224 scans. >>> Please correct me if I'm >>> wrong: >>> File name: Pat1 >>> Number of scans in Pat1: 2 (81334010 and 81334011) >>> >>> On terminal: >>> Input command: >>> 1. recon-all -s Patient1 -i >>> /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >>> (this is executed free >>> from errors) >>> 2. recon-all -s Patient1 -all >>> My error becomes: >>> #@# Talairach Failure Detection Сб. апр. 25 18:25:07 >>> CST 2015 >>> >>> recon-all -s Patient1 exited with ERRORS at Сб. апр. >>> 25 18:25:32 CST 2015 >>> >>> Besides if I try to use the tkmedit I get this >>> following: >>> Tkmedit couldn't read the volume you specified. >>> This could be because the image format wasn't >>> recognized, >>> or it couldn't find the proper header, >>> or the file(s) were unreadable, >>> or it was the wrong size. >>> >>> >>> Please do you possibly know how to go around this >>> problem. >>> >>> Thank you in advance! >>> >>> >>> Best regards; Cecilio. >>> >>> 2015-04-24 21:20 GMT+08:00 Bruce Fischl >>> : >>> Hi Cecilio >>> >>> this means that the automatic checking >>> determined that the >>> Talairach transform to be very unlikely and >>> probably a failure. >>> What was your input data? If you bring it up >>> in tkmedit or >>> freeview do the directions on the screen >>> correspond to true >>> anatomical ones (e.g. is A really anterior)? >>> >>> cheers >>> Bruce >>> >>> >>> On Fri, 24 Apr 2015, Cecilio C Baro Perez >>> wrote: >>> >>> >>> >>> >>> Hi! >>> My name is Cecilio! I'm using the >>> freesurfer 5.3 and >>> I'm having some issues >>>
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Thank you so much for your quick and helpful response! Best regards, Cecilio. 2015-04-26 20:27 GMT+08:00 Bruce Fischl : > sorry Cecilio, it is pretty compute intensive. If you have multiple cores > you can use -openmp to speed things up a bit, or just run more than one > recon-all at a time. Note that you don't need to invoke it twice - just run: > > recon-all -s - -i --- -all > > cheers > Bruce > > > > On Sun, 26 Apr 2015, Cecilio C Baro Perez wrote: > > Dear professor Bruce! >> >> Thank you so much for your help, it help me a lot! I have a silly >> question, >> sorry for that, I'm using the Freesurfer to extract the hippocampal volume >> of two different groups. Right using this two commands: >> >> "recon-all -s - -i followed by"recon-all -s --all" >> >> Is taking like a day of processing for just one patient. Is there any >> faster >> way as I'm only interested on the hippocampal volume? >> >> Once again thank you for your help! >> >> Best regards; Cecilio. >> >> 2015-04-25 22:10 GMT+08:00 Bruce Fischl : >> Hi Cecilio >> >> what do you mean "224 scans"? I assume you mean 224 slices in >> each scan? And do you have two different runs of the same scan >> type (e.g. mprage) for each subject? You can try: >> >> mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> >> and >> >> freeview /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> >> to find out the scan parameters and also visualize it. >> >> cheers >> Bruce >> >> >> On Sat, 25 Apr 2015, Cecilio C Baro Perez wrote: >> >> Hi Bruce! >> Thank you for your quick replay! I appreciate that! >> Well my data is T1 dicom >> images. And For every subject I have 224 scans. >> Though as I'm using >> freesurfer I'm trying by only using 2 of 224 scans. >> Please correct me if I'm >> wrong: >> File name: Pat1 >> Number of scans in Pat1: 2 (81334010 and 81334011) >> >> On terminal: >> Input command: >> 1. recon-all -s Patient1 -i >> /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> (this is executed free >> from errors) >> 2. recon-all -s Patient1 -all >> My error becomes: >> #@# Talairach Failure Detection Сб. апр. 25 18:25:07 >> CST 2015 >> >> recon-all -s Patient1 exited with ERRORS at Сб. апр. >> 25 18:25:32 CST 2015 >> >> Besides if I try to use the tkmedit I get this >> following: >> Tkmedit couldn't read the volume you specified. >> This could be because the image format wasn't >> recognized, >> or it couldn't find the proper header, >> or the file(s) were unreadable, >> or it was the wrong size. >> >> >> Please do you possibly know how to go around this >> problem. >> >> Thank you in advance! >> >> >> Best regards; Cecilio. >> >> 2015-04-24 21:20 GMT+08:00 Bruce Fischl >> : >> Hi Cecilio >> >> this means that the automatic checking >> determined that the >> Talairach transform to be very unlikely and >> probably a failure. >> What was your input data? If you bring it up >> in tkmedit or >> freeview do the directions on the screen >> correspond to true >> anatomical ones (e.g. is A really anterior)? >> >> cheers >> Bruce >> >> >> On Fri, 24 Apr 2015, Cecilio C Baro Perez >> wrote: >> >> >> >> >> Hi! >> My name is Cecilio! I'm using the >> freesurfer 5.3 and >> I'm having some issues >> that I hope you could help me with. When >> I perform: >> >>recon-all -s patienttesta -all >> >> I get this error: >>recon-all -s patienttesta exited with >> ERRORS >>ERROR: talairach_afd: Talairach >> Transform: >> transforms/talairach.xfm >> >> After reading on the internet I even try >> this >> command: >> recon-all -s patienttesta -all >> -use-mritotal >> >> But it stills give me the same error >> >> >> Could you please tell me what the >> problem could be? >> >> Thank you in advance! >> >> Best regards, Cecilio. >> >> >> >> >> __
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
sorry Cecilio, it is pretty compute intensive. If you have multiple cores you can use -openmp to speed things up a bit, or just run more than one recon-all at a time. Note that you don't need to invoke it twice - just run: recon-all -s - -i --- -all cheers Bruce On Sun, 26 Apr 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Thank you so much for your help, it help me a lot! I have a silly question, sorry for that, I'm using the Freesurfer to extract the hippocampal volume of two different groups. Right using this two commands: "recon-all -s - -i followed by"recon-all -s --all" Is taking like a day of processing for just one patient. Is there any faster way as I'm only interested on the hippocampal volume? Once again thank you for your help! Best regards; Cecilio. 2015-04-25 22:10 GMT+08:00 Bruce Fischl : Hi Cecilio what do you mean "224 scans"? I assume you mean 224 slices in each scan? And do you have two different runs of the same scan type (e.g. mprage) for each subject? You can try: mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 and freeview /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 to find out the scan parameters and also visualize it. cheers Bruce On Sat, 25 Apr 2015, Cecilio C Baro Perez wrote: Hi Bruce! Thank you for your quick replay! I appreciate that! Well my data is T1 dicom images. And For every subject I have 224 scans. Though as I'm using freesurfer I'm trying by only using 2 of 224 scans. Please correct me if I'm wrong: File name: Pat1 Number of scans in Pat1: 2 (81334010 and 81334011) On terminal: Input command: 1. recon-all -s Patient1 -i /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 (this is executed free from errors) 2. recon-all -s Patient1 -all My error becomes: #@# Talairach Failure Detection Сб. апр. 25 18:25:07 CST 2015 recon-all -s Patient1 exited with ERRORS at Сб. апр. 25 18:25:32 CST 2015 Besides if I try to use the tkmedit I get this following: Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Please do you possibly know how to go around this problem. Thank you in advance! Best regards; Cecilio. 2015-04-24 21:20 GMT+08:00 Bruce Fischl : Hi Cecilio this means that the automatic checking determined that the Talairach transform to be very unlikely and probably a failure. What was your input data? If you bring it up in tkmedit or freeview do the directions on the screen correspond to true anatomical ones (e.g. is A really anterior)? cheers Bruce On Fri, 24 Apr 2015, Cecilio C Baro Perez wrote: Hi! My name is Cecilio! I'm using the freesurfer 5.3 and I'm having some issues that I hope you could help me with. When I perform: recon-all -s patienttesta -all I get this error: recon-all -s patienttesta exited with ERRORS ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm After reading on the internet I even try this command: recon-all -s patienttesta -all -use-mritotal But it stills give me the same error Could you please tell me what the problem could be? Thank you in advance! Best regards, Cecilio. ___ 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 Complian
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Dear professor Bruce! Thank you so much for your help, it help me a lot! I have a silly question, sorry for that, I'm using the Freesurfer to extract the hippocampal volume of two different groups. Right using this two commands: "recon-all -s - -i followed by"recon-all -s --all" Is taking like a day of processing for just one patient. Is there any faster way as I'm only interested on the hippocampal volume? Once again thank you for your help! Best regards; Cecilio. 2015-04-25 22:10 GMT+08:00 Bruce Fischl : > Hi Cecilio > > what do you mean "224 scans"? I assume you mean 224 slices in each scan? > And do you have two different runs of the same scan type (e.g. mprage) for > each subject? You can try: > > mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 > > and > > freeview /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 > > to find out the scan parameters and also visualize it. > > cheers > Bruce > > > > On Sat, 25 Apr 2015, Cecilio C Baro Perez wrote: > > Hi Bruce! >> Thank you for your quick replay! I appreciate that! Well my data is T1 >> dicom >> images. And For every subject I have 224 scans. Though as I'm using >> freesurfer I'm trying by only using 2 of 224 scans. Please correct me if >> I'm >> wrong: >> File name: Pat1 >> Number of scans in Pat1: 2 (81334010 and 81334011) >> >> On terminal: >> Input command: >> 1. recon-all -s Patient1 -i >> /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 (this is executed free >> from errors) >> 2. recon-all -s Patient1 -all >> My error becomes: >> #@# Talairach Failure Detection Сб. апр. 25 18:25:07 CST 2015 >> >> recon-all -s Patient1 exited with ERRORS at Сб. апр. 25 18:25:32 CST 2015 >> >> Besides if I try to use the tkmedit I get this following: >> Tkmedit couldn't read the volume you specified. >> This could be because the image format wasn't recognized, >> or it couldn't find the proper header, >> or the file(s) were unreadable, >> or it was the wrong size. >> >> >> Please do you possibly know how to go around this problem. >> >> Thank you in advance! >> >> >> Best regards; Cecilio. >> >> 2015-04-24 21:20 GMT+08:00 Bruce Fischl : >> Hi Cecilio >> >> this means that the automatic checking determined that the >> Talairach transform to be very unlikely and probably a failure. >> What was your input data? If you bring it up in tkmedit or >> freeview do the directions on the screen correspond to true >> anatomical ones (e.g. is A really anterior)? >> >> cheers >> Bruce >> >> >> On Fri, 24 Apr 2015, Cecilio C Baro Perez wrote: >> >> >> >> >> Hi! >> My name is Cecilio! I'm using the freesurfer 5.3 and >> I'm having some issues >> that I hope you could help me with. When I perform: >> >>recon-all -s patienttesta -all >> >> I get this error: >>recon-all -s patienttesta exited with ERRORS >>ERROR: talairach_afd: Talairach Transform: >> transforms/talairach.xfm >> >> After reading on the internet I even try this >> command: >> recon-all -s patienttesta -all -use-mritotal >> >> But it stills give me the same error >> >> >> Could you please tell me what the problem could be? >> >> Thank you in advance! >> >> Best regards, Cecilio. >> >> >> >> >> ___ >> 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 > > > 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-mai
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi Cecilio what do you mean "224 scans"? I assume you mean 224 slices in each scan? And do you have two different runs of the same scan type (e.g. mprage) for each subject? You can try: mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 and freeview /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 to find out the scan parameters and also visualize it. cheers Bruce On Sat, 25 Apr 2015, Cecilio C Baro Perez wrote: Hi Bruce! Thank you for your quick replay! I appreciate that! Well my data is T1 dicom images. And For every subject I have 224 scans. Though as I'm using freesurfer I'm trying by only using 2 of 224 scans. Please correct me if I'm wrong: File name: Pat1 Number of scans in Pat1: 2 (81334010 and 81334011) On terminal: Input command: 1. recon-all -s Patient1 -i /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 (this is executed free from errors) 2. recon-all -s Patient1 -all My error becomes: #@# Talairach Failure Detection Сб. апр. 25 18:25:07 CST 2015 recon-all -s Patient1 exited with ERRORS at Сб. апр. 25 18:25:32 CST 2015 Besides if I try to use the tkmedit I get this following: Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Please do you possibly know how to go around this problem. Thank you in advance! Best regards; Cecilio. 2015-04-24 21:20 GMT+08:00 Bruce Fischl : Hi Cecilio this means that the automatic checking determined that the Talairach transform to be very unlikely and probably a failure. What was your input data? If you bring it up in tkmedit or freeview do the directions on the screen correspond to true anatomical ones (e.g. is A really anterior)? cheers Bruce On Fri, 24 Apr 2015, Cecilio C Baro Perez wrote: Hi! My name is Cecilio! I'm using the freesurfer 5.3 and I'm having some issues that I hope you could help me with. When I perform: recon-all -s patienttesta -all I get this error: recon-all -s patienttesta exited with ERRORS ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm After reading on the internet I even try this command: recon-all -s patienttesta -all -use-mritotal But it stills give me the same error Could you please tell me what the problem could be? Thank you in advance! Best regards, Cecilio. ___ 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 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] Fwd: Problem with Freesurfer 5.3
Hi Bruce! Thank you for your quick replay! I appreciate that! Well my data is T1 dicom images. And For every subject I have 224 scans. Though as I'm using freesurfer I'm trying by only using 2 of 224 scans. Please correct me if I'm wrong: File name: Pat1 Number of scans in Pat1: 2 (81334010 and 81334011) On terminal: Input command: 1. recon-all -s Patient1 -i /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 (this is executed free from errors) 2. recon-all -s Patient1 -all My error becomes: #@# Talairach Failure Detection Сб. апр. 25 18:25:07 CST 2015 recon-all -s Patient1 exited with ERRORS at Сб. апр. 25 18:25:32 CST 2015 Besides if I try to use the tkmedit I get this following: Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Please do you possibly know how to go around this problem. Thank you in advance! Best regards; Cecilio. 2015-04-24 21:20 GMT+08:00 Bruce Fischl : > Hi Cecilio > > this means that the automatic checking determined that the Talairach > transform to be very unlikely and probably a failure. What was your input > data? If you bring it up in tkmedit or freeview do the directions on the > screen correspond to true anatomical ones (e.g. is A really anterior)? > > cheers > Bruce > > > > On Fri, 24 Apr 2015, Cecilio C Baro Perez wrote: > > >> >> >> Hi! >> My name is Cecilio! I'm using the freesurfer 5.3 and I'm having some >> issues >> that I hope you could help me with. When I perform: >> >>recon-all -s patienttesta -all >> >> I get this error: >>recon-all -s patienttesta exited with ERRORS >>ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> >> After reading on the internet I even try this command: >> recon-all -s patienttesta -all -use-mritotal >> >> But it stills give me the same error >> >> >> Could you please tell me what the problem could be? >> >> Thank you in advance! >> >> Best regards, Cecilio. >> >> >> >> > ___ > 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 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] Fwd: Problem with Freesurfer 5.3
Hi Cecilio this means that the automatic checking determined that the Talairach transform to be very unlikely and probably a failure. What was your input data? If you bring it up in tkmedit or freeview do the directions on the screen correspond to true anatomical ones (e.g. is A really anterior)? cheers Bruce On Fri, 24 Apr 2015, Cecilio C Baro Perez wrote: Hi! My name is Cecilio! I'm using the freesurfer 5.3 and I'm having some issues that I hope you could help me with. When I perform: recon-all -s patienttesta -all I get this error: recon-all -s patienttesta exited with ERRORS ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm After reading on the internet I even try this command: recon-all -s patienttesta -all -use-mritotal But it stills give me the same error Could you please tell me what the problem could be? Thank you in advance! Best regards, Cecilio. ___ 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] Fwd: Problem with Freesurfer 5.3
Hi! My name is Cecilio! I'm using the freesurfer 5.3 and I'm having some issues that I hope you could help me with. When I perform: recon-all -s patienttesta -all I get this error: recon-all -s patienttesta exited with ERRORS ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm After reading on the internet I even try this command: recon-all -s patienttesta -all -use-mritotal But it stills give me the same error Could you please tell me what the problem could be? Thank you in advance! Best regards, Cecilio. ___ 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.
